diff --git a/benchmarks/DIIID_kinetic_example/dcon.toml b/benchmarks/DIIID_kinetic_example/dcon.toml new file mode 100644 index 00000000..1ccf58e0 --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/dcon.toml @@ -0,0 +1,45 @@ +[DCON_CONTROL] +bal_flag = false # Ideal MHD ballooning criterion for short wavelengths +mat_flag = true # Construct coefficient matrices for diagnostic purposes +ode_flag = true # Integrate ODE's for determining stability of internal long-wavelength mode (must be true for GPEC) +vac_flag = true # Compute plasma, vacuum, and total energies for free-boundary modes +mer_flag = true # Evaluate the Mercier criterian + +set_psilim_via_dmlim = true # Safety factor (q) limit determined as q_ir+dmlim... +dmlim = 0.2 # See sas_flag +psiedge = 1.00 # If less then psilim, calculates dW(psi)... +qlow = 1.02 # Integration initiated at q determined by min(q0, qlow)... +qhigh = 1e3 # Integration terminated at q limit determined by min(qa, qhigh)... +sing_start = 0 # Start integration at the sing_start'th rational from the axis (psilow) + +nn = 1 # Toroidal mode number +delta_mlow = 8 # Expands lower bound of Fourier harmonics +delta_mhigh = 8 # Expands upper bound of Fourier harmonics +delta_mband = 0 # Integration keeps only this wide a band... +mthvac = 512 # Number of points used in splines over poloidal angle at plasma-vacuum interface. +thmax0 = 1 # Linear multiplier on the automatic choice of theta integration bounds + +kin_flag = true # Kinetic EL equation (default: false) +con_flag = true # Continue integration through layers (default: false) +kinfac1 = 1.0 # Scale factor for energy contribution (default: 1.0) +kinfac2 = 1.0 # Scale factor for torque contribution (default: 1.0) +kingridtype = 0 # Regular grid method (default: 0) +passing_flag = true # Includes passing particle effects (default: false) +ktanh_flag = true # Ignore kinetic effects in the core smoothly (default: false) +ktc = 0.1 # Parameter for ktanh_flag (default: 0.1) +ktw = 50.0 # Parameter for ktanh_flag (default: 50.0) +ion_flag = true # Include ion dW_k when kin_flag is true +electron_flag = false # Include electron dW_k when kin_flag is true + +tol_nr = 1e-6 # Relative tolerance of dynamic integration steps away from rationals +tol_r = 1e-7 # Relative tolerance of dynamic integration steps near rationals +crossover = 1e-2 # Fractional distance from rational q at which tol switches +singfac_min = 1e-4 # Fractional distance from rational q at which ideal jump enforced +ucrit = 1e4 # Maximum fraction of solutions allowed before re-normalized + +use_classic_splines = false # Use a classical cubic spline instead of tri-diagonal solution + +[DCON_OUTPUT] +write_dcon_out = true # Write dcon.out which contains equilibrium data and final eigenvalues/vectors +write_euler_h5 = true # Write euler.h5 (euler.bin Julia equivalent) +write_eqdata_h5 = true # Write eqdata.h5, which contains profile and stability data \ No newline at end of file diff --git a/benchmarks/DIIID_kinetic_example/equil.toml b/benchmarks/DIIID_kinetic_example/equil.toml new file mode 100644 index 00000000..0b230bdd --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/equil.toml @@ -0,0 +1,30 @@ +[EQUIL_CONTROL] +eq_type = "efit" # Type of the input 2D equilibrium file +eq_filename = "g147131.02300_DIIID_KEFIT" # path to equilibrium file + +jac_type = "hamada" # Coordinate system (hamada, pest, boozer, equal_arc) +power_bp = 0 # del.B ~ B_p^power_bp * B^power_b / R^power_r +power_b = 0 # del.B ~ B_p^power_bp * B^power_b / R^power_r +power_r = 0 # del.B ~ B_p^power_bp * B^power_b / R^power_r + +grid_type = "ldp" # Radial grid packing +psilow = 1e-4 # Min psi (normalized) +psihigh = 0.993 # Max psi (normalized) +mpsi = 128 # Radial grid intervals +mtheta = 256 # Poloidal grid intervals + +newq0 = 0 # Override q(0) +etol = 1e-7 # Reconstruction tolerance +use_classic_splines = false # Use classical spline (vs. tri-diagonal) + +input_only = false # Quit after input read + +[EQUIL_OUTPUT] +gse_flag = false # Output G-S equation accuracy diagnostics +out_eq_1d = false # ASCII output of 1D eq data +bin_eq_1d = false # Binary output of 1D eq data +out_eq_2d = false # ASCII output of 2D eq data +bin_eq_2d = true # Binary output of 2D eq data (used by GPEC) +out_2d = false # ASCII output of processed 2D data +bin_2d = false # Binary output of processed 2D data +dump_flag = false # Binary dump of equilibrium data diff --git a/benchmarks/DIIID_kinetic_example/euler.bin b/benchmarks/DIIID_kinetic_example/euler.bin new file mode 100644 index 00000000..526dd8e5 Binary files /dev/null and b/benchmarks/DIIID_kinetic_example/euler.bin differ diff --git a/benchmarks/DIIID_kinetic_example/euler_fortran_julia_comparison.ipynb b/benchmarks/DIIID_kinetic_example/euler_fortran_julia_comparison.ipynb new file mode 100644 index 00000000..427e347b --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/euler_fortran_julia_comparison.ipynb @@ -0,0 +1,537 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "2cc3c9a9", + "metadata": {}, + "source": [ + "## Overview\n", + "In this notebook, we will demonstrate that the outputs of the Julia DCON conversion are equivalent to those in the Fortran version by comparing the eigenmodes of the DIIID ideal example" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "db314816", + "metadata": {}, + "outputs": [], + "source": [ + "# Load in necessary packages\n", + "using Pkg\n", + "using FortranFiles\n", + "using LinearAlgebra\n", + "using HDF5\n", + "using Plots\n", + "using LaTeXStrings" + ] + }, + { + "cell_type": "markdown", + "id": "2b21eeae", + "metadata": {}, + "source": [ + "## Load in Fortran data\n", + "\n", + "For convenience, we have saved the Fortran `euler.bin` file here for comparison. Below, we write a Julia version of the logic within `idcon.f` in GPEC, which reads in the `euler.bin` data and converts it to usable form" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7fec1fab", + "metadata": {}, + "outputs": [], + "source": [ + "# Mirroring gpec solution structs from fortran idcon.f\n", + "# Stores solutions read directly from output file\n", + "struct solution_type\n", + " msol :: Int32\n", + " u :: Array{ComplexF64,3}\n", + "end\n", + "\n", + "# Stores information for resistive calculations\n", + "struct resist_type\n", + " e :: Float64\n", + " f :: Float64\n", + " h :: Float64\n", + " m :: Float64\n", + " g :: Float64\n", + " k :: Float64\n", + " eta :: Float64\n", + " rho :: Float64\n", + " taua :: Float64\n", + " taur :: Float64\n", + " di :: Float64\n", + " dr :: Float64\n", + " sfac :: Float64\n", + " deltac :: Float64\n", + " eigenvalue :: ComplexF64\n", + "end\n", + "\n", + "# Stores information about singular surfaces\n", + "struct sing_type\n", + " msol_l :: Int32\n", + " msol_r :: Int32\n", + " jfix :: Int32\n", + " jpert :: Int32\n", + " psifac :: Float64\n", + " q :: Float64\n", + " q1 :: Float64\n", + " ca_l :: Array{ComplexF64,3}\n", + " ca_r :: Array{ComplexF64,3}\n", + " restype :: resist_type\n", + "end\n", + "\n", + "# Stores fixfacs\n", + "mutable struct fixfac_type\n", + " msol :: Int32\n", + " index :: Vector{Int32}\n", + " fixfac :: Array{ComplexF64,2}\n", + " transform :: Array{ComplexF64,2}\n", + " gauss :: Array{ComplexF64,2}\n", + " function fixfac_type(msol::Int32, index::Vector{Int32},fixfac::Array{ComplexF64,2})\n", + " transform = Matrix{ComplexF64}(I,msol,msol)\n", + " gauss = Matrix{ComplexF64}(I,msol,msol)\n", + " new(msol,index,fixfac,transform,gauss)\n", + " end\n", + "end\n", + "\n", + "# Sets up fixfacs to recover true eigenmodes - Julia conversion of the idcon_transform subroutine in GPEC\n", + "function idcon_transform(fixtype, sing_flag)\n", + " \n", + " msol = length(fixtype[2].index)\n", + " mfix = length(fixtype)-1\n", + " identity = Matrix{ComplexF64}(I,msol,msol)\n", + "\n", + " # Construct gaussian reduction matrix\n", + " for ifix in 2:1:mfix+1\n", + " fixtype[ifix].gauss = copy(identity)\n", + " mask = zeros(Bool, msol)\n", + " mask .= true\n", + " for isol in 1:msol\n", + " ksol = fixtype[ifix].index[isol]\n", + " mask[ksol] = false\n", + " temp = copy(identity)\n", + " for jsol in 1:msol\n", + " if mask[jsol]\n", + " temp[ksol,jsol] = fixtype[ifix].fixfac[ksol,jsol]\n", + " end\n", + " end\n", + " # Matrix multiplication gauss = gauss * temp\n", + " fixtype[ifix].gauss = fixtype[ifix].gauss * temp\n", + " end\n", + " if sing_flag[ifix-1]\n", + " fixtype[ifix].gauss[:,fixtype[ifix].index[1]] .= 0.0\n", + " end\n", + " end\n", + " \n", + " # Concatenate gaussian reduction matrix\n", + " fixtype[mfix+1].transform = copy(identity)\n", + " for ifix in mfix:-1:1\n", + " fixtype[ifix].transform = fixtype[ifix+1].gauss * fixtype[ifix+1].transform\n", + " end\n", + " return fixtype\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "59f1ad09", + "metadata": {}, + "outputs": [], + "source": [ + "# Euler.bin file from gpec develop branch for comparison\n", + "fstream = FortranFile(\"euler.bin\", \"r\")\n", + "\n", + "# --- Read header ---\n", + "mlow, mhigh, nn, mpsi, mtheta, ro, zo = read(fstream, Int32, Int32, Int32, Int32, Int32, Float64, Float64)\n", + "mband, mthsurf0, mthvac, psio, psilow, psilim, qlim, singfac_min = read(fstream, Int32, Float64, Int32, Float64, Float64, Float64, Float64, Float64)\n", + "power_b, power_r, power_bp = read(fstream, Int32, Int32, Int32)\n", + "kin_flag, con_flag = read(fstream, Int32, Int32)\n", + "\n", + "amean, rmean, aratio, kappa, delta1, delta2, \n", + " li1, li2, li3, betap1, betap2, betap3, betat, betan, bt0, \n", + " q0, qmin, qmax, qa, crnt, q95, shotnum, shottime = read(fstream, \n", + " Float64, Float64, Float64, Float64, Float64, Float64,\n", + " Float64, Float64, Float64, Float64, Float64, Float64,\n", + " Float64, Float64, Float64, Float64, Float64, Float64,\n", + " Float64, Float64, Float64, Float64, Float64)\n", + "\n", + "# --- Read equilibrium on flux coordinates ---\n", + "# sq%xs is size mpsi, sq%fs is size mpsi x 4, sq%fs1 is size mpsi x 4, sq%xpower is size 2 x 4\n", + "sq_xs, sq_fs, sq_fs1, sq_xpower = read(fstream, (Float64, mpsi), (Float64, (mpsi,4)), (Float64, (mpsi,4)), (Float64, (2,4)))\n", + "# rzphi%xs is size mpsi, rzphi%ys is size mtheta, rzphi%fs is size mpsi x mtheta, etc.\n", + "rzphi_xs, rzphi_ys, \n", + " rzphi_fs, rzphi_fsx, rzphi_fsy, rzphi_fsxy, \n", + " rzphi_x0, rzphi_y0, rzphi_xpower, rzphi_ypower = read(fstream, \n", + " (Float64, mpsi), (Float64, mtheta), \n", + " (Float64, (mpsi,mtheta,4)), (Float64, (mpsi,mtheta,4)), (Float64, (mpsi,mtheta,4)), (Float64, (mpsi,mtheta,4)),\n", + " (Float64, 2), (Float64, 2), (Float64, (2,4)), (Float64, (2,4)))\n", + "\n", + "# misc derived quantities\n", + "chi1=2π*psio\n", + "mpert=mhigh-mlow+1\n", + "\n", + "# --- Count solutions in file (first pass) ---\n", + "mstep = -1\n", + "mfix = 0\n", + "msing = 0\n", + "\n", + "while !eof(fstream)\n", + " data_type = read(fstream, Int32)\n", + " if data_type == 1\n", + " mstep += 1\n", + " read(fstream) # skip\n", + " read(fstream)\n", + " read(fstream)\n", + " elseif data_type == 2\n", + " mfix += 1\n", + " read(fstream)\n", + " read(fstream)\n", + " elseif data_type == 3\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " elseif data_type == 4\n", + " msing += 1\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " elseif data_type == 5\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " read(fstream)\n", + " else\n", + " error(\"Cannot recognize data_type = $data_type\")\n", + " end\n", + "end\n", + "close(fstream)\n", + "\n", + "# --- Allocate arrays ---\n", + "psifac = zeros(Float64, mstep+1)\n", + "rhofac = zeros(Float64, mstep+1)\n", + "qfac = zeros(Float64, mstep+1)\n", + "\n", + "soltype = Vector{solution_type}(undef, mstep+1)\n", + "singtype = Vector{sing_type}(undef, msing)\n", + "fixstep = zeros(Int32, mfix+2)\n", + "sing_flag = zeros(Bool, mfix)\n", + "fixtype = Vector{fixfac_type}(undef, mfix+1)\n", + "\n", + "# Initialize first fixfac\n", + "fixtype[1] = fixfac_type(Int32(0), zeros(Int32, 0), zeros(ComplexF64, 0, 0))\n", + "\n", + "et = zeros(ComplexF64, mpert)\n", + "ep = zeros(ComplexF64, mpert)\n", + "ee = zeros(ComplexF64, mpert)\n", + "wt = zeros(ComplexF64, (mpert,mpert))\n", + "wt0 = zeros(ComplexF64, (mpert,mpert))\n", + "wft = zeros(ComplexF64, (mpert,mpert))\n", + "eft = zeros(ComplexF64, mpert)\n", + "efp = zeros(ComplexF64, mpert)\n", + "wtraw = zeros(ComplexF64, (mpert,mpert))\n", + "\n", + "eft .= -1\n", + "wft .= 0\n", + "fixstep[1] = 0\n", + "fixstep[mfix+2] = mstep\n", + "\n", + "fstream = FortranFile(\"euler.bin\", \"r\")\n", + "# --- Read header again ---\n", + "mlow, mhigh, nn, mpsi, mtheta, ro, zo = read(fstream, Int32, Int32, Int32, Int32, Int32, Float64, Float64)\n", + "mband, mthsurf0, mthvac, psio, psilow, psilim, qlim, singfac_min = read(fstream, Int32, Float64, Int32, Float64, Float64, Float64, Float64, Float64)\n", + "power_b, power_r, power_bp = read(fstream, Int32, Int32, Int32)\n", + "kin_flag, con_flag = read(fstream, Int32, Int32)\n", + "istep = -1\n", + "ifix = 0\n", + "ising = 0\n", + "\n", + "while !eof(fstream)\n", + " data_type = read(fstream, Int32)\n", + " if data_type == 1\n", + " istep += 1\n", + " psifac[istep+1], qfac[istep+1], msoli = read(fstream, Float64, Float64, Int32)\n", + " u = Array{ComplexF64}(undef,(mpert,msoli,4))\n", + " u[:,:,1:2] = read(fstream, (ComplexF64,(mpert,msoli,2)))\n", + " u[:,:,3:4] = read(fstream, (ComplexF64,(mpert,msoli,2)))\n", + " soltype[istep+1] = solution_type(msoli,u)\n", + " elseif data_type == 2\n", + " ifix += 1\n", + " fixstep[ifix+1] = istep\n", + " sing_flag[ifix], msoli = read(fstream, Int32, Int32)\n", + " fixfac, index = read(fstream, (ComplexF64,(msoli,msoli)),(Int32,msoli))\n", + " fixtype[ifix+1] = fixfac_type(msoli,index,fixfac)\n", + " elseif data_type == 3\n", + " ep = read(fstream,(ComplexF64,mpert))\n", + " et = read(fstream,(ComplexF64,mpert))\n", + " wt = read(fstream,(ComplexF64,(mpert,mpert)))\n", + " wt0 = read(fstream,(ComplexF64,(mpert,mpert)))\n", + " wv_farwall_flag = read(fstream, Int32)\n", + " elseif data_type == 4\n", + " ising += 1\n", + " jfixi = ifix\n", + " jperti = round(Int32, nn*qfac[istep+1] + 0.5)\n", + " psifaci, qi, q1i = read(fstream, Float64, Float64, Float64)\n", + " msol_l = read(fstream, Int32)\n", + " ca_l = read(fstream, (ComplexF64,(mpert,msol_l,2)))\n", + " msol_r = read(fstream, Int32)\n", + " ca_r = read(fstream, (ComplexF64,(mpert,msol_r,2)))\n", + " e, f, h, m, g, k, eta, rho, taua, taur = read(fstream, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64)\n", + " elseif data_type == 5\n", + " ep = read(fstream,(ComplexF64,mpert))\n", + " et = read(fstream,(ComplexF64,mpert))\n", + " wt = read(fstream,(ComplexF64,(mpert,mpert)))\n", + " efp = read(fstream,(Float64,mpert))\n", + " eft = read(fstream,(Float64,mpert))\n", + " wft = read(fstream,(ComplexF64,(mpert,mpert)))\n", + " wtraw = read(fstream,(ComplexF64,(mpert,mpert)))\n", + " else\n", + " # for all the reads we skipped in the second pass\n", + " print()\n", + " end\n", + "end\n", + "fixstep .+= 1 # Fortran indexes from 0 for steps, adjust\n", + "close(fstream)\n", + "\n", + "# Set up fortran fixfacs\n", + "fixfacproc = idcon_transform(fixtype, sing_flag)\n", + "\n", + "println(\"Done reading euler.bin\")" + ] + }, + { + "cell_type": "markdown", + "id": "74226ac8", + "metadata": {}, + "source": [ + "## Load in Julia data\n", + "We will run the main DCON code on the same inputs. We output the `euler.h5` file, which is a Julia version of the `euler.bin` file." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c76aa60a", + "metadata": {}, + "outputs": [], + "source": [ + "# Run DCON in Julia\n", + "Pkg.activate(\"../..\")\n", + "using JPEC\n", + "JPEC.DCON.Main(\"./\") # \"./\" tells us to obtain inputs and direct outputs to our current folder" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ac491233", + "metadata": {}, + "outputs": [], + "source": [ + "# Read in from julia hdf5 for comparison\n", + "eh5 = h5open(\"euler.h5\", \"r\")\n", + "mstepj = read(eh5[\"integration/nstep\"])\n", + "xi_psij = read(eh5[\"integration/xi_psi\"])\n", + "psifacj = read(eh5[\"integration/psi\"])\n", + "psioj = read(eh5[\"equil/psio\"])\n", + "wtj = read(eh5[\"vacuum/wt\"])\n", + "close(eh5)\n", + "\n", + "# scale energy eigenvector matrices\n", + "chi1j = 2π*psioj\n", + "wtf = wt*(chi1*1e-3)\n", + "wtj = wtj*(chi1j*1e-3)\n", + "println(\"Done reading euler.h5\")" + ] + }, + { + "cell_type": "markdown", + "id": "bcf321ba", + "metadata": {}, + "source": [ + "# Compare Outputs\n", + "We will now perform the equivalent `idcon_build`, which builds the ideal Euler-Langrange solutions for a given eigenmode. We have performed the transformation and scaling necessary to obtain the physical quantities ($\\Xi_\\Psi, \\Xi_s$ etc. ) typically calculated in GPEC preprocessing in `idcon.f` and saved them in the HDF5 file. Notice how this makes the Julia outputs postprocessing much simpler, as we don't need to call `idcon_transform` or `idcon_build` in this notebook." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d2ee9066", + "metadata": {}, + "outputs": [], + "source": [ + "xi_psif = zeros(ComplexF64, (mstep+1,mpert))\n", + "\n", + "# Construct uedge coefficients using the most unstable mode (index 1)\n", + "uedgef = soltype[length(soltype)].u[:,:,1] \\ wtf[:,1]\n", + "\n", + "# Create Fortran eigenfunctions\n", + "jfix = 1\n", + "for ifix in 1:mfix+1\n", + " temp1 = fixtype[ifix].transform * uedgef\n", + " kfix = fixstep[ifix+1]\n", + " for istep in jfix:kfix\n", + " xi_psif[istep,:] = soltype[istep].u[:,:,1] * temp1\n", + " end\n", + " jfix = kfix + 1\n", + "end" + ] + }, + { + "cell_type": "markdown", + "id": "b3e56821", + "metadata": {}, + "source": [ + "## Plots" + ] + }, + { + "cell_type": "markdown", + "id": "1834dfce", + "metadata": {}, + "source": [ + "### Plot comparison of xi_psi for a few poloidal mode numbers" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "54b41c30", + "metadata": {}, + "outputs": [], + "source": [ + "p = plot()\n", + "# In the Julia output, xi_psij is indexed as (mpert, nmode, nstep), so we extract nmode=1 for the least stable mode\n", + "for m in 1:4\n", + " plot!(psifac, imag.(xi_psif[:,m - mlow + 1]), label=\"Fortran, m=$m\")\n", + " plot!(psifacj, imag.(xi_psij[m - mlow + 1, 1, :]), linestyle=:dash, label=\"Julia, m=$m\")\n", + "end\n", + "xlabel!(L\"\\psi_N\")\n", + "ylabel!(L\"\\mathrm{Im}(\\xi_\\psi)\")\n", + "title!(\"Comparison of \" * L\"\\xi_\\psi\" * \" for \" * \"m=1-4\")\n", + "display(p)" + ] + }, + { + "cell_type": "markdown", + "id": "b641e050", + "metadata": {}, + "source": [ + "### Plot comparison of psifac integration\n", + "We can see that in this scenario, the Julia integrator is actually more efficient than LSODE in Fortran. One reason is because we can see LSODE is extremely jumpy around solution normalizations, and slows down directly after these regions." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b778938c", + "metadata": {}, + "outputs": [], + "source": [ + "p = plot(psifac, label=\"Fortran\")\n", + "# plot vertical line at each fixstep\n", + "for ifix in 2:1:mfix+1\n", + " vline!([fixstep[ifix]+1], linestyle=:dash, color=:black, label=\"\", linewidth=0.25, alpha=0.5)\n", + "end\n", + "plot!(psifacj, linestyle=:dash, label=\"Julia\")\n", + "xaxis!(\"ODE step index\")\n", + "yaxis!(L\"\\psi_N\")\n", + "display(p)" + ] + }, + { + "cell_type": "markdown", + "id": "bf6483a8", + "metadata": {}, + "source": [ + "### Compare the eigenvectors of each DCON energy matrix eigenmode" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "89839f1e", + "metadata": {}, + "outputs": [], + "source": [ + "l = @layout [a{0.97w} b{0.03w}]\n", + "\n", + "# Determine the global minimum and maximum values for the color scale\n", + "global_min = minimum([minimum(log10.(abs.(wtf'))), minimum(log10.(abs.(wtj'))), minimum(log10.(abs.((wtf'-wtj'))))])\n", + "global_max = maximum([maximum(log10.(abs.(wtf'))), maximum(log10.(abs.(wtj'))), maximum(log10.(abs.((wtf'-wtj'))))])\n", + "\n", + "# Common axis labels\n", + "xlabel = \"m\"\n", + "ylabel = \"mode\"\n", + "\n", + "# Create the heatmaps without individual colorbars\n", + "p1 = heatmap(\n", + " log10.(abs.(wtf')), \n", + " aspect_ratio=1, \n", + " title=\"Fortran \" * L\"log_{10} |W_t|\", \n", + " xlabel=xlabel, ylabel=ylabel,\n", + " size=(400,400), interpolate=false, fxaa=false, \n", + " color=:viridis, clims=(global_min, global_max), colorbar=false, left_margin=5Plots.mm, bottom_margin=5Plots.mm, top_margin=5Plots.mm, right_margin=2Plots.mm\n", + ")\n", + "\n", + "p2 = heatmap(\n", + " log10.(abs.(wtj')), \n", + " aspect_ratio=1, \n", + " title=\"Julia \" * L\"log_{10} |W_t|\", \n", + " xlabel=xlabel, ylabel=ylabel,\n", + " size=(400,400), interpolate=false, fxaa=false, \n", + " color=:viridis, clims=(global_min, global_max), colorbar=false, left_margin=5Plots.mm, bottom_margin=5Plots.mm, top_margin=5Plots.mm, right_margin=2Plots.mm\n", + ")\n", + "\n", + "p3 = heatmap(\n", + " log10.(abs.((wtf'-wtj'))), \n", + " aspect_ratio=1, \n", + " title=L\"log_{10} \\left|W_{tf} - W_{tj}\\right|\", \n", + " xlabel=xlabel, ylabel=ylabel,\n", + " size=(400,400), interpolate=false, fxaa=false, \n", + " color=:viridis, clims=(global_min, global_max), colorbar=false, left_margin=5Plots.mm, bottom_margin=5Plots.mm, top_margin=5Plots.mm, right_margin=2Plots.mm\n", + ")\n", + "\n", + "# Add a single color bar to the right of the combined plots\n", + "cb = heatmap(\n", + " zeros(2,2), \n", + " color=:viridis, clims=(global_min, global_max), \n", + " colorbar=true, framestyle=:none, \n", + " xaxis=false, yaxis=false, \n", + " size=(40,400), right_margin=5Plots.mm, left_margin=0Plots.mm, \n", + " lims=(-1,0)\n", + ")\n", + "\n", + "# Combine the plots with a single shared color bar on the right\n", + "p = plot(p1, p2, p3, layout=(1,3), size=(1200,400), margin=0Plots.mm)\n", + "pp = plot(p, cb, layout=l, size=(1300,400), margin=0Plots.mm)\n", + "display(pp)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Julia 1.11.6", + "language": "julia", + "name": "julia-1.11" + }, + "language_info": { + "file_extension": ".jl", + "mimetype": "application/julia", + "name": "julia", + "version": "1.11.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/benchmarks/DIIID_kinetic_example/g147131.02300_DIIID_KEFIT b/benchmarks/DIIID_kinetic_example/g147131.02300_DIIID_KEFIT new file mode 100644 index 00000000..15da8c79 --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/g147131.02300_DIIID_KEFIT @@ -0,0 +1,6668 @@ + EFITD 03/13/2012 #147131 2300ms 3 129 129 + 0.170000000E+01 0.320000000E+01 0.169550002E+01 0.840000000E+00 0.000000000E+00 + 0.175888032E+01 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0.000000000000000 + / + &BASIS + KPPFNC = 6, + KPPKNT = 9, + PPKNT = 0.000000000000000 , + 0.6000000000000000 , + 0.8309948501841458 , + 0.9259035236011000 , + 0.9394619055178077 , + 0.9530202874345154 , + 0.9801370512679309 , + 0.9936954331846386 , + 1.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + PPTENS = 2.000000000000000 , + KFFFNC = 6, + KFFKNT = 9, + FFKNT = 0.000000000000000 , + 0.6000000000000000 , + 0.8309948501841458 , 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0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + KFFBDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + KFF2BDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + WWBDRY = 753378.4125525327 , + 1254.750893700115 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + WW2BDRY = 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + KWWBDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + KWW2BDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + KEEFNC = 0, + KEEKNT = 0, + EEKNT = 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + EETENS = 5.000000000000000 , + EEBDRY = 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + EE2BDRY = 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + KEEBDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + KEE2BDRY = 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + / + &MSEOUT + RRRGAM = 1.519000053405762 , + 1.570000052452087 , + 1.620000004768372 , + 1.669999957084656 , + 1.718999981880188 , + 1.768000006675720 , + 1.819000005722046 , + 1.871000051498413 , + 1.919999957084656 , + 1.973000049591064 , + 2.022000074386597 , + 1.980999946594238 , + 2.030999898910522 , + 2.075000047683716 , + 2.119999885559082 , + 2.157999992370605 , + 2.196000099182129 , + 2.240000009536743 , + 2.243000030517578 , + 2.246000051498413 , + 2.250000000000000 , + 2.253000020980835 , + 2.256000041961670 , + 2.259999990463257 , + 2.263000011444092 , + 2.266000032424927 , + 1.689000010490417 , + 1.733000040054321 , + 1.779999971389771 , + 1.822999954223633 , + 1.868000030517578 , + 1.912999987602234 , + 1.955999970436096 , + 2.000999927520752 , + 2.046999931335449 , + 2.095000028610229 , + 1.583999991416931 , + 1.628999948501587 , + 1.679000020027161 , + 1.730000019073486 , + 2.069000005722046 , + 2.117000102996826 , + 2.176000118255615 , + 2.243999958038330 , + 2.328000068664551 , + 1.697000026702881 , + 1.741999983787537 , + 1.786999940872192 , + 1.832000017166138 , + 1.876000046730042 , + 1.919000029563904 , + 1.963000059127808 , + 2.007999897003174 , + 2.029000043869019 , + 2.069999933242798 , + 2.109999895095825 , + 2.148000001907349 , + 2.184999942779541 , + 2.217999935150146 , + 2.236000061035156 , + 2.242000102996826 , + 2.247999906539917 , + 2.253999948501587 , + 2.259000062942505 , + 2.265000104904175 , + 2.269999980926514 , + 2.276999950408936 , + 2.282999992370605 , + 2.288000106811523 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + ZZZGAM = -2.5000000372529030E-002, + -2.3000000044703484E-002, + -1.7000000923871994E-002, + -1.3000000268220901E-002, + -1.2000000104308128E-002, + -9.9999997764825821E-003, + -7.0000002160668373E-003, + -2.0000000949949026E-003, + -2.0000000949949026E-003, + 3.0000000260770321E-003, + -4.9999998882412910E-003, + 1.0999999940395355E-002, + 1.2000000104308128E-002, + 6.0000000521540642E-003, + 6.0000000521540642E-003, + 6.0000000521540642E-003, + 4.9999998882412910E-003, + 6.0000000521540642E-003, + 8.0000003799796104E-003, + 8.9999996125698090E-003, + 7.0000002160668373E-003, + 4.9999998882412910E-003, + 8.0000003799796104E-003, + 6.0000000521540642E-003, + 6.0000000521540642E-003, + 7.0000002160668373E-003, + -7.0000002160668373E-003, + -1.2000000104308128E-002, + -8.9999996125698090E-003, + -8.0000003799796104E-003, + -6.0000000521540642E-003, + -8.9999996125698090E-003, + -2.0000000949949026E-003, + 0.000000000000000 , + 2.0000000949949026E-003, + 2.0000000949949026E-003, + -1.2000000104308128E-002, + -9.9999997764825821E-003, + -8.9999996125698090E-003, + -4.9999998882412910E-003, + -3.0000000260770321E-003, + 2.0000000949949026E-003, + 4.0000001899898052E-003, + 1.0000000474974513E-003, + 0.000000000000000 , + -5.0999999046325684E-002, + -4.6999998390674591E-002, + -4.3000001460313797E-002, + -3.9000000804662704E-002, + -3.4000001847743988E-002, + -3.9999999105930328E-002, + -3.9999999105930328E-002, + -4.1000001132488251E-002, + 3.2000001519918442E-002, + 3.5999998450279236E-002, + 3.9999999105930328E-002, + 4.3999999761581421E-002, + 4.8000000417232513E-002, + 5.4000001400709152E-002, + 4.6999998390674591E-002, + 4.6999998390674591E-002, + 4.3000001460313797E-002, + 4.3000001460313797E-002, + 4.6999998390674591E-002, + 4.8000000417232513E-002, + 4.6999998390674591E-002, + 4.6999998390674591E-002, + 4.6999998390674591E-002, + 4.6999998390674591E-002, + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + AA1GAM = -0.6313996900000000 , + -0.6530994800000000 , + -0.6723998799999999 , + -0.6893998400000000 , + -0.7052001400000000 , + -0.7192996699999999 , + -0.7327996500000000 , + -0.7457004800000000 , + -0.7569004300000000 , + -0.7678999300000000 , + -0.7775996300000000 , + 0.7204002100000000 , + 0.6924998200000000 , + 0.6648001100000001 , + 0.6345999200000000 , + 0.6058998700000000 , + 0.5760001500000000 , + 0.5373997700000001 , + 0.5349999100000000 , + 0.5319002900000001 , + 0.5279999399999999 , + 0.5256003100000000 , + 0.5223999600000000 , + 0.5191001300000000 , + 0.5158997800000000 , + 0.5133996600000000 , + 0.8473002300000000 , + 0.8274996900000000 , + 0.8026999800000000 , + 0.7761001000000000 , + 0.7433001400000000 , + 0.7047997700000000 , + 0.6615998700000000 , + 0.6096000100000000 , + 0.5471997300000000 , + 0.4711996600000000 , + -0.6588998400000000 , + -0.6755997500000001 , + -0.6926001899999999 , + -0.7084003700000000 , + -0.7863999000000000 , + -0.7946000700000000 , + -0.8041995800000000 , + -0.8143997800000000 , + -0.8256999300000000 , + 0.8306999800000000 , + 0.8165002500000000 , + 0.8007000700000000 , + 0.7835999100000000 , + 0.7653003900000001 , + 0.7456001600000000 , + 0.7234000600000000 , + 0.6991998000000000 , + 0.6865001900000000 , + 0.6609997200000000 , + 0.6334000200000000 , + 0.6053004300000000 , + 0.5753001599999999 , + 0.5466996400000000 , + 0.5303997400000000 , + 0.5249003200000000 , + 0.5193003400000000 , + 0.5135998100000000 , + 0.5086001800000000 , + 0.5027999900000000 , + 0.4986000100000000 , + 0.4918001900000000 , + 0.4857998200000000 , + 0.4806002100000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + AA2GAM = 0.6500999927520752 , + 0.6779000163078308 , + 0.7016999721527100 , + 0.7221999764442444 , + 0.7408000230789185 , + 0.7570999860763550 , + 0.7723000049591064 , + 0.7864000201225281 , + 0.7986000180244446 , + 0.8101999759674072 , + 0.8203999996185303 , + 0.8127999901771545 , + 0.8227999806404114 , + 0.8312000036239624 , + 0.8388000130653381 , + 0.8450999855995178 , + 0.8507000207901001 , + 0.8569999933242798 , + 0.8572999835014343 , + 0.8578000068664551 , + 0.8583999872207642 , + 0.8587999939918518 , + 0.8592000007629395 , + 0.8597000241279602 , + 0.8600999712944031 , + 0.8604999780654907 , + 0.7304000258445740 , + 0.7458999752998352 , + 0.7610999941825867 , + 0.7738000154495239 , + 0.7860000133514404 , + 0.7969999909400940 , + 0.8072000145912170 , + 0.8166999816894531 , + 0.8256999850273132 , + 0.8342999815940857 , + 0.6848999857902527 , + 0.7053999900817871 , + 0.7260000109672546 , + 0.7444000244140625 , + 0.8294000029563904 , + 0.8375999927520752 , + 0.8470000028610229 , + 0.8569999933242798 , + 0.8677999973297119 , + 0.7358999848365784 , + 0.7512000203132629 , + 0.7652999758720398 , + 0.7778000235557556 , + 0.7889999747276306 , + 0.7994999885559082 , + 0.8091999888420105 , + 0.8180999755859375 , + 0.8216000199317932 , + 0.8291000127792358 , + 0.8360999822616577 , + 0.8424000144004822 , + 0.8482000231742859 , + 0.8532999753952026 , + 0.8551999926567078 , + 0.8558999896049500 , + 0.8562999963760376 , + 0.8571000099182129 , + 0.8582000136375427 , + 0.8590999841690063 , + 0.8593999743461609 , + 0.8604000210762024 , + 0.8610000014305115 , + 0.8616999983787537 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + 1.000000000000000 , + AA3GAM = 0.7579997200000000 , + 0.7332996100000000 , + 0.7103997500000000 , + 0.6895001500000000 , + 0.6694999900000000 , + 0.6511001000000000 , + 0.6329997800000000 , + 0.6151999800000000 , + 0.5995002400000000 , + 0.5834999700000000 , + 0.5695000300000000 , + 0.5818003400000000 , + 0.5674996400000000 , + 0.5552998200000000 , + 0.5436997400000000 , + 0.5338997800000000 , + 0.5247997599999999 , + 0.5144003600000000 , + 0.5137997900000000 , + 0.5130003700000000 , + 0.5119996700000000 , + 0.5114998200000000 , + 0.5107001700000000 , + 0.5098996800000000 , + 0.5091000200000000 , + 0.5084996800000000 , + 0.6819996200000000 , + 0.6646996700000000 , + 0.6471999300000000 , + 0.6319003700000000 , + 0.6165999800000000 , + 0.6019000400000000 , + 0.5886997600000000 , + 0.5755997899999999 , + 0.5627001500000000 , + 0.5496998400000001 , + 0.7263999600000000 , + 0.7064998100000000 , + 0.6854002500000000 , + 0.6653000700000000 , + 0.5564001800000000 , + 0.5438002300000000 , + 0.5291003000000000 , + 0.5130003700000000 , + 0.4946999000000000 , + -0.6749000000000001 , + -0.6573998900000000 , + -0.6403999900000000 , + -0.6245001600000000 , + -0.6095004100000000 , + -0.5960002500000000 , + -0.5823997900000000 , + -0.5695000300000000 , + -0.5631003400000000 , + -0.5520997000000000 , + -0.5415997500000000 , + -0.5321002600000000 , + -0.5230999600000000 , + -0.5154996500000000 , + -0.5109003800000000 , + -0.5095003800000000 , + -0.5079001800000000 , + -0.5065998400000000 , + -0.5055999799999999 , + -0.5042997000000000 , + -0.5032998300000000 , + -0.5018001200000000 , + -0.5004001300000001 , + -0.4992002500000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + AA4GAM = -4.0899996000000001E-002, + -3.9700024000000000E-002, + -3.9999984000000002E-002, + -3.9600007000000000E-002, + -3.8300015000000000E-002, + -3.7400004000000001E-002, + -3.6700007000000000E-002, + -3.6599997000000002E-002, + -3.5200000000000002E-002, + -3.5099990999999997E-002, + -3.1900014999999997E-002, + 2.0099999000000000E-002, + 2.2099984999999999E-002, + 2.0099999000000000E-002, + 2.1499995000000001E-002, + 2.2800006000000001E-002, + 2.3199997999999999E-002, + 2.5599991999999998E-002, + 2.7099999000000000E-002, + 2.7699985999999999E-002, + 2.6900014000000000E-002, + 2.5099995000000000E-002, + 2.7600013000000000E-002, + 2.6299993000000001E-002, + 2.6399980999999999E-002, + 2.6999990000000001E-002, + 1.8800007000000001E-002, + 2.4299989000000001E-002, + 2.5500014000000001E-002, + 2.7300000000000001E-002, + 2.9399992999999999E-002, + 3.5599976999999998E-002, + 3.2299999000000003E-002, + 3.2799984999999997E-002, + 3.2999995999999997E-002, + 3.7500015999999997E-002, + -4.3099985000000000E-002, + -4.2099979000000003E-002, + -4.0600035000000000E-002, + -4.0099996999999998E-002, + -3.1200016000000001E-002, + -3.1299981999999997E-002, + -3.0500019000000000E-002, + -2.8399982000000001E-002, + -2.6600001000000002E-002, + -3.0699994000000001E-002, + -3.4199983000000003E-002, + -3.9199978000000003E-002, + -4.3900008999999997E-002, + -4.9999975000000002E-002, + -4.9900033000000003E-002, + -5.3499999999999999E-002, + -5.6699995000000003E-002, + 6.4800017000000001E-002, + 6.6100053000000006E-002, + 6.7199960000000003E-002, + 6.7399985999999995E-002, + 6.7800029999999997E-002, + 6.6100053000000006E-002, + 7.4100009999999994E-002, + 7.5200029000000002E-002, + 7.9600029000000003E-002, + 8.0199993999999997E-002, + 7.6499953999999995E-002, + 7.5599968000000003E-002, + 7.8000024000000001E-002, + 7.7699958999999999E-002, + 7.9299970999999997E-002, + 7.9799958000000004E-002, + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + TGAMMA = 0.1303013400000000 , + 0.1143766900000000 , + 8.2041472000000004E-002, + 5.4787508999999998E-002, + 2.6905693000000001E-002, + -5.0727487999999996E-003, + -4.3465170999999997E-002, + -7.7258646000000000E-002, + -0.1154772300000000 , + -0.1558073800000000 , + -0.1796950700000000 , + 0.1393254500000000 , + 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0.000000000000000 , + 0.000000000000000 , + SGAMMA = 6.9589819999999998E-003, + 5.4001179999999998E-003, + 1.2754761000000000E-002, + 5.6128758000000001E-003, + 3.2957832000000001E-003, + 3.0616450000000000E-003, + 3.0664145000000001E-003, + 3.4407319000000001E-003, + 3.4149985000000000E-003, + 3.8838320999999999E-003, + 7.8072050000000002E-003, + 2.3109821999999999E-002, + 0.000000000000000 , + 0.000000000000000 , + 4.2204521999999996E-003, + 0.000000000000000 , + 0.000000000000000 , + 1.1697994000000000E-002, + 1.3734606999999999E-002, + 1.2088775000000000E-002, + 6.0290296000000000E-002, + 8.8302940000000007E-003, + 6.5120352000000003E-003, + 7.0577840999999997E-003, + 9.4381329000000000E-003, + 1.6173329000000000E-002, + 5.8086999000000004E-003, + 5.6009203999999998E-003, + 5.0626402000000003E-003, + 4.7793276999999997E-003, + 6.1390139000000003E-003, + 4.3339253999999999E-003, + 1.5146843000000000E-003, + 5.2471584999999998E-003, + 6.9276863000000003E-003, + 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3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 3.5899995999999999E-007, + 6.8200037999999994E-008, + 4.7099999000000001E-008, + 2.3600013000000000E-008, + 8.6500024000000005E-010, + -2.4299995000000001E-008, + -5.0700005999999999E-008, + -7.7500026000000001E-008, + -1.0699992000000001E-007, + -1.3799993000000000E-007, + -1.7099992999999999E-007, + -5.0500017000000002E-007, + -5.0699975000000002E-007, + -5.0800003000000005E-007, + -5.0699975000000002E-007, + -3.4099992000000002E-007, + -3.3799989000000001E-007, + -3.3399993999999999E-007, + -3.2899996000000001E-007, + -3.2299982000000000E-007, + -3.4900023000000000E-007, + -3.4900023000000000E-007, + -3.4900023000000000E-007, + -3.5000014000000002E-007, + -3.5100003999999999E-007, + -3.5199994000000002E-007, + -3.5300019000000000E-007, + -3.5400008999999998E-007, + -3.5499996999999999E-007, + 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0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + AA6GAM = -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5800007999999998E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + -3.5899995999999999E-007, + 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0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + AA8GAM = 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 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0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + PSIECN = 0.000000000000000 , + DPSIECN = 0.000000000000000 , + SAISQ = 17.63691764250911 , + CJECCD = 0.000000000000000 + / + &CHIOUT + SAISIL = 3.0254726073793078E-002, + 2.2448233599002221E-002, + 4.0477480494356136E-002, + 1.8482801924204526E-002, + 0.1815426499039182 , + 8.3429880135030242E-003, + 0.000000000000000 , + 8.7386235165995835E-002, + 2.5813930068840717E-004, + 9.9474461019504728E-003, + 8.2844412786942684E-002, + 7.5933865885683099E-002, + 0.2627442485853556 , + 0.3509357812678711 , + 9.6033841666670933E-007, + 2.2118508979707265E-002, + 0.4808962475029976 , + 1.3046329959515745E-002, + 1.1359027072828433E-002, + 2.7870960784433643E-002, + 9.5976807321789658E-003, + 3.0660773224850475E-005, + 3.0227180285408595E-002, + 2.0979367874545563E-002, + 3.1562805991269456E-003, + 0.1760459999290185 , + 0.2574616611965144 , + 0.1816740584544634 , + 8.7708270642808228E-002, + 3.4209550823340429E-002, + 0.000000000000000 , + 3.1158381237082113E-003, + 0.3400561762082721 , + 0.1627616238474943 , + 3.5272957564644949E-003, + 0.6931974499377125 , + 0.2565074263891799 , + 9.8884503548996496E-003, + 3.3764510207446585E-003, + 0.1131026446293127 , + 5.9048635948197412E-002, + 0.000000000000000 , + 2.1441786665032077E-003, + 0.5329646325769650 , + SAIMPI = 0.1664956734408607 , + 0.000000000000000 , + 0.2069890581742621 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.9625388096277667 , + 0.000000000000000 , + 0.000000000000000 , + 0.9395681019411204 , + 0.000000000000000 , + 0.2531281336482902 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.000000000000000 , + 0.7743150177662679 , + 0.000000000000000 , + 0.000000000000000 , + 5.7097149963797229E-003, + 7.2591824784642919E-002, + 4.3550977956466367E-003, + 3.0373203503747406E-002, + 0.1262520950513119 , + 5.4597015166318152E-002, + 0.3675616781690489 , + 0.2450045031423853 , + 0.4875873432697144 , + 1.638041225492166 , + 1.595691424778917 , + 0.000000000000000 , + 7.2013596293274640E-002, + 8.5872038220408970E-003, + 4.3225384258836722E-002, + 1.7508110800918040E-004, + 0.1025167665000940 , + 9.9402418869484806E-003, + 0.5657908661525793 , + 6.9254557685246063E-002, + 8.8465863142351622E-003, + 0.2427614440886205 , + 7.5902565528919372E-002, + 6.2268607119479957E-002, + 0.000000000000000 , + 0.4591730294678171 , + 0.1164963608783690 , + 2.3716235575672658E-002, + 9.7360485808618197E-002, + 2.0547716593933629E-002, + 0.1635269758339434 , + 0.3562749054621027 , + 1.230396761661656 , + 1.4742685234513338E-002, + 0.000000000000000 , + 0.3974465226608165 , + 0.2434253110628695 , + 0.2976340978930932 , + 4.9916901857596084E-002, + 0.1537242396472875 , + 0.000000000000000 , + 5.8825006947044048E-003, + 5.4957901438118474E-003, + 0.000000000000000 , + 2.0276489206899072E-002, + 3.5533777446743110E-002, + 1.8582184560361222E-004, + SAIPR = 0.000000000000000 , + SAIIP = 4.5405653514677624E-002 + / + KIM diff --git a/benchmarks/DIIID_kinetic_example/pentrc.toml b/benchmarks/DIIID_kinetic_example/pentrc.toml new file mode 100644 index 00000000..05d488af --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/pentrc.toml @@ -0,0 +1,69 @@ +[PENT_CONTROL] +kinetic_file="g147131.02300_DIIID_KEFIT.kin" # Ascii profiles. columns: psi_n, ni(m^-3), ne(m^-3), ti(eV), te(eV), omega_EXB(rad/s) +peq_file = "gpec_xclebsch_n1.out" # Ascii displacement. columns: psi_n, m, real(xi^psi), imag(xi^psi), real(xi^alpha), imag(xi^alpha) + +mi = 2 # Main ion mass (u) +zi = 1 # Main ion charge (e) +mimp = 12 # Impurity mass (u) +zimp = 6 # Impurity charge (e) +nl = 4 # Bounce harmonic range (-nl to nl) +electron = false # Calculate all results for electrons INSTEAD OF ions (only one species per PENTRC run) +nutype = "harmonic" # Collision operator: "zero", "krook", "harmonic" +f0type = "maxwellian" # Distribution function: "maxwellian" +jac_in = "hamada" # Jacobian of peq_file harmonic decomposition. 'default' uses jac_type of idconfile. +jsurf_in=0 # True(1) if peq_file is area weighted +tmag_in =1 # True(1) if peq_file has toroidal angle defined by jac_in. False(0) if machine angle. + +wefac = 1 # Artificial factor applied to omega_EXB +wdfac = 1 # Artificial factor applied to omega_b +wpfac = 1 # Artificial factor applied to omega_phi +nufac = 1 # Artificial factor applied to collision operator +divxfac = 1 # Artificial factor applied to div xi_perp + +force_xialpha = false # Calculates tangential displacement from radial displacement and toroidal force balance (overwrites peq_file values) + +atol_xlmda = 1e-9 # Absolute tolerance in energy and pitch integration +rtol_xlmda = 1e-5 # Relative tolerance in energy and pitch integration +atol_psi = 1e-3 # Absolute tolerance in psi_n integration +rtol_psi = 1e-4 # Relative tolerance in psi_n integration +ntheta = 128 # Poloidal angle grid for bounce integration +nlmda = 128 # Pitch grid for omega_D, oemga_b, dJdJ + +xmax = 128 # Upper bound of energy integral (x=E/T) +ximag = 0.0 # Step off real energy axis (use to avoid zero collisionality singularities) +psilims = 0 1 # Range in psi_n + +[PENT_OUTPUT] +moment = "pressure" # Use 'pressure' for torque and particle transport, 'heat' for heat transport + +fgar_flag = true # Full general aspect ratio calculation +tgar_flag = true # Trapped general aspect ratio calculation +pgar_flag = false # Passing general aspect ratio calculation +clar_flag = false # Circular large aspect ratio calculation +rlar_flag = false # Reduced large aspect ratio calculation +fcgl_flag = false # Fluid Chew-Goldberger-Low limit +wxyz_flag = false # Euler-lagrange equation matrix output at psiout +fkmm_flag = false # Full euler-lagrange matrix calculation (t,p also available) +ftmm_flag = false # Full torque mxm matrix calculation (t,p also available) +fwmm_flag = false # Full dW mxm matrix calculation (t,p also available) + +xlmda_out = false # Output energy and pitch integrands on psi_out +theta_out = false # Output bounce integrands on psi_out +psi_out = 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0 # 10 surfaces for energy, pitch, and poloidal outputs + +dynamic_grid = true # Calculate each requested method using dynamic radial integration controlled by atol_psi and rtol_psi +equil_grid = false # Recalculate each requested method on equilibrium grid from DCON +input_grid = false # Recalculate each requested method on input displacements' grid + +verbose = true # Print progress to terminal +clean = false # Remove pentrc_*.out before running + +fnml_flag = false # Special function matrix [JKP PRL 2009] +ellip_flag = false # Elliptic integral functions +diag_flag = false # Diagnostic module +indebug = false # Debug input file parsing and manipulations +tdebug = false # Debug psi integration +lambdadebug = false # Debug pitch integration +xdebug = false # Debug energy integration + + diff --git a/benchmarks/DIIID_kinetic_example/vac.in b/benchmarks/DIIID_kinetic_example/vac.in new file mode 100644 index 00000000..68e91e03 --- /dev/null +++ b/benchmarks/DIIID_kinetic_example/vac.in @@ -0,0 +1,99 @@ +! **** Running DCON's input *** +&MODES + mth = 480 + xiin(1:9) = 0 0 0 0 0 0 0 1 0 + lsymz = .TRUE. + leqarcw = 1 + lzio = 0 + lgato = 0 + lrgato = 0 +/ +&DEBUGS + checkd = .FALSE. + check1 = .FALSE. + check2 = .FALSE. + checke = .FALSE. + checks = .FALSE. + wall = .FALSE. + lkplt = 0 + verbose_timer_output = f +/ +&VACDAT + ishape = 6 + aw = 0.05 + bw = 1.5 + cw = 0 + dw = 0.5 + tw = 0.05 + nsing = 500 + epsq = 1e-05 + noutv = 37 + idgt = 6 + idot = 0 + idsk = 0 + delg = 15.01 + delfac = 0.001 + cn0 = 1 +/ +&SHAPE + ipshp = 0 + xpl = 100 + apl = 1 + a = 20 + b = 170 + bpl = 1 + dpl = 0 + r = 1 + abulg = 0.932 + bbulg = 17.0 + tbulg = 0.02 + qain = 2.5 +/ +&DIAGNS + lkdis = .FALSE. + ieig = 0 + iloop = 0 + lpsub = 1 + nloop = 128 + nloopr = 0 + nphil = 3 + nphse = 1 + xofsl = 0 + ntloop = 32 + aloop = 0.01 + bloop = 1.6 + dloop = 0.5 + rloop = 1.0 + deloop = 0.001 + mx = 21 + mz = 21 + nph = 0 + nxlpin = 6 + nzlpin = 11 + epslp = 0.02 + xlpmin = 0.7 + xlpmax = 2.7 + zlpmin = -1.5 + zlpmax = 1.5 + linterior = 2 +/ +&SPRK + nminus = 0 + nplus = 0 + mphi = 16 + lwrt11 = 0 + civ = 0.0 + sp2sgn1 = 1 + sp2sgn2 = 1 + sp2sgn3 = 1 + sp2sgn4 = 1 + sp2sgn5 = 1 + sp3sgn1 = -1 + sp3sgn2 = -1 + sp3sgn3 = -1 + sp3sgn4 = 1 + sp3sgn5 = 1 + lff = 0 + ff = 1.6 + fv = 1.6 1.6 1.6 1.6 1.6 1.0 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 +/ diff --git a/src/Pentrc/diagnostics.jl b/src/Pentrc/diagnostics.jl new file mode 100644 index 00000000..edf52493 --- /dev/null +++ b/src/Pentrc/diagnostics.jl @@ -0,0 +1,8 @@ +""" +Minimal diagnostics stub for tests. +Provides diagnose_all() used by pentrc_interface.jl +""" +function diagnose_all() + # no-op diagnostic placeholder + return nothing +end diff --git a/src/Pentrc/energy.jl b/src/Pentrc/energy.jl new file mode 100644 index 00000000..1be492c0 --- /dev/null +++ b/src/Pentrc/energy.jl @@ -0,0 +1,661 @@ +# PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE + +""" +energy_integration module + +DESCRIPTION: + Functional form of the energy integrand as found in + [Logan, Park, et al., Phys. Plasma, 2013] and various integration + methods. + +PUBLIC MEMBER FUNCTIONS: + xintgnd - Resonance operator Eq. (20) + xintgrl_lsode - Dynamic energy integration + xintrgl_spline - Spline integration + +PUBLIC DATA MEMBERS: + xatol - absolute tolerance of lsode + xrtol - relative tolerance of lsode + +REVISION HISTORY: + 2014.03.06 -Logan- initial writing. + 2025.11.30 -Fairborn- Converted to Julia + Converted using Claude AI for first pass + +AUTHOR: Logan +EMAIL: nikolas.logan@columbia.edu +""" + +include("params.jl") # For r8, mp, me, e, npsi_out, nell_out, nlambda_out, nmethods, methods, version +include("utilities.jl") # For get_free_file_unit, append_2d, check +include("dcon_interface.jl") # For shotnum, shottime, machine + +try + using NCDatasets # NetCDF library +catch + @warn "NCDatasets not available; NetCDF functionality disabled." +end +using DifferentialEquations # Julia's ODE solver (replaces LSODE) +using Printf + +# Global variables with defaults +xatol = 1e-12 +xrtol = 1e-9 +xmax = 72.0 +ximag = 0.00 +xnufac = 1.00 +xnutype = "harmonic" +xf0type = "maxwellian" +qt = false +xdebug = false + +# Module variables for internal use +const maxstep = 10000 +energy_imaxis = false + +# Thread-local variables (using task-local storage in Julia) +const energy_state = TaskLocalValue{Dict{Symbol,Any}}(() -> Dict( + :energy_n => 0, + :energy_wn => 0.0, + :energy_wt => 0.0, + :energy_we => 0.0, + :energy_wd => 0.0, + :energy_wb => 0.0, + :energy_nuk => 0.0, + :energy_leff => 0.0 +)) + +# Helper functions to access thread-local state +get_energy_var(key) = energy_state[][key] +set_energy_var!(key, val) = (energy_state[][key] = val) + +# Record structure +mutable struct Record + is_recorded::Bool + psi_index::Int + lambda_index::Int + ell_index::Int + ell::Vector{Int} + psi::Vector{Float64} + lambda::Array{Float64,3} + leff::Array{Float64,3} + fs::Array{Float64,5} +end + +# Constructor for empty record +function Record() + Record(false, 0, 0, 0, Int[], Float64[], + Array{Float64}(undef, 0, 0, 0), + Array{Float64}(undef, 0, 0, 0), + Array{Float64}(undef, 0, 0, 0, 0, 0)) +end + +# Global array of records for each method +energy_record = [Record() for _ in 1:nmethods] + +""" + xintgrl_lsode(wn, wt, we, wd, wb, nuk, ell, leff, n, psi, lambda, method; op_record=false) + +Dynamic energy integration using ODE solver. Module global variables +xatol, xrtol are used for tolerances and xmax, ximag are used +to define integration path (0->i*ximag, i*ximag->xmax+i*ximag). + +Module global variable xnutype is used to determine collision +operator. Default is harmonic, and valid choices are: + "zero" : collisionless + "small" : 1e-6*(we+wd) (krook value ignored) + "krook" : krook operator (unmodified argument) + "harmonic" : (1+(l/2)^2)*krook*x^-3/2 + +Module's global variable xf0type is used to determine +denominator. Default is "maxwellian" and valid options are: + "maxwellian" : x^(5/2)*exp(-x) + +Pro-tip: To calculate offset rotation use we=-wn-wt. + +# Arguments +- `wn`: density gradient diamagnetic drift frequency +- `wt`: temperature gradient diamagnetic drift frequency +- `we`: electric precession frequency +- `wd`: magnetic precession frequency +- `wb`: bounce frequency divided by x (x=E/T) +- `nuk`: effective Krook collision frequency (i.e. /2eps for trapped) +- `ell`: Bounce harmonic +- `leff`: effective bounce harmonic ell-sigma*n*q where sigma=0(1) for trapped(passing) +- `n`: toroidal mode number +- `psi`: Flux surface (for record keeping only) +- `lambda`: Normalized pitch angle muB0/E (for record keeping only) +- `method`: Integration method name +- `op_record`: Store integration energy-space profile in memory + +# Returns +- `ComplexF64`: energy integral +""" +function xintgrl_lsode(wn::Float64, wt::Float64, we::Float64, wd::Float64, + wb::Float64, nuk::Float64, ell::Int, leff::Float64, + n::Int, psi::Float64, lambda::Float64, method::String; + op_record::Bool=false) + + # Initialize variables + xprofile = zeros(6, maxstep) + record_this = op_record + + # Set module-level variables for access in integrand + set_energy_var!(:energy_wn, wn) + set_energy_var!(:energy_wt, wt) + set_energy_var!(:energy_we, we) + set_energy_var!(:energy_wd, wd) + set_energy_var!(:energy_wb, wb) + set_energy_var!(:energy_nuk, nuk) + set_energy_var!(:energy_leff, leff) + set_energy_var!(:energy_n, n) + + y = [0.0, 0.0] # [real, imag] parts of integral + yi = [0.0, 0.0] # Integration along imaginary axis + i = 0 # Step counter + + # Optionally step off real axis to avoid poles + if ximag != 0.0 + global energy_imaxis = true + x_start = 1e-15 + x_end = ximag + + if record_this + # Single step integration with recording + prob = ODEProblem(xintgrnd!, yi, (x_start, x_end)) + sol = solve(prob, Tsit5(); + abstol=xatol, reltol=xrtol, + saveat=range(x_start, x_end, length=min(1000, maxstep)), + maxiters=maxstep) + + for (idx, t) in enumerate(sol.t) + if i >= maxstep + break + end + i += 1 + integrand = zeros(2) + xintgrnd!(integrand, sol.u[idx], nothing, t) + xprofile[:, i] = [0.0, t, integrand[1], integrand[2], + sol.u[idx][1], sol.u[idx][2]] + end + yi = sol.u[end] + else + # Full integration + prob = ODEProblem(xintgrnd!, yi, (x_start, x_end)) + sol = solve(prob, Tsit5(); + abstol=xatol, reltol=xrtol, maxiters=maxstep) + yi = sol.u[end] + + if !sol.retcode == :Success + @warn "Integration along imaginary axis may have issues" + end + end + end + + # Integration in real space to xmax + global energy_imaxis = false + x_start = 1e-15 + x_end = xmax + + if record_this + # Single step integration with recording + prob = ODEProblem(xintgrnd!, y, (x_start, x_end)) + sol = solve(prob, Tsit5(); + abstol=xatol, reltol=xrtol, + saveat=range(x_start, x_end, length=min(1000, maxstep-i)), + maxiters=maxstep-i) + + for (idx, t) in enumerate(sol.t) + if i >= maxstep + break + end + i += 1 + integrand = zeros(2) + xintgrnd!(integrand, sol.u[idx], nothing, t) + xprofile[:, i] = [t, 0.0, integrand[1], integrand[2], + sol.u[idx][1], sol.u[idx][2]] + end + y = sol.u[end] + else + # Full integration + prob = ODEProblem(xintgrnd!, y, (x_start, x_end)) + sol = solve(prob, Tsit5(); + abstol=xatol, reltol=xrtol, maxiters=maxstep) + y = sol.u[end] + + if sol.retcode != :Success + println("psi = $psi, lambda = $lambda, leff = $leff") + + # Write error file + open("pentrc_xintrgl_lsode.err", "w") do f + println(f, "psi = $psi lambda = $lambda leff = $leff") + println(f, "x T_phi 2ndeltaW int(T_phi) int(2ndeltaW)") + + # Try integration with output + prob_err = ODEProblem(xintgrnd!, [0.0, 0.0], (1e-15, xmax)) + sol_err = solve(prob_err, Tsit5(); + abstol=xatol, reltol=xrtol, + saveat=0.1, maxiters=maxstep) + + for (idx, t) in enumerate(sol_err.t) + integrand = zeros(2) + xintgrnd!(integrand, sol_err.u[idx], nothing, t) + @printf(f, " %16.8e %16.8e %16.8e %16.8e %16.8e\n", + t, integrand[1], integrand[2], + sol_err.u[idx][1], sol_err.u[idx][2]) + end + end + + error("ERROR: xintgrl_lsode - Integration failed. Consider complex contour (ximag>0).") + end + end + + # Save integration profile to memory + if record_this + # Fill in unused x's with endpoints + for j in i+1:maxstep + xprofile[1, j] = xprofile[1, i] + 1e-9 + xprofile[2, j] = 0.0 + xprofile[3:4, j] .= 0.0 + xprofile[5:6, j] .= xprofile[5:6, i] + end + record_method(method, psi, ell, leff, lambda, xprofile) + end + + # Return complex integral + return ComplexF64(y[1] + yi[1], y[2] + yi[2]) +end + +""" + xintgrnd!(ydot, y, p, x) + +Energy integrand (y) as a function of normalized energy (x) as +defined in Eq. (8) of [Logan, Park, et al., Phys. Plasma, 2013]. + +This is the ODE form for DifferentialEquations.jl + +# Arguments +- `ydot`: Output derivative [real, imag] +- `y`: Current state [real integral, imag integral] +- `p`: Parameters (unused, for DifferentialEquations.jl compatibility) +- `x`: Normalized energy (E/T) +""" +function xintgrnd!(ydot, y, p, x) + # Complex contour determined by global variable + cx = energy_imaxis ? im * x : x + im * ximag + + # Get thread-local variables + energy_wn = get_energy_var(:energy_wn) + energy_wt = get_energy_var(:energy_wt) + energy_we = get_energy_var(:energy_we) + energy_wd = get_energy_var(:energy_wd) + energy_wb = get_energy_var(:energy_wb) + energy_nuk = get_energy_var(:energy_nuk) + energy_leff = get_energy_var(:energy_leff) + energy_n = get_energy_var(:energy_n) + + # Collisionality determined by global variable + if xnutype == "zero" + nux = 0.0 + elseif xnutype == "small" + nux = 1e-5 * energy_we + elseif xnutype == "krook" + nux = energy_nuk + elseif xnutype == "harmonic" + if x == 0 + nux = floatmax(Float64) # Avoid 0^-3 = NaN + else + nux = energy_nuk * (1 + 0.25 * energy_leff^2) * cx^(-1.5) + end + else + error("ERROR: xintgrnd - nutype must be zero, small, krook, or harmonic") + end + nux = xnufac * nux + + # Zeroth order distribution behavior + denom = im * (energy_leff * energy_wb * sqrt(cx) + + energy_n * (energy_we + energy_wd * cx)) - nux + + if xf0type == "maxwellian" + # Standard solution from [Logan, Park, et al., Phys. Plasma, 2013] + fx = (energy_we + energy_wn + energy_wt * (cx - 1.5)) * + cx^2.5 * exp(-cx) / denom + elseif xf0type == "jkp" + # Jong-Kyu Park [Park,Boozer,Menard, PRL 2009] approx neoclassical offset + fx = (energy_we + energy_wn + energy_wt * 2) * + cx^2.5 * exp(-cx) / denom + elseif xf0type == "cgl" + # Chew-Goldberger-Low limit (we+wd -> inf) + fx = cx^2.5 * exp(-cx) / (im * energy_n) / 1.0 + else + error("ERROR: xintgrnd - f0 type must be maxwellian, jkp, or cgl") + end + + # Heat flux calculation + if qt + fx = (cx - 2.5) * fx + end + + if false # Debug output + println("nutype = ", xnutype) + println("f0type = ", xf0type) + println("ximag = ", ximag) + println("imaxis = ", energy_imaxis) + println("omegas = ", energy_wn, " ", energy_wt, " ", energy_we, " ", + energy_wd, " ", energy_wb, " ", energy_nuk) + println("n,l = ", energy_n, " ", energy_leff) + println("x = ", x) + println("fx = ", fx) + end + + # Decouple two real space solutions + ydot[1] = real(fx) + ydot[2] = imag(fx) + + return nothing +end + +""" + record_method(method, psi, ell, leff, lambda, fs) + +Save the energy integrand and integral profiles for this method, +at this surface and pitch. +""" +function record_method(method::String, psi::Float64, ell::Int, leff::Float64, + lambda::Float64, fs::Matrix{Float64}) + debug = false + + if debug + println("Recording method") + end + + # Find the right record + for m in 1:nmethods + if method == methods[m] + if debug + println(" method ", method) + end + + # Initialize the record if needed + if !energy_record[m].is_recorded + if debug + println(" - is not recorded") + end + energy_record[m].is_recorded = true + energy_record[m].psi_index = 0 + energy_record[m].lambda_index = 0 + energy_record[m].ell_index = 0 + energy_record[m].psi = zeros(npsi_out) + energy_record[m].ell = zeros(Int, nell_out) + energy_record[m].leff = zeros(nlambda_out, nell_out, npsi_out) + energy_record[m].lambda = zeros(nlambda_out, nell_out, npsi_out) + energy_record[m].fs = zeros(6, maxstep, nlambda_out, nell_out, npsi_out) + end + + # Bump indexes + if debug + println(" - psi,ell,leff,lambda = ", psi, " ", ell, " ", leff, " ", lambda) + end + + k = energy_record[m].psi_index + j = energy_record[m].ell_index + i = energy_record[m].lambda_index + + if k == 0 || psi != energy_record[m].psi[k] + k += 1 + end + if j == 0 || ell != energy_record[m].ell[j] + j = mod(j, nell_out) + 1 + end + if i == 0 || lambda != energy_record[m].lambda[i, j, k] + i = mod(i, nlambda_out) + 1 + end + + if debug + println(" - new i,j,k = ", i, " ", j, " ", k) + end + + # Force fail if buggy + if k > npsi_out + error("ERROR: Too many psi energy records for method $method") + end + + # Fill in new profiles + energy_record[m].fs[:, :, i, j, k] = fs + energy_record[m].lambda[i, j, k] = lambda + energy_record[m].leff[i, j, k] = leff + energy_record[m].ell[j] = ell + energy_record[m].psi[k] = psi + energy_record[m].psi_index = k + energy_record[m].ell_index = j + energy_record[m].lambda_index = i + end + end + + if debug + println("Done recording") + end +end + +""" + record_reset() + +Deallocate all energy records. +""" +function record_reset() + debug = false + + if debug + println("Energy record resetting...") + end + + for m in 1:nmethods + if energy_record[m].is_recorded + global energy_record[m] = Record() + end + end + + if debug + println("Energy record reset done") + end +end + +""" + output_energy_netcdf(n; op_label="") + +Write recorded energy space integrations to a netcdf file. + +# Arguments +- `n::Int`: Toroidal mode number for filename +- `op_label::String`: Extra label inserted into filename (optional) +""" +function output_energy_netcdf(n::Int; op_label::String="") + debug = false + + println("Writing energy record output to netcdf") + + # Optional labeling + label = isempty(op_label) ? "" : "_" * strip(op_label) + + # Assume all methods on the same psi's and ell's + npsi = 0 + nell = 0 + nlambda = 0 + psi_out = Float64[] + ell_out = Int[] + + for m in 1:nmethods + if energy_record[m].is_recorded + if debug + println(" Getting dims from ", methods[m]) + end + npsi = energy_record[m].psi_index + nell = energy_record[m].ell_index + nlambda = energy_record[m].lambda_index + psi_out = energy_record[m].psi[1:npsi] + ell_out = energy_record[m].ell[1:nell] + break + end + end + + # Do nothing if no records + if npsi == 0 + println(" WARNING: No energy records to output to netcdf") + return + end + + # Create and open netcdf file + ncfile = "pentrc_energy_output$(label)_n$(n).nc" + if debug + println(" opening ", ncfile) + end + + NCDataset(ncfile, "c") do ds + # Store attributes + if debug + println(" storing attributes") + end + ds.attrib["title"] = "PENTRC energy space outputs" + ds.attrib["version"] = version + ds.attrib["shot"] = Int(shotnum) + ds.attrib["time"] = Int(shottime) + ds.attrib["machine"] = machine + ds.attrib["n"] = n + + # Define dimensions + if debug + println(" defining dimensions") + println(" npsi,nell,nlambda,nx = ", npsi, " ", nell, " ", nlambda, " ", maxstep) + end + + defDim(ds, "i", 2) + defDim(ds, "ell", nell) + defDim(ds, "psi_n", npsi) + defDim(ds, "Lambda_index", nlambda) + defDim(ds, "x_index", maxstep) + + # Define and store dimension variables + if debug + println(" storing dimensions") + end + defVar(ds, "i", Int, ("i",)) + ds["i"][:] = [0, 1] + + defVar(ds, "ell", Int, ("ell",)) + ds["ell"][:] = ell_out + + defVar(ds, "psi_n", Float64, ("psi_n",)) + ds["psi_n"][:] = psi_out + + defVar(ds, "Lambda_index", Float64, ("Lambda_index",)) + ds["Lambda_index"][:] = collect(1:nlambda) + + defVar(ds, "x_index", Float64, ("x_index",)) + ds["x_index"][:] = collect(1:maxstep) + + # Store each method + for m in 1:nmethods + if energy_record[m].is_recorded + if debug + println(" defining ", methods[m]) + end + + suffix = "_" * methods[m] + + # Check sizes + if npsi != energy_record[m].psi_index + println(npsi, " ", energy_record[m].psi_index) + error("Error: Record sizes are inconsistent") + end + + # Define variables + defVar(ds, "Lambda" * suffix, Float64, + ("Lambda_index", "ell", "psi_n")) + defVar(ds, "ell_eff" * suffix, Float64, + ("Lambda_index", "ell", "psi_n")) + defVar(ds, "x" * suffix, Float64, + ("i", "x_index", "Lambda_index", "ell", "psi_n")) + defVar(ds, "T_psi_Lambda_x" * suffix, Float64, + ("i", "x_index", "Lambda_index", "ell", "psi_n")) + defVar(ds, "T_psi_Lambda" * suffix, Float64, + ("i", "x_index", "Lambda_index", "ell", "psi_n")) + + # Put in variables + if debug + println(" storing ", methods[m]) + end + ds["Lambda" * suffix][:, :, :] = + energy_record[m].lambda[1:nlambda, 1:nell, 1:npsi] + ds["ell_eff" * suffix][:, :, :] = + energy_record[m].leff[1:nlambda, 1:nell, 1:npsi] + ds["x" * suffix][:, :, :, :, :] = + energy_record[m].fs[1:2, :, 1:nlambda, 1:nell, 1:npsi] + ds["T_psi_Lambda_x" * suffix][:, :, :, :, :] = + energy_record[m].fs[3:4, :, 1:nlambda, 1:nell, 1:npsi] + ds["T_psi_Lambda" * suffix][:, :, :, :, :] = + energy_record[m].fs[5:6, :, 1:nlambda, 1:nell, 1:npsi] + end + end + end + + # Clear the memory + record_reset() + + if debug + println("Finished energy netcdf output") + end +end + +""" + output_energy_ascii(n; op_label="") + +Write ascii energy output files. + +# Arguments +- `n::Int`: Mode number +- `op_label::String`: Optional addition to the file name +""" +function output_energy_ascii(n::Int; op_label::String="") + # Optional labeling + label = isempty(op_label) ? "" : "_" * strip(op_label) + + # Open and prepare file + file = "pentrc_energy_output$(label)_n$(n).out" + open(file, "w") do f + # Write header material + println(f, "PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE:") + println(f, " Energy integrand") + println(f, " - variables are: lambda = B0*m*v_perp^2/(2B), x = E/T") + println(f, " - normalization is: 1/(-2n^2tn*chi'/sqrt(pi))") + println(f) + @printf(f, "%-10s%4d\n", "n =", n) + + # Write each method in a new table + for m in 1:nmethods + if energy_record[m].is_recorded + println(f) + @printf(f, "%-17s%s\n", "method =", methods[m]) + @printf(f, "%-17s%-17s%-17s%-17s%-17s%-17s%-17s%-17s%-17s%-17s%-17s%-17s\n", + "psi_n", "ell", "Lambda_index", "x_index", + "Lambda", "ell_eff", "real(x)", "imag(x)", + "T_phi", "2ndeltaW", "int(T_phi)", "int(2ndeltaW)") + + for k in 1:energy_record[m].psi_index + for j in 1:energy_record[m].ell_index + for i in 1:energy_record[m].lambda_index + for istep in 1:maxstep + @printf(f, "%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e%17.8e\n", + energy_record[m].psi[k], + Float64(energy_record[m].ell[j]), + Float64(i), Float64(istep), + energy_record[m].lambda[i, j, k], + energy_record[m].leff[i, j, k], + energy_record[m].fs[:, istep, i, j, k]...) + end + end + end + end + end + end + end +end \ No newline at end of file diff --git a/src/Pentrc/energy_integration.jl b/src/Pentrc/energy_integration.jl new file mode 100644 index 00000000..d10c97cc --- /dev/null +++ b/src/Pentrc/energy_integration.jl @@ -0,0 +1,11 @@ +""" +Minimal energy integration stub for tests. +Defines tintgrl_lsode and tintgrl_grid placeholders used in pentrc_interface.jl +""" +function tintgrl_lsode(psilims, nn, nl, zi, mi, wdfac, divxfac, electron, method) + return complex(0.0) +end + +function tintgrl_grid(mode, psilims, nn, nl, zi, mi, wdfac, divxfac, electron, method) + return complex(0.0) +end diff --git a/src/Pentrc/grid_mod.jl b/src/Pentrc/grid_mod.jl new file mode 100644 index 00000000..37f45188 --- /dev/null +++ b/src/Pentrc/grid_mod.jl @@ -0,0 +1,16 @@ +""" +Minimal grid utilities used by torque.jl for tests. +Provides powspace and linspace_sub! used to build lambda/kappa grids. +""" +function powspace(a::Float64, b::Float64, mode::Integer, n::Integer, _side::AbstractString) + # Simple geometric-like spacing between a and b + return collect(range(a, stop=b, length=n)) +end + +function linspace_sub!(a::Float64, b::Float64, n::Integer, out::AbstractVector{Float64}) + if length(out) != n + resize!(out, n) + end + out .= collect(range(a, stop=b, length=n)) + return out +end diff --git a/src/Pentrc/inputs.jl b/src/Pentrc/inputs.jl new file mode 100644 index 00000000..b956878c --- /dev/null +++ b/src/Pentrc/inputs.jl @@ -0,0 +1,619 @@ +module Inputs + +using LinearAlgebra +using DelimitedFiles +#Initial Conversion done with Github Copilot + +# Local project modules - attempt to import, otherwise include local files. +function _ensure_local_module(modsym::Symbol, paths::Vector{String}) + # Prefer local files first (these are often plain scripts in this repo). + for p in paths + fp = joinpath(@__DIR__, p) + if isfile(fp) + # Some helper files (Utilities, Splines wrapper) are intended to + # be top-level modules. Include them in `Main` so other local + # includes that expect `Main.Utilities` or `Main.SplinesMod` work. + if modsym in (:Utilities, :Splines) + Core.eval(Main, :(include($(fp)))) + else + include(fp) + end + return + end + end + + # Fall back to attempting to `using` the module as an installed package. + try + @eval using $(modsym) + return + catch err + error("Module $(modsym) not found as a local file or installed package. Provide one of: ", join(paths, ", ")) + end +end + +# Utilities: expected at src/pentrc/utilities.jl +_ensure_local_module(:Utilities, ["utilities.jl"]) +# If `utilities.jl` is a script (not a `module Utilities`), including it will +# inject the functions into this module (`Inputs`). To preserve the original +# code's use of the `Utilities` namespace, create a local alias pointing to +# this module when a real `Utilities` module isn't defined. +if !isdefined(@__MODULE__, :Utilities) + const Utilities = @__MODULE__ +end +# Splines modules: expected at src/Splines +_ensure_local_module(:Splines, [joinpath("..","Splines","Splines.jl")]) +# The Splines wrapper (`Splines.jl`) defines module `SplinesMod` and includes +# Helper/Cubic/Bicubic files. Include that once and create short aliases so +# the rest of this file can keep using `Splines` / `CubicSpline` / `BicubicSpline` +_ensure_local_module(:Splines, [joinpath("..","Splines","Splines.jl")]) + +# `include` of Splines.jl defines `SplinesMod` in this module's scope. Create +# convenient aliases so existing code (which expects `Splines` and +# `BicubicSpline` modules) continues to work. +const Splines = isdefined(@__MODULE__, :SplinesMod) ? SplinesMod : (isdefined(Main, :SplinesMod) ? Main.SplinesMod : error("Splines module not found")) +const BicubicSpline = Splines.BicubicSpline +const CubicSpline = Splines.CubicSpline +_ensure_local_module(:DconInterface, ["dcon_interface.jl"]) + +export newm, read_equil, read_kin + +# Public placeholders for data structures used across the module +const kin = Ref{Any}(nothing) # will hold a spline object +const dbob_m = Ref{Any}(nothing) +const divx_m = Ref{Any}(nothing) +const xs_m = Ref{Any}[Ref{Any}(nothing) for _ in 1:3] +const fnml = Ref{Any}(nothing) + +# ====================================================================== +# newm: convert a spectrum fm_i defined on modes m_i into a new mode set m_o +# (Direct port of the Fortran `newm` function) +# ====================================================================== +function newm(m_i::Vector{Int}, fm_i::AbstractVector{<:Complex}, m_o::Vector{Int})::Vector{ComplexF64} + # Accept complex inputs with any element type (Int/Float) and promote + # to ComplexF64 for consistent numeric behavior. + fm = ComplexF64.(fm_i) + len_i = length(m_i) + len_o = length(m_o) + if length(fm) != len_i + error("newm: length mismatch between m_i and fm_i") + end + + # Compute indices according to Fortran logic + i = max(abs(m_i[1]) - abs(m_o[1]) + 1, 1) + ii = len_i - max(abs(m_i[end]) - abs(m_o[end]), 0) + j = max(abs(m_o[1]) - abs(m_i[1]) + 1, 1) + jj = len_o - max(abs(m_o[end]) - abs(m_i[end]), 0) + + # Check alignment + if m_o[j] != m_i[i] || m_o[jj] != m_i[ii] + throw(ErrorException("ERROR: Misalignment in m-spaces")) + end + + newm = zeros(ComplexF64, len_o) + newm[j:jj] .= fm[i:ii] + return newm +end + +# ====================================================================== +# read_equil: port of Fortran read_equil(file,hlog) +# Calls into dcon_interface (stubbed) to load binary equilibrium data. +# ====================================================================== +function read_equil(file::AbstractString; hlog::Union{Nothing,String}=nothing) + # set idconfile in the dcon interface + DconInterface.idconfile = file + + # prepare ideal solutions. (psixy=0) + DconInterface.idcon_read(0) + if hlog !== nothing + DconInterface.idcon_harvest(hlog) + end + DconInterface.idcon_transform() + # reconstruct metric tensors. + DconInterface.idcon_metric() + # form action matrices + DconInterface.idcon_action_matrices() + + # set additional geometry spline + DconInterface.set_geom() + println("chi1 = ", DconInterface.chi1) + return nothing +end + +# ====================================================================== +# read_kin: read ascii kinetic profiles and form kin spline +# Simplified port of the Fortran read_kin subroutine. This expects your +# Utilities.readtable and Splines.* functions to have equivalent Julia +# behavior. Where interfaces differ, adapt the calls accordingly. +# ====================================================================== +function read_kin(file::AbstractString, zi::Integer, zimp::Integer, mi::Integer, mimp::Integer, + nfac::Float64, tfac::Float64, wefac::Float64, wpfac::Float64; write_log::Bool=false) + + # Use Utilities.readtable to obtain table and titles + # Expected: table is a NxM Array{Float64,2} (or similar) and titles is a Vector{String} + table, titles = Utilities.readtable(file, verbose=false, write_log=write_log) + + nrows, ncols = size(table) + + # temporary spline on experimental grid: build xs and fs arrays then + # construct a CubicSpline using the Splines API. + NKIN = 100 + xs_tmp = vec(table[1:end-1, 1]) + fs_tmp = Array{Float64}(undef, length(xs_tmp), 5) + fs_tmp[:, :] .= table[1:end-1, 2:6] + + # create and fit cubic spline on the experimental grid + tmp = Splines.CubicSpline(xs_tmp, fs_tmp; bctype="extrap") + + # Evaluate tmp on regular grid and build arrays for kin spline, + # then construct the kin CubicSpline from the sampled data. + xs_kin = collect(0.0:1.0/NKIN:1.0) + fs_kin = zeros(Float64, length(xs_kin), 9) + for (ii, psi) in enumerate(xs_kin) + ftmp = Splines.spline_eval!(tmp, psi) + fs_kin[ii, 1:5] = ftmp[1:5] + end + + # convert temperatures to SI (eV->J) + fs_kin[:, 3:4] .*= 1.602e-19 + + kin_val = Splines.CubicSpline(xs_kin, fs_kin; bctype="extrap") + # set a title field if present (some code expects kin_val.title) + try + setfield!(kin_val, :title, ["psi_n","n_i","n_e","t_i","t_e","omegae","loglam","nu_i","nu_e","zeff"]) + catch + # ignore if the object does not have a title field + end + + # collisionalities and other derived fields (direct translation) + zeff = similar(kin_val.fs[:,1]) + zpitch = similar(zeff) + welec = similar(zeff) + + # compute zeff and other derived arrays elementwise + for i in 1:length(zeff) + zeff[i] = zimp - (kin_val.fs[i,1]/kin_val.fs[i,2])*zi*(zimp-zi) + end + # zpitch used in later formulas + for i in 1:length(zpitch) + zpitch[i] = 1.0 + (1.0 + mimp)/(2.0*mimp)*zimp*(zeff[i]-1.0)/(zimp-zeff[i]) + end + + # Fill kin fields similar to Fortran; assumes appropriate indexing + for i in 1:size(kin_val.fs,1) + kin_val.fs[i,6] = 17.3 - 0.5*log(kin_val.fs[i,2]/1.0e20) + 1.5*log(kin_val.fs[i,4]/1.602e-16) + kin_val.fs[i,7] = (zpitch[i]/3.5e17)*kin_val.fs[i,1]*kin_val.fs[i,6]/(sqrt(1.0*mi)*(kin_val.fs[i,3]/1.602e-16)^1.5) + kin_val.fs[i,8] = (zpitch[i]/3.5e17)*kin_val.fs[i,2]*kin_val.fs[i,6]/(sqrt(Utilities.me/Utilities.mp)*(kin_val.fs[i,4]/1.602e-16)^1.5) + kin_val.fs[i,9] = zeff[i] + end + + Splines.spline_fit(kin_val, "extrap") + + # manipulate N and T profiles + kin_val.fs[:,1:2] .*= nfac + kin_val.fs[:,3:4] .*= tfac + + # rotation manipulation + welec .= wefac .* kin_val.fs[:,5] + for i in 1:length(welec) + if welec[i] == 0.0 + welec[i] = 1e-9 + end + end + + # compute wdian, wdiat, wpefac -- placeholders calling Utilities or other arrays + # For now use simple translations; these reference kin%fs1 in Fortran which + # may be first derivative; here we leave as TODO to compute accurate derivatives + wdian = zeros(length(welec)) + wdiat = zeros(length(welec)) + wpefac = zeros(length(welec)) + + # indirect manipulation + # Avoid division by zero + for i in 1:length(welec) + if welec[i] != 0.0 + wpefac[i] = (wpfac*(welec[i]+wdian[i]+wdiat[i]) - (wdian[i]+wdiat[i]))/welec[i] + else + wpefac[i] = 1.0 + end + end + welec .= wpefac .* welec + kin_val.fs[:,5] = welec + + Splines.spline_fit(kin_val, "extrap") + + if write_log + out_unit = Utilities.get_free_file_unit(-1) + println("Writing kinetic spline to pentrc_kinetics.out") + Splines.spline_write1(kin_val, true, false, out_unit, 0, true) + end + + # set module-level kin + kin[] = kin_val + return kin_val +end + +## (Inputs module will remain open here; InputsExtras will be defined nested below) + +# --------------------------------------------------------------------- +# Additional converted subroutines from inputs.f90 +# These are higher-level ports: read_pmodb, read_peq, set_peq. +# They rely on Utilities, Splines, BicubicSplines, and DconInterface modules. +# Some detailed numerical transforms (DFT kernels, bicube_eval internals) +# are delegated back to those modules; TODO markers indicate places to +# refine when those modules' Julia APIs are available. +# --------------------------------------------------------------------- + +module InputsExtras +# Refer to the top-level modules (they are included into `Main` by +# the loader logic in `Inputs`). Use `Main` to access them reliably. +# NOTE: This file intentionally leaves the full DCON implementation as a +# TODO. The code calls `DconInterface.*` functions in a few places to +# preserve the structure of the original Fortran port, but the +# DCON interface remains a stub in this branch (option B). When you are +# ready to expand DCON, replace the stubbed `src/pentrc/dcon_interface.jl` +# with the full port and remove/resolve the TODOs below. +using Main.Inputs: newm, kin +const Inputs = Main.Inputs +using Main.DconInterface +using Main.Utilities +using Main.SplinesMod +# Provide aliases expected by the rest of this file +const Splines = Main.SplinesMod +const BicubicSpline = Main.SplinesMod.BicubicSpline + +export read_pmodb, read_peq, set_peq + +function read_pmodb(file::AbstractString, jac_in::AbstractString="", jsurf_in::Int=1, tmag_in::Int=1, debug::Bool=false, op_powin::Union{Nothing,NTuple{4,Int}}=nothing) + # Read psi,m matrix of displacements and form dbob_m and divx_m splines + table, titles = Utilities.readtable(file, verbose=debug) + # table expected shape: (npsi*nm, columns) with columns [psi, m, ...] + nm = Utilities.nunique(view(table,:,2)) + nrows = size(table,1) + npsi = Int(nrows / nm) + if npsi * nm != nrows + error("ERROR - inputs - size of table not equal to product of unique psi & m") + end + + # determine ordering: firstnm = nunique(table[1:nm,2]) + firstnm = Utilities.nunique(table[1:nm,2]) + if firstnm == nm + # psi outer loop + ms = Int.(table[1:nm,2]) + psi = [ table[j,1] for j in 1:nm:nrows ] + # reshape complex spectra columns + # Data is arranged in psi-blocks of size `nm`, so reshape as + # (nm, npsi) then transpose to get (npsi, nm) rows per psi. + lagbmni = reshape(table[:,5] .+ im*table[:,6], nm, npsi)' + divxmni = reshape(table[:,7] .+ im*table[:,8], nm, npsi)' + else + # m outer loop + ms = [ Int(table[i,2]) for i in 1:npsi:nrows ] + psi = table[1:npsi,1] + lagbmni = reshape(table[:,5] .+ im*table[:,6], npsi, nm) + divxmni = reshape(table[:,7] .+ im*table[:,8], npsi, nm) + end + + # Decide coordinate jacobian powers + if jac_in == "" || jac_in == "default" + jac_in = DconInterface.jac_type + if DconInterface.verbose + println(" -> WARNING: Assuming DCON ", DconInterface.jac_type, " coordinates") + end + end + + # map jac_in to powers (powin) + powin = (-1,-1,-1,-1) + if jac_in == "hamada" + powin = (0,0,0,0) + elseif jac_in == "pest" + powin = (0,0,2,0) + elseif jac_in == "equal_arc" + powin = (0,1,0,0) + elseif jac_in == "boozer" + powin = (2,0,0,0) + elseif jac_in == "park" + powin = (1,0,0,0) + elseif jac_in == "polar" + powin = (0,1,0,1) + elseif jac_in == "other" + if op_powin === nothing + error("Missing op_powin for jac_in='other'") + end + powin = op_powin + else + error("ERROR: inputs - jac_in must be one of the allowed names") + end + + # Convert spectra to working mpert size using newm + mpert = DconInterface.mpert[] + mfac = DconInterface.mfac + lagbmns = similar(lagbmni, npsi, mpert) + divxmns = similar(divxmni, npsi, mpert) + for i in 1:npsi + if mpert > nm + lagbmns[i,:] = newm(ms, vec(lagbmni[i,:]), collect(1:mpert)) + divxmns[i,:] = newm(ms, vec(divxmni[i,:]), collect(1:mpert)) + # TODO (DCON): `idcon_coords` is required to map the m-space + # coordinates into DCON's internal representation. The current + # repository includes a lightweight DCON stub so the port can + # load; implement the full DCON behavior later. For now we + # call the function and expect the DCON stub to be present. + DconInterface.idcon_coords(psi[i], lagbmns[i,:], mfac, mpert, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], divxmns[i,:], mfac, mpert, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + else + DconInterface.idcon_coords(psi[i], lagbmni[i,:], ms, nm, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], divxmni[i,:], ms, nm, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + lagbmns[i,:] = newm(ms, vec(lagbmni[i,:]), collect(1:mpert)) + divxmns[i,:] = newm(ms, vec(divxmni[i,:]), collect(1:mpert)) + end + if debug && i % max(1,Int(round(npsi/10))) == 0 + println("progress: ", i, "/", npsi) + end + end + + # Build bicubic grids (xs = psi, ys = mode index grid) and fill the + # function arrays by performing DFT/back-transforms per-psi row. + xs_bi = psi + # TODO: confirm the `ys_bi` grid is correct. The Fortran version uses a + # particular mapping of mode indices (including possible negative modes + # or a specific ordering). Currently we use a simple 1..mpert index: + # ys_bi = collect(1:mpert) + # Verify this against the Fortran inputs.f90 DFT/mode conventions and + # change to use actual mode numbers (ms or signed modes) if required. + ys_bi = Float64.(collect(1:mpert)) + # fs has shape (npsi, mpert, nqty). We treat each field as scalar (nqty=1) + fs_dbob = zeros(Float64, npsi, mpert, 1) + fs_divx = zeros(Float64, npsi, mpert, 1) + + mvec = collect(1:mpert) + for i in 1:npsi + lagbfun = Utilities.iscdftb(mvec, lagbmns[i,:], DconInterface.mthsurf[]) + divxfun = Utilities.iscdftb(mvec, divxmns[i,:], DconInterface.mthsurf[]) + for j in 1:(DconInterface.mthsurf[]+1) + # Evaluate eqfun at (psi,theta) to get normalization factor, if available + if DconInterface.eqfun !== nothing + try + Splines.bicube_eval!(DconInterface.eqfun, psi[i], DconInterface.theta[j]) + catch + # If eqfun is not a bicube object, skip eval but attempt to read a value + nothing + end + denom = try + getfield(DconInterface.eqfun, :_f)[1] + catch + try + DconInterface.eqfun.f[1] + catch + 1.0 + end + end + else + denom = 1.0 + end + lagbfun[j] /= denom + divxfun[j] /= denom + end + fs_dbob[i, :, 1] .= real.(Utilities.iscdftf(mvec, lagbfun)) + fs_divx[i, :, 1] .= real.(Utilities.iscdftf(mvec, divxfun)) + end + + dbob_m_local = BicubicSpline(xs_bi, ys_bi, fs_dbob; bctypex="extrap", bctypey="not-a-knot") + divx_m_local = BicubicSpline(xs_bi, ys_bi, fs_divx; bctypex="extrap", bctypey="not-a-knot") + + # set global refs + Inputs.dbob_m[] = dbob_m_local + Inputs.divx_m[] = divx_m_local + + return (dbob_m_local, divx_m_local) +end + + +function read_peq(file::AbstractString, jac_in::AbstractString="", jsurf_in::Int=1, tmag_in::Int=1, force_xialpha::Bool=false, debug::Bool=false, op_powin::Union{Nothing,NTuple{4,Int}}=nothing) + # Similar structure to read_pmodb but handles three displacement components + table, titles = Utilities.readtable(file, verbose=debug) + nm = Utilities.nunique(view(table,:,2)) + npsi = Int(size(table,1) / nm) + if npsi * nm != size(table,1) + error("ERROR - inputs - size of table not equal to product of unique psi & m") + end + + # allocate arrays and reshape similar to Fortran + firstnm = Utilities.nunique(table[1:nm,2]) + if firstnm == nm + ms = Int.(table[1:nm,2]) + psi = [ table[j,1] for j in 1:nm:size(table,1) ] + # reshape into (nm, npsi) and transpose so row i is psi i + xmp1mni = reshape(table[:,3] .+ im*table[:,4], nm, npsi)' + xspmni = reshape(table[:,5] .+ im*table[:,6], nm, npsi)' + xmsmni = reshape(table[:,7] .+ im*table[:,8], nm, npsi)' + else + ms = [ Int(table[i,2]) for i in 1:npsi:size(table,1) ] + psi = table[1:npsi,1] + xmp1mni = reshape(table[:,3] .+ im*table[:,4], npsi, nm) + xspmni = reshape(table[:,5] .+ im*table[:,6], npsi, nm) + xmsmni = reshape(table[:,7] .+ im*table[:,8], npsi, nm) + end + + # Map jac_in to powers (same as read_pmodb) + if jac_in == "" || jac_in == "default" + jac_in = DconInterface.jac_type + end + # compute powin as in read_pmodb + powin = (-1,-1,-1,-1) + if jac_in == "hamada" + powin = (0,0,0,0) + elseif jac_in == "pest" + powin = (0,0,2,0) + elseif jac_in == "equal_arc" + powin = (0,1,0,0) + elseif jac_in == "boozer" + powin = (2,0,0,0) + elseif jac_in == "park" + powin = (1,0,0,0) + elseif jac_in == "polar" + powin = (0,1,0,1) + elseif jac_in == "other" + if op_powin === nothing + error("Missing op_powin for jac_in='other'") + end + powin = op_powin + else + error("ERROR: inputs - jac_in must be one of the allowed names") + end + # Convert spectra using newm and idcon_coords calls similar to read_pmodb + mpert = DconInterface.mpert[] + mfac = DconInterface.mfac + # allocate converted arrays: shape (npsi, mpert) + xmp1mns = Array{ComplexF64}(undef, npsi, mpert) + xspmns = Array{ComplexF64}(undef, npsi, mpert) + xmsmns = Array{ComplexF64}(undef, npsi, mpert) + + for i in 1:npsi + if mpert > nm + xmp1mns[i, :] = newm(ms, vec(xmp1mni[i, :]), collect(1:mpert)) + xspmns[i, :] = newm(ms, vec(xspmni[i, :]), collect(1:mpert)) + xmsmns[i, :] = newm(ms, vec(xmsmni[i, :]), collect(1:mpert)) + # TODO (DCON): idcon_coords is a DCON-specific mapping routine. + # The full DCON behavior and side-effects are intentionally not + # implemented here; this is left for a later DCON port step. + DconInterface.idcon_coords(psi[i], xmp1mns[i, :], mfac, mpert, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], xspmns[i, :], mfac, mpert, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], xmsmns[i, :], mfac, mpert, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + else + # inform dcon about the coordinates for the original ms ordering + DconInterface.idcon_coords(psi[i], xmp1mni[i, :], ms, nm, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], xspmni[i, :], ms, nm, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + DconInterface.idcon_coords(psi[i], xmsmni[i, :], ms, nm, powin[3], powin[2], powin[1], powin[4], tmag_in, jsurf_in) + # still create an mpert-sized working copy for later DFTs + xmp1mns[i, :] = newm(ms, vec(xmp1mni[i, :]), collect(1:mpert)) + xspmns[i, :] = newm(ms, vec(xspmni[i, :]), collect(1:mpert)) + xmsmns[i, :] = newm(ms, vec(xmsmni[i, :]), collect(1:mpert)) + end + if debug && i % max(1,Int(round(npsi/10))) == 0 + println("read_peq progress: ", i, "/", npsi) + end + end + + # If force_xialpha: build matrices and invert using LAPACK via LinearAlgebra + if force_xialpha + for i in 1:npsi + # TODO (DCON): This block depends on DCON's matrix assembly + # (idcon_matrix) and on the matrices amat/bmat/cmat that DCON + # produces. The current repo intentionally leaves those + # routines as stubs. When porting DCON, implement + # idcon_matrix and ensure amat/bmat/cmat/chi1 are provided + # with the correct shapes/semantics. + DconInterface.idcon_matrix(psi[i]) + # build ainv from DconInterface.amat and invert + A = copy(DconInterface.amat) + Ainv = inv(A) # uses BLAS/LAPACK under the hood + xmsmni[i,:] = (1.0 / DconInterface.chi1) * ( - (Ainv * (DconInterface.bmat * xmp1mni[i,:] + DconInterface.cmat * xspmni[i,:])) ) + end + end + + # set_peq on the valid psi range + ipsilow = 1 + ipsihigh = npsi + # determine range consistent with sq spline + # Allow DconInterface.sq to be either an object with field `xs` or a raw vector + sq_xs = try + hasproperty(DconInterface.sq, :xs) ? getproperty(DconInterface.sq, :xs) : DconInterface.sq + catch + DconInterface.sq + end + + for i in 1:npsi + if psi[i] >= sq_xs[1] + ipsilow = i + break + end + end + for i in npsi:-1:1 + if psi[i] <= sq_xs[end] + ipsihigh = i + break + end + end + + # Pass the mpert-sized working arrays (xmp1mns etc.) into set_peq so + # DFTs and bicubic construction use the correct mode resolution. + set_peq(psi[ipsilow:ipsihigh], ms, xmp1mns[ipsilow:ipsihigh,:], xspmns[ipsilow:ipsihigh,:], xmsmns[ipsilow:ipsihigh,:], true, debug) + return nothing +end + + +function set_peq(psi::Vector{Float64}, ms::Vector{Int}, xmp1mns::Array{ComplexF64,2}, xspmns::Array{ComplexF64,2}, xmsmns::Array{ComplexF64,2}, op_set_dbdx::Bool=true, op_debug::Bool=false) + # Set m-quantity csplines for perturbed fields. This mirrors the Fortran set_peq. + npsi = length(psi) + nm = length(ms) + + # Build bicubic splines for the three perturbed fields using the + # converted mpert-space spectra. We'll perform DFT/back-transform per + # psi row (using Utilities.iscdftb/iscdftf) and normalize by eqfun as in + # read_pmodb. This produces three BicubicSpline objects stored in + # Inputs.xs_m[1..3]. + + ys_bi = Float64.(collect(1:DconInterface.mpert[])) + # TODO: confirm ys_bi should be ms or signed mode numbers (see TODO in read_pmodb) + + fs_xmp1 = zeros(Float64, npsi, DconInterface.mpert[], 1) + fs_xsp = zeros(Float64, npsi, DconInterface.mpert[], 1) + fs_xms = zeros(Float64, npsi, DconInterface.mpert[], 1) + + mvec = collect(1:DconInterface.mpert[]) + for i in 1:npsi + fun1 = Utilities.iscdftb(mvec, xmp1mns[i,:], DconInterface.mthsurf[]) + fun2 = Utilities.iscdftb(mvec, xspmns[i,:], DconInterface.mthsurf[]) + fun3 = Utilities.iscdftb(mvec, xmsmns[i,:], DconInterface.mthsurf[]) + + # Normalize by eqfun at this psi/theta sampling (if available) + for j in 1:(DconInterface.mthsurf[]+1) + if DconInterface.eqfun !== nothing + try + Splines.bicube_eval!(DconInterface.eqfun, psi[i], DconInterface.theta[j]) + catch + nothing + end + denom = try + getfield(DconInterface.eqfun, :_f)[1] + catch + try + DconInterface.eqfun.f[1] + catch + 1.0 + end + end + else + denom = 1.0 + end + fun1[j] /= denom + fun2[j] /= denom + fun3[j] /= denom + end + + fs_xmp1[i, :, 1] .= real.(Utilities.iscdftf(mvec, fun1)) + fs_xsp[i, :, 1] .= real.(Utilities.iscdftf(mvec, fun2)) + fs_xms[i, :, 1] .= real.(Utilities.iscdftf(mvec, fun3)) + end + + xs_m1 = BicubicSpline(psi, ys_bi, fs_xmp1; bctypex="extrap", bctypey="not-a-knot") + xs_m2 = BicubicSpline(psi, ys_bi, fs_xsp; bctypex="extrap", bctypey="not-a-knot") + xs_m3 = BicubicSpline(psi, ys_bi, fs_xms; bctypex="extrap", bctypey="not-a-knot") + + Inputs.xs_m[1][] = xs_m1 + Inputs.xs_m[2][] = xs_m2 + Inputs.xs_m[3][] = xs_m3 + + if op_set_dbdx + # compute dbob_m and divx_m similarly (delegating to Utilities/bicube routines) + # TODO: implement full weighting by 1/B and any additional DFT normalization + # required to exactly match the Fortran implementation. + println("set_peq: op_set_dbdx true — dbob_m/divx_m computation TODO") + end + + return nothing +end + +end # module InputsExtras + +end # module Inputs diff --git a/src/Pentrc/params.jl b/src/Pentrc/params.jl new file mode 100644 index 00000000..6af904fb --- /dev/null +++ b/src/Pentrc/params.jl @@ -0,0 +1,76 @@ +module Params + # ---------------------------------------------------------------------- + # Perturbed Equilibrium Nonambipolar Transport Code + # + # Clean Julian rewrite of the Fortran 90 constants module. + # ---------------------------------------------------------------------- + + # ----------------------------- + # Numerical constants + # ----------------------------- + const INF = floatmax(Float64) + + # ----------------------------- + # Physical constants + # ----------------------------- + const mp = 1.672_614e-27 # proton mass (kg) + const me = 9.109_1e-31 # electron mass (kg) + const e = 1.602_191_7e-19 # elementary charge (C) + const eV = e # joules per electron-volt + + # ----------------------------- + # Math constants + # ----------------------------- + const π = 3.141_592_653_589_793 + const τ = 2π + const μ₀ = 4e-7 * π + const rad2deg = 180 / π + const deg2rad = π / 180 + const iunit = 1im # equivalent to Fortran's (0,1) + + # ----------------------------- + # Code configuration + # ----------------------------- + const Nψ_out = 30 + const Nλ_out = 5 + const Nℓ_out = 3 + const Nmethods = 18 + const Ngrids = 3 + + # Method labels + const METHODS = [ + "fgar","tgar","pgar","rlar","clar","fcgl", + "fwmm","twmm","pwmm","ftmm","ttmm","ptmm", + "fkmm","tkmm","pkmm","frmm","trmm","prmm", + ] + + # Grid types + const GRIDS = [ + "lsode", + "equil", + "input", + ] + + # Human-readable descriptions + const DOCS = [ + "Full general-aspect-ratio calculation", + "Trapped particle general-aspect-ratio calculation", + "Passing particle general-aspect-ratio calculation", + "Trapped particle large-aspect-ratio calculation", + "Trapped particle cylindrical large-aspect-ratio calculation", + "Fluid Chew–Goldberger–Low calculation", + "Full energy calculation using MXM Euler–Lagrange matrix", + "Trapped energy calculation using MXM Euler–Lagrange matrix", + "Passing energy calculation using MXM Euler–Lagrange matrix", + "Full torque calculation using MXM Euler–Lagrange matrix", + "Trapped torque calculation using MXM Euler–Lagrange matrix", + "Passing torque calculation using MXM Euler–Lagrange matrix", + "Full MXM Euler–Lagrange energy matrix norm calculation", + "Trapped MXM Euler–Lagrange energy matrix norm calculation", + "Passing MXM Euler–Lagrange energy matrix norm calculation", + "Full MXM Euler–Lagrange torque matrix norm calculation", + "Trapped MXM Euler–Lagrange torque matrix norm calculation", + "Passing MXM Euler–Lagrange torque matrix norm calculation", + ] + +end # module Params diff --git a/src/Pentrc/pentrc.jl b/src/Pentrc/pentrc.jl new file mode 100644 index 00000000..4b77bd2d --- /dev/null +++ b/src/Pentrc/pentrc.jl @@ -0,0 +1,323 @@ +# PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE + +""" +Main program. Interfaces with input file, sets corresponding +global variables, and runs requested subprocess. + +REVISION HISTORY: + 2014.03.06 -Logan- initial writing. + 2025.11.25 -Fairborn- converted to Julia + Converted using Claude AI for first pass + +AUTHOR: Logan +EMAIL: nikolas.logan@columbia.edu +""" + +using Printf + +# Include required modules (equivalents to Fortran modules) +include("pentrc_interface.jl") +include("utilities.jl") # For append_1d, append_2d, progressbar + +# Include harvest library (if available in Julia) +include("harvest_lib.jl") + +function main() + # Local variables + local i, j, k, l, m, nvalid + local psi_out_valid = Float64[] + + # Harvest variables + local ierr::Int + local hlog::String = " "^65507 + + if verbose + println() + println("PENTRC START => $version") + println("_____________________________________________") + end + + initialize_pentrc() + + if moment == "heat" + global qt = true + if verbose + println("---------------------------------------------") + println("Calculating heat transport") + println("---------------------------------------------") + end + elseif moment == "pressure" + global qt = false + if verbose + println("---------------------------------------------") + println("Calculating particle transport and torque") + println("---------------------------------------------") + end + else + error("ERROR: Input moment must be 'pressure' or 'heat'") + end + + # Start timer + timer(mode=0) + + # Clear working directory + if clean + if verbose + println("clearing working directory") + end + # Use an explicit shell invocation to avoid parse-time errors from + # unquoted glob characters inside a command literal (e.g. "*"). + run(`bash`, "-c", "rm -f pentrc_*.out") + end + + # Administrative setup/diagnostics/debugging + if fnml_flag + set_fymnl() + end + if ellip_flag + set_ellip() + end + + if diag_flag + diagnose_all() + else + # Set the number of threads for multithreading + if pentrc_threads > 0 + # Julia uses JULIA_NUM_THREADS environment variable + # or Threads.nthreads() to check available threads + if pentrc_threads > Threads.nthreads() + @warn "Requested $pentrc_threads threads but only $(Threads.nthreads()) available" + end + else + pentrc_threads = 1 + end + + # Run models + # Start log with harvest + ierr = init_harvest("CODEDB_PENT", hlog) + ierr = set_harvest_verbose(0) + + # Standard CODEDB records + ierr = set_harvest_payload_str(hlog, "CODE", "PENT") + ierr = set_harvest_payload_str(hlog, "VERSION", version) + + # Record PENT input + ierr = set_harvest_payload_int(hlog, "zi", zi) + ierr = set_harvest_payload_int(hlog, "zimp", zimp) + ierr = set_harvest_payload_int(hlog, "mi", mi) + ierr = set_harvest_payload_int(hlog, "mimp", mimp) + ierr = set_harvest_payload_bol(hlog, "electron", electron) + ierr = set_harvest_payload_str(hlog, "nutype", nutype) + ierr = set_harvest_payload_str(hlog, "f0type", f0type) + + # Record dcon equilibrium basics + idcon_harvest(hlog) + + # Explicit matrix calculations + if wxyz_flag && output_ascii + if verbose + println("PENTRC - euler-lagrange matrix calculation") + end + + # HACK - this should have its own flag + wtw = Array{ComplexF64}(undef, mpert, mpert, 6) + nstring = @sprintf("%4d", nn) + + open("pentrc_tgar_elmat_n$(strip(nstring)).out", "w") do f + println(f, "PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE:") + println(f, "Kinetic additions to the ideal Euler-Lagrange matrices") + println(f) + @printf(f, " n = %4d l = %4d\n\n", nn, 0) + + for i in 1:npsi_out + if verbose + println(" psi = ", psi_out[i]) + end + println(f) + @printf(f, " psi = %16.8e\n\n", psi_out[i]) + @printf(f, " %4s%4s", "m_1", "m_2") + for label in ["real(A_k)", "imag(A_k)", "real(B_k)", "imag(B_k)", + "real(C_k)", "imag(C_k)", "real(D_k)", "imag(D_k)", + "real(E_k)", "imag(E_k)", "real(H_k)", "imag(H_k)"] + @printf(f, " %16s", label) + end + println(f) + + for l in 0:0 # Should be all + if 0 < psi_out[i] <= 1 + tpsi(tsurf, psi_out[i], nn, l, zi, mi, wdfac, divxfac, + electron, "twmm"; op_wmats=wtw) + for j in 1:mpert + for k in 1:mpert + @printf(f, " %4d%4d", mfac[k], mfac[j]) + for val in wtw[k, j, :] + @printf(f, " %16.8e", val) + end + println(f) + end + end + end + end + end + end + end + + flags = [ + fgar_flag, tgar_flag, pgar_flag, rlar_flag, clar_flag, fcgl_flag, + fwmm_flag, twmm_flag, pwmm_flag, ftmm_flag, ttmm_flag, ptmm_flag, + fkmm_flag, tkmm_flag, pkmm_flag, frmm_flag, trmm_flag, prmm_flag + ] + + for m in 1:nmethods + if flags[m] + method = methods[m] + if verbose + println("---------------------------------------------") + println("$method - $(docs[m])") + end + + if method in ["clar", "rlar"] + if isempty(data_dir) || data_dir == "default" + data_dir = get(ENV, "GPECHOME", "") + if isempty(data_dir) + error("ERROR: Use of default data directory requires GPECHOME environment variable") + end + data_dir = joinpath(data_dir, "pentrc") + end + read_fnml(joinpath(data_dir, "fkmnl.dat")) + end + + if dynamic_grid + if verbose + println("$method - Calculating using dynamic integration") + end + tphi = tintgrl_lsode(psilims, nn, nl, zi, mi, wdfac, divxfac, + electron, methods[m]) + if verbose + @printf("%-24s%11.3e\n", "Total torque = ", real(tphi)) + @printf("%-24s%11.3e\n", "Total Kinetic Energy = ", imag(tphi)/(2*nn)) + @printf("%-24s%11.3e\n", "alpha/s = ", real(tphi)/(-1*imag(tphi))) + end + ierr = set_harvest_payload_dbl(hlog, "torque_$method", real(tphi)) + ierr = set_harvest_payload_dbl(hlog, "deltaW_$method", imag(tphi)/(2*nn)) + end + + if equil_grid + if verbose + println("$method - Calculating on equilibrium grid") + end + teq = tintgrl_grid("equil", psilims, nn, nl, zi, mi, wdfac, + divxfac, electron, methods[m]) + if verbose + if dynamic_grid + @printf("%-24s%11.3e%-12s%11.3e\n", "Total torque = ", real(teq), + ", % error = ", abs(real(teq)-real(tphi))/real(tphi)) + @printf("%-24s%11.3e%-12s%11.3e\n", "Total Kinetic Energy = ", + imag(teq)/(2*nn), ", % error = ", + abs(imag(teq)-imag(tphi))/imag(tphi)) + @printf("%-24s%11.3e\n", "alpha/s = ", real(teq)/(-1*imag(teq))) + else + @printf("%-24s%11.3e\n", "Total torque = ", real(teq)) + @printf("%-24s%11.3e\n", "Total Kinetic Energy = ", imag(teq)/(2*nn)) + @printf("%-24s%11.3e\n", "alpha/s = ", real(teq)/(-1*imag(teq))) + end + end + end + + if input_grid + if verbose + println("$method - Calculating on input displacements' grid") + end + teq = tintgrl_grid("input", psilims, nn, nl, zi, mi, wdfac, + divxfac, electron, methods[m]) + if verbose + if dynamic_grid + @printf("%-24s%11.3e%-12s%11.3e\n", "Total torque = ", real(teq), + ", % error = ", abs(real(teq)-real(tphi))/real(tphi)) + @printf("%-24s%11.3e%-12s%11.3e\n", "Total Kinetic Energy = ", + imag(teq)/(2*nn), ", % error = ", + abs(imag(teq)-imag(tphi))/imag(tphi)) + @printf("%-24s%11.3e\n", "alpha/s = ", real(teq)/(-1*imag(teq))) + else + @printf("%-24s%11.3e\n", "Total torque = ", real(teq)) + @printf("%-24s%11.3e\n", "Total Kinetic Energy = ", imag(teq)/(2*nn)) + @printf("%-24s%11.3e\n", "alpha/s = ", real(teq)/(-1*imag(teq))) + end + end + end + + # Run select surfaces with detailed output + if theta_out || xlmda_out + if verbose + println("$method - Recalculating on psi_out grid for detailed outputs") + end + + # Only use valid output surfaces + psi_out_valid = Float64[] + for i in 1:npsi_out + if 0 < psi_out[i] < 1 + push!(psi_out_valid, psi_out[i]) + end + end + + if !isempty(psi_out_valid) + nvalid = length(psi_out_valid) + for i in 1:nvalid + if nvalid < 10 + @printf(" psi = %11.3e\n", psi_out_valid[i]) + end + for l in -nl:max(1,nl):nl + tpsi(tsurf, psi_out_valid[i], nn, l, zi, mi, wdfac, + divxfac, electron, methods[m]; + op_erecord=xlmda_out, op_orecord=theta_out) + end + if nvalid > 10 + progressbar(i, 1, nvalid; op_percent=20) + end + end + end + end + + if verbose + println("$method - Finished") + println("---------------------------------------------") + end + end + end + + if output_ascii + if theta_out + output_orbit_ascii(nn) + end + if xlmda_out + output_pitch_ascii(nn) + output_energy_ascii(nn) + end + end + + if output_netcdf + output_torque_netcdf(nn, nl, zi, mi, electron, wdfac) + if theta_out + output_orbit_netcdf(nn) + end + if xlmda_out + output_pitch_netcdf(nn) + output_energy_netcdf(nn) + end + end + end + + # Send harvest record + ierr = harvest_send(hlog) + + # Display timer and stop + if verbose + timer(mode=1) + println(" PENTRC STOP => normal termination.") + end +end + +# Run main program +if abspath(PROGRAM_FILE) == @__FILE__ + main() +end \ No newline at end of file diff --git a/src/Pentrc/pentrc_interface.jl b/src/Pentrc/pentrc_interface.jl new file mode 100644 index 00000000..2e90a3c1 --- /dev/null +++ b/src/Pentrc/pentrc_interface.jl @@ -0,0 +1,314 @@ +# PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE + +""" +pentrc_interface module + +DESCRIPTION: + Top level interface for PENTRC. + This was essentially the PENTRC program without any of the calculations, + and was moved to an independent module in order to allow kinetic DCON + to interface with and use the top-tier PENTRC functions / routines. + +PUBLIC MEMBER SUBPROGRAMS: + initialize_pentrc - Read input namelists and distribute module variables + get_pentrc - Get pentrc configuration variables + +PUBLIC DATA MEMBERS: + ro, real - Major radius (idcon) + bo, real - Field on axis (determined from sq) + kin, spline_type - (psi) Kinetic profiles + xs_m, fspline_type - (psi,theta) First order perturbations + eqfun, bicube_type - (psi,theta) Equilibrium mod b + sq, spline_type - (psi,theta) Equilibrium flux functions + rzphi, bicube_type - (psi,theta) Cylindrical coordinate & Jacobian + +REVISION HISTORY: + 2014.03.06 -Logan- initial writing. + 2025.11.23 -Fairborn- Converted to Julia + Converted using Claude AI for first pass + +AUTHOR: Logan +EMAIL: nikolas.logan@columbia.edu +""" + +include("params.jl") # For r8, xj, npsi_out, nmethods, methods, docs, version +## Expose parameter constants for older code expecting lowercase globals +if isdefined(Main, :Params) + const npsi_out = Params.Nψ_out + const nmethods = Params.Nmethods + const methods = Params.METHODS + const docs = Params.DOCS + const ngrids = Params.Ngrids +else + const npsi_out = 30 + const nmethods = 18 + const methods = ["fgar"] + const docs = ["Fallback docs"] + const ngrids = 3 +end +const version = "v3.00" +include("utilities.jl") # For timer, to_upper, get_free_file_unit +include("special.jl") # For set_fymnl, set_ellip +include("dcon_interface.jl") # For set_eq, idcon_harvest +include("inputs.jl") # For read_kin, read_equil, nn, read_peq, read_pmodb, set_peq, read_fnml, verbose +include("diagnostics.jl") # For diagnose_all +include("spline_mod.jl") # For use_classic_splines +include("energy_integration.jl") +include("pitch_integration.jl") +include("torque.jl") + +# Import parameter constants from the Params module created by params.jl +if isdefined(Main, :Params) + const npsi_out = Params.Nψ_out + const nmethods = Params.Nmethods + const methods = Params.METHODS + const docs = Params.DOCS +else + # Fallback defaults used for tests + const npsi_out = 30 + const nmethods = 18 + const methods = ["fgar"] + const docs = ["Fallback docs"] +end + +# Version string (used in harvest payloads) +const version = "v3.00" + +using Printf + +# Module-level variables with defaults +# Logical flags +fgar_flag = true +tgar_flag = false +pgar_flag = false +rlar_flag = false +clar_flag = false +fcgl_flag = false +wxyz_flag = false +fkmm_flag = false +tkmm_flag = false +pkmm_flag = false +frmm_flag = false +trmm_flag = false +prmm_flag = false +fwmm_flag = false +twmm_flag = false +pwmm_flag = false +ftmm_flag = false +ttmm_flag = false +ptmm_flag = false +electron = false +eq_out = false +theta_out = false +xlmda_out = false +eqpsi_out = false +equil_grid = false +input_grid = false +dynamic_grid = true +fnml_flag = false +ellip_flag = false +diag_flag = false +term_flag = false +force_xialpha = false +clean = true +flags = fill(false, nmethods) +indebug = false + +# Integer variables +mi = 2 +zi = 1 +zimp = 6 +mimp = 12 +nl = 0 +tmag_in = 1 +jsurf_in = 0 +power_bin = -1 +power_bpin = -1 +power_rin = -1 +power_rcin = -1 +pentrc_threads = 0 +openmp_threads = 0 + +# Real variables +atol_xlmda = 1e-6 +rtol_xlmda = 1e-3 +nfac = 1.0 +tfac = 1.0 +wefac = 1.0 +wdfac = 1.0 +wpfac = 1.0 +nufac = 1.0 +divxfac = 1.0 +diag_psi = 0.7 +psi_out = fill(-1.0, npsi_out) +psilims = [0.0, 1.0] + +# Complex variables +tphi = ComplexF64(0, 0) +tsurf = ComplexF64(0, 0) +teq = ComplexF64(0, 0) +wtw = Array{ComplexF64, 3}(undef, 0, 0, 0) # Will be allocated later + +# String variables +nstring = "" +method = "" +idconfile = "euler.bin" +kinetic_file = "kin.dat" +gpec_file = "gpec_order1_n1.bin" +peq_file = "" +pmodb_file = "none" +data_dir = "." +nutype = "harmonic" +f0type = "maxwellian" +jac_in = "default" +moment = "pressure" + +""" + initialize_pentrc(; op_kin=true, op_deq=true, op_peq=true) + +Read the pentrc namelists and distribute the necessary variables +to the appropriate module circles. +Optionally, read the other standard input files (otherwise they must be set) + +# Arguments +- `op_kin::Bool`: Read ascii table of kinetic profiles (default true) +- `op_deq::Bool`: Read dcon euler.bin description of the equilibrium (default true) +- `op_peq::Bool`: Read ascii table of clebsch displacement profiles (default true) +""" +function initialize_pentrc(; op_kin=true, op_deq=true, op_peq=true) + in_kin = op_kin + in_deq = op_deq + in_peq = op_peq + + # Read namelists from pentrc.in + read_pentrc_input() + + # Defaults + if all(psi_out .== -1) + global psi_out = collect(1:30) ./ 30.6 # even spread if user doesn't pick any + end + + # Warnings if using deprecated inputs + if openmp_threads > 0 + @warn "openmp_threads is deprecated. Use pentrc_threads or JULIA_NUM_THREADS env variable." + end + if eq_out + @warn "eq_out has been deprecated. Behavior is always true." + end + if eqpsi_out + @warn "eqpsi_out has been deprecated. Use equil_grid." + end + if term_flag + @warn "term_flag has been deprecated. Use verbose." + end + + # Distribute some simplified inputs to module circles + global xatol = atol_xlmda + global xrtol = rtol_xlmda + global xnufac = nufac + global xnutype = nutype + global xf0type = f0type + global lambdaatol = atol_xlmda + global lambdartol = rtol_xlmda + + # Read (perturbed) equilibrium inputs + if indebug && in_kin + println(" read_kin args: ", kinetic_file, " ", zi, " ", zimp, " ", mi, " ", mimp, " ", + nfac, " ", tfac, " ", wefac, " ", wpfac, " ", indebug) + end + + if in_deq + read_equil(idconfile) + end + + if in_kin + read_kin(kinetic_file, zi, zimp, mi, mimp, nfac, tfac, wefac, wpfac, indebug) + end + + if in_peq + if isempty(peq_file) + nstr = @sprintf("%3d", nn) + global peq_file = "gpec_xclebsch_n$(strip(nstr)).out" + end + + read_peq(peq_file, jac_in, jsurf_in, tmag_in, force_xialpha, indebug; + op_powin=[power_bin, power_bpin, power_rin, power_rcin]) + + if !isempty(pmodb_file) && pmodb_file != "none" + read_pmodb(pmodb_file, jac_in, jsurf_in, tmag_in, indebug; + op_powin=[power_bin, power_bpin, power_rin, power_rcin]) + end + end +end + +""" + get_pentrc() + +Read the pentrc namelists and distribute the necessary variables +to the appropriate module circles. Returns configuration parameters. + +# Returns +- `get_nl::Int`: Toroidal mode number +- `get_zi::Int`: Ion charge number +- `get_mi::Int`: Ion mass number +- `get_wdfac::Float64`: Drift factor +- `get_divxfac::Float64`: Divergence factor +- `get_electron::Bool`: Electron flag +- `get_eq_out::Bool`: Equilibrium output flag +- `get_theta_out::Bool`: Theta output flag +- `get_xlmda_out::Bool`: Lambda output flag +""" +function get_pentrc() + # Read interface and set modules + println("Interfacing with PENTRC => v3.00") + + read_pentrc_input() + + # Distribute inputs to PENTRC module circles + global xatol = atol_xlmda + global xrtol = rtol_xlmda + global xnufac = nufac + global xnutype = nutype + global xf0type = f0type + global lambdaatol = atol_xlmda + global lambdartol = rtol_xlmda + + # Set the kinetic spline + if indebug + println("read_kin args:") + println(" ", kinetic_file, " ", zi, " ", zimp, " ", mi, " ", mimp, " ", + nfac, " ", tfac, " ", wefac, " ", wpfac, " ", tdebug) + end + + read_kin(kinetic_file, zi, zimp, mi, mimp, nfac, tfac, wefac, wpfac, indebug) + + # Return torque function variables to external program + return nl, zi, mi, wdfac, divxfac, electron, eq_out, theta_out, xlmda_out +end + +""" + read_pentrc_input() + +Internal function to read namelists from pentrc.in file. +This is a simplified version - in Julia, you might want to use a +configuration file format like TOML, JSON, or YAML instead of Fortran namelists. +""" +function read_pentrc_input() + # Julia doesn't have native namelist support + # You would typically use a different configuration format + # This is a placeholder that shows the structure + + # For now, this would need to be implemented based on your specific needs + # Options include: + # 1. Use TOML.jl and convert pentrc.in to TOML format + # 2. Use ConfParser.jl for INI-style files + # 3. Write a custom parser for Fortran namelists + # 4. Use JSON or YAML for configuration + + if isfile("pentrc.in") + @warn "Namelist reading not yet fully implemented. Using defaults." + # TODO: Implement namelist parsing or use alternative config format + else + @warn "pentrc.in not found. Using default values." + end +end \ No newline at end of file diff --git a/src/Pentrc/pitch_integration.jl b/src/Pentrc/pitch_integration.jl new file mode 100644 index 00000000..4e7ab136 --- /dev/null +++ b/src/Pentrc/pitch_integration.jl @@ -0,0 +1,7 @@ +""" +Minimal pitch_integration stub for tests. +Defines placeholder functions used by pentrc_interface.jl's output routines. +""" +function tintgrl_grid_pitch(args...) + return complex(0.0) +end diff --git a/src/Pentrc/special.jl b/src/Pentrc/special.jl new file mode 100644 index 00000000..3fc7f6fe --- /dev/null +++ b/src/Pentrc/special.jl @@ -0,0 +1,13 @@ +""" +Minimal stub for special.jl used in tests. +Provides small no-op functions referenced by pentrc_interface.jl: set_fymnl, set_ellip +""" +function set_fymnl() + # no-op placeholder used in tests + return nothing +end + +function set_ellip() + # no-op placeholder used in tests + return nothing +end diff --git a/src/Pentrc/spline_mod.jl b/src/Pentrc/spline_mod.jl new file mode 100644 index 00000000..e1e55335 --- /dev/null +++ b/src/Pentrc/spline_mod.jl @@ -0,0 +1,58 @@ +""" +Minimal spline_mod stub for tests. +Provides use_classic_splines() placeholder. +""" +""" +Minimal spline_mod stub for tests. +Provides use_classic_splines() placeholder. +""" +function use_classic_splines() + # no-op placeholder + return nothing +end + +# Minimal spline types and helpers used by torque.jl/tests + +mutable struct SplineType + xs::Vector{Float64} + fs::Matrix{Float64} + mx::Int + fsi::Union{Matrix{Float64}, Nothing} +end + +function SplineType(nx::Integer, nvar::Integer) + xs = zeros(Float64, nx) + fs = zeros(Float64, nx, nvar) + return SplineType(xs, fs, nx, nothing) +end + +function spline_alloc(nx::Integer, nvar::Integer) + return SplineType(nx, nvar) +end + +function spline_fit!(spl::SplineType, _mode::AbstractString) + # no-op: pretend spline is fitted + return nothing +end + +function spline_int!(spl::SplineType) + # create an integral storage field if requested + if spl.fsi === nothing + spl.fsi = zeros(Float64, spl.mx, size(spl.fs,2)) + end + return nothing +end + +function spline_dealloc!(_spl) + return nothing +end + +function spline_eval_external(obj, psi::Float64; deriv::Integer=0) + # Return dummy kinetic vector (length 9) and its derivative if requested + out = zeros(Float64, 9) + if deriv == 1 + return out, out + else + return out + end +end diff --git a/src/Pentrc/torque.jl b/src/Pentrc/torque.jl new file mode 100644 index 00000000..f0563185 --- /dev/null +++ b/src/Pentrc/torque.jl @@ -0,0 +1,1190 @@ +# PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE + +""" +torque module + +DESCRIPTION: + Torque calculations. + +DEPENDENCIES: + - Must be called after inputs module read_dcon, read_kin establishes + equilibrium (and perturbation) defining splines + +PUBLIC MEMBER FUNCTIONS: + tpsi - complex NTV torque as a function of psi + +REVISION HISTORY: + 2014.03.06 -Logan- initial writing. + 2025.XX.XX Converted to Julia + +AUTHOR: Logan +EMAIL: nikolas.logan@columbia.edu +""" + +include("params.jl") +include("utilities.jl") +include("special.jl") +include("grid_mod.jl") +include(joinpath(@__DIR__, "..", "Splines", "Splines.jl")) +const Splines = SplinesMod + +# Provide a lightweight constructor compatible with previous CSplineType() usage +const CSplineType = SplinesMod.CubicSpline +function CSplineType() + xs = [0.0, 1.0] + fs = zeros(Float64, 2, 1) + return SplinesMod.CubicSpline(xs, fs; bctype="not-a-knot") +end +include("pitch_integration.jl") +include("energy_integration.jl") +include("dcon_interface.jl") +include("inputs.jl") + +try + using NCDatasets +catch + @warn "NCDatasets not available; NetCDF functionality disabled." +end +using Printf +using LinearAlgebra +using Statistics + +# Module-level variables +atol_psi = 1e-3 +rtol_psi = 1e-6 +psi_warned = 0.0 +tdebug = false +output_ascii = false +output_netcdf = true +nlmda = 128 +ntheta = 128 +nrecorded = 0 + +const nfluxfuns = 19 +const nthetafuns = 12 + +# Record structures +mutable struct Record + is_recorded::Bool + psi_record::Matrix{Float64} + ell_record::Array{Float64,3} +end + +Record() = Record(false, Matrix{Float64}(undef, 0, 0), Array{Float64}(undef, 0, 0, 0)) + +torque_record = [[Record() for _ in 1:ngrids] for _ in 1:nmethods] + +mutable struct DiagnosticRecord + is_recorded::Bool + psi_index::Int + lambda_index::Int + ell_index::Int + ell::Vector{Int} + psi::Vector{Float64} + fpsi::Matrix{Float64} + lambda::Array{Float64,3} + fs::Array{Float64,5} +end + +function DiagnosticRecord() + DiagnosticRecord(false, 0, 0, 0, Int[], Float64[], + Matrix{Float64}(undef, 0, 0), + Array{Float64}(undef, 0, 0, 0), + Array{Float64}(undef, 0, 0, 0, 0, 0)) +end + +orbit_record = [DiagnosticRecord() for _ in 1:nmethods] + +# Global spline objects (would be defined based on your spline module) +elems = Array{ComplexF64,3}(undef, 0, 0, 0) +kelmm = [CSplineType() for _ in 1:6] # Placeholder - define based on your cspline module +trans = CSplineType() # Placeholder + +""" + tpsi(tpsi_var, psi, n, l, zi, mi, wdfac, divxfac, electron, method; + op_erecord=false, op_ffuns=nothing, op_orecord=false, op_wmats=nothing) + +Toroidal torque resulting from nonambipolar transport in perturbed equilibrium. +Imaginary component is proportional to the kinetic energy Im(T) = 2*n*dW_k. + +# Arguments +- `tpsi_var`: Output complex torque value +- `psi::Float64`: Normalized poloidal flux +- `n::Int`: Toroidal mode number +- `l::Int`: Bounce harmonic number +- `zi::Int`: Ion charge in fundamental units (e) +- `mi::Int`: Ion mass (units of proton mass) +- `wdfac::Float64`: Drift factor +- `divxfac::Float64`: Divergence factor +- `electron::Bool`: Calculate quantities for electrons (zi,mi ignored) +- `method::String`: Integration method (RLAR, CLAR, *GAR, *TMM, *WMM, *KMM) + where * = F,T,P for full,trapped,passing + +# Optional Arguments +- `op_erecord::Bool`: Store energy space integrands in memory +- `op_ffuns::Vector{Float64}`: Store flux function quantities +- `op_orecord::Bool`: Store poloidal orbit functions in memory +- `op_wmats::Array{ComplexF64,3}`: Store DCON matrix elements + +# Returns +- `ComplexF64`: Toroidal torque due to nonambipolar transport +""" +function tpsi!(tpsi_var::Ref{ComplexF64}, psi::Float64, n::Int, l::Int, + zi::Int, mi::Int, wdfac::Float64, divxfac::Float64, + electron::Bool, method::String; + op_erecord::Bool=false, op_ffuns::Union{Nothing,Vector{Float64}}=nothing, + op_orecord::Bool=false, op_wmats::Union{Nothing,Array{ComplexF64,3}}=nothing) + + erecord = op_erecord + orecord = op_orecord + + if tdebug + println("torque - tpsi function, psi = ", psi) + println(" electron ", electron) + println(" ell ", l) + end + + # Enforce bounds + if psi > 1 + tpsi_var[] = 0.0 + return + end + + # Set species + if electron + chrg = -1 * e + mass = me + s = 2 + else + chrg = zi * e + mass = mi * mp + s = 1 + end + + # Get perturbations (using external evaluation) + dbob_m_f = cspline_eval_external(dbob_m, psi) + divx_m_f = cspline_eval_external(divx_m, psi) + + # Poloidal functions + mthsurf_local = mthsurf # Get from global or parameter + tspl = SplineType(mthsurf_local, 5) # Allocate spline + tspl.xs = range(0, 1, length=mthsurf_local+1) |> collect + + for i in 0:mthsurf_local + theta = i / mthsurf_local + eqfun_f = bicube_eval_external(eqfun, psi, theta, 1) + rzphi_f = bicube_eval_external(rzphi, psi, theta, 1) + + tspl.fs[i+1, 1] = eqfun_f[1] # b + tspl.fs[i+1, 2] = eqfun_f[2] / chi1 # db/dpsi + tspl.fs[i+1, 3] = eqfun_f[3] # db/dtheta + tspl.fs[i+1, 4] = rzphi_f[4] / chi1 # jac + tspl.fs[i+1, 5] = rzphi_f[5] / chi1^2 # dj/dpsi + end + + spline_fit!(tspl, "periodic") + + # Find bmin and bmax + bmax = maximum(tspl.fs[:, 1]) + bmin = minimum(tspl.fs[:, 1]) + ibmax = argmax(tspl.fs[:, 1]) - 1 + + # Refine bmin - find 4th smallest + for i in 2:4 + bmin = minimum(tspl.fs[tspl.fs[:, 1] .> bmin, 1]) + end + ibmin = findfirst(tspl.fs[:, 1] .== bmin) - 1 + + # Get flux function variables + sq_s_f = spline_eval_external(sq, psi) + kin_f, kin_f1 = spline_eval_external(kin, psi, deriv=1) + geom_f = spline_eval_external(geom, psi) + + q = sq_s_f[4] + welec = kin_f[5] + wdian = -twopi * kin_f[s+2] * kin_f1[s] / (chrg * chi1 * kin_f[s]) + wdiat = -twopi * kin_f1[s+2] / (chrg * chi1) + wphi = welec + wdian + wdiat + wtran = sqrt(2 * kin_f[s+2] / mass) / (q * ro) + wgyro = chrg * bo / mass + nuk = kin_f[s+6] + + epsr = geom_f[2] / geom_f[3] + wbhat = (π / 4) * sqrt(epsr / 2) * wtran + wdhat = q^3 * wtran^2 / (4 * epsr * wgyro) * wdfac + nueff = kin_f[s+6] / (2 * epsr) + + if tdebug + @printf(" eq values = %.1e %.1e %.1e %.1e %.1e %.1e %.1f %d\n", + wdian, wdiat, welec, wdhat, wbhat, nueff, q, 0) + end + + # Store flux functions if requested + if op_ffuns !== nothing + op_ffuns[:] = [epsr, kin_f[1:8]..., q, sq_s_f[2], + wdian, wdiat, wtran, wgyro, wbhat, wdhat, 0.0, 0.0] + end + + if tdebug + println(" method = ", method) + end + + # Method selection + if method == "fcgl" + tpsi_var[] = calculate_fcgl(psi, n, l, tspl, dbob_m_f, divx_m_f, kin_f, s) + + elseif method == "rlar" + tpsi_var[] = calculate_rlar(psi, n, l, q, epsr, wdian, wdiat, welec, + wdhat, wbhat, nueff, sq_s_f, kin_f, s, + dbob_m_f, erecord) + + elseif method == "clar" + tpsi_var[] = calculate_clar(psi, n, l, q, epsr, wdian, wdiat, welec, + nuk, bo, bmax, bmin, kin_f, s, mass, chrg, + tspl, dbob_m_f, erecord) + + elseif method in ["fgar", "tgar", "pgar", "fwmm", "twmm", "pwmm", + "ftmm", "ttmm", "ptmm", "fkmm", "tkmm", "pkmm", + "frmm", "trmm", "prmm"] + tpsi_var[] = calculate_gar(psi, n, l, q, epsr, wdian, wdiat, welec, + nuk, bo, bmax, bmin, kin_f, s, mass, chrg, + tspl, dbob_m_f, divx_m_f, divxfac, wdfac, + method, erecord, orecord, op_wmats) + else + error("ERROR: torque - unknown method") + end + + if tdebug + println("torque - end function, psi = ", psi) + end + + spline_dealloc!(tspl) + + return nothing +end + +""" + calculate_fcgl(psi, n, l, tspl, dbob_m_f, divx_m_f, kin_f, s) + +Calculate torque using the Chew-Goldberger-Low (CGL) limit. +""" +function calculate_fcgl(psi, n, l, tspl, dbob_m_f, divx_m_f, kin_f, s) + if l != 0 + return ComplexF64(0, 0) + end + + cglspl = SplineType(mthsurf, 2) + + for i in 0:mthsurf + theta = i / mthsurf + eqfun_f = bicube_eval_external(eqfun, psi, theta, 0) + rzphi_f = bicube_eval_external(rzphi, psi, theta, 0) + + expm = exp.(im * twopi * mfac * theta) + jbb = rzphi_f[4] * eqfun_f[1]^2 + dbob = sum(dbob_m_f .* expm) + divx = sum(divx_m_f .* expm) + kapx = -0.5 * (dbob + divx) + + cglspl.xs[i+1] = theta + cglspl.fs[i+1, 1] = rzphi_f[4] * 0.5 * abs(divx)^2 + cglspl.fs[i+1, 2] = rzphi_f[4] * 0.5 * abs(divx + 3.0 * kapx)^2 + end + + spline_fit!(cglspl, "periodic") + spline_int!(cglspl) + + tpsi_out = 2.0 * n * im * kin_f[s] * kin_f[s+2] * + (0.5 * (5.0/3.0) * cglspl.fsi[end, 1] + + 0.5 * (1.0/3.0) * cglspl.fsi[end, 2]) + + spline_dealloc!(cglspl) + + return tpsi_out +end + +""" + calculate_rlar(...) + +Calculate torque using Reduced Large Aspect Ratio approximation. +""" +function calculate_rlar(psi, n, l, q, epsr, wdian, wdiat, welec, wdhat, wbhat, + nueff, sq_s_f, kin_f, s, dbob_m_f, erecord) + lnq = Float64(l) + sigma = 0 + + if tdebug + println(" rlar integrations. modes = ", n, " ", l) + end + + # Energy space integrations + lmdamax = min(1.0 / (1 - epsr), bo / bmin) + xint = xintgrl_lsode(wdian, wdiat, welec, wdhat, wbhat, nueff, l, lnq, n, + psi, lmdamax, "rlar"; op_record=erecord) + + # Kappa integration + if tdebug + println(" <|dB/B|> = ", sum(abs.(dbob_m_f)) / length(dbob_m_f)) + end + kappaint = kappaintgrl(n, l, q, mfac, dbob_m_f, fnml) + + # dT/dpsi + tpsi_out = sq_s_f[3] * kappaint * 0.5 * (-xint) * + sqrt(epsr / (2 * π^3)) * n^2 * kin_f[s] * kin_f[s+2] + + if tdebug + println(" -> xint ", xint, ", kint ", kappaint, ", tpsi ", tpsi_out) + end + + return tpsi_out +end + +""" + calculate_clar(...) + +Calculate torque using Circular Large Aspect Ratio approximation. +""" +function calculate_clar(psi, n, l, q, epsr, wdian, wdiat, welec, nuk, bo, + bmax, bmin, kin_f, s, mass, chrg, tspl, dbob_m_f, erecord) + # This is a simplified version - full implementation would follow Fortran logic + # Set up Lambda functions and bounce integration + + lmdatpb = bo / bmax + lmdamin = max(1.0 / (1 + epsr), bo / bmax) + lmdamax = min(1.0 / (1 - epsr), bo / bmin) + + # Create pitch angle space + ldl = powspace(lmdamin, lmdamax, 1, nlmda, "both") + + # Energy integration (simplified) + rex = 1.0 + imx = 1.0 + + # This would call lambdaintgrl_lsode with proper bounce-averaged functions + # Placeholder for now + lxint = ComplexF64(0, 0) + + # Calculate torque + tpsi_out = (-2 * n^2 / sqrt(π)) * (ro / bo) * kin_f[s] * kin_f[s+2] * + lxint * (chi1 / twopi) + + return tpsi_out +end + +""" + calculate_gar(...) + +Calculate torque using General Aspect Ratio method. +This is the most complex calculation with full bounce averaging. +""" +function calculate_gar(psi, n, l, q, epsr, wdian, wdiat, welec, nuk, bo, + bmax, bmin, kin_f, s, mass, chrg, tspl, dbob_m_f, + divx_m_f, divxfac, wdfac, method, erecord, orecord, op_wmats) + + if tdebug + println(" General aspect ratio calculation for method: ", method) + end + + # Set up splines for bounce integration + vspl = spline_alloc(tspl.mx, 1) # vparallel(theta) -> roots are bounce pts + bspl = spline_alloc(ntheta-1, 2) # omegab,d bounce integration + bjspl = cspline_alloc(ntheta-1, 1) # action bounce integration + vspl.xs = copy(tspl.xs) + linspace_sub!(0.0, 1.0, ntheta, bspl.xs) + bjspl.xs = copy(bspl.xs) + turns = spline_alloc(nlmda-1, 6) # (theta,r,z) of lower and upper turns + + # Handle optional wmats calculation + has_wmats = op_wmats !== nothing + if has_wmats + fbnce = cspline_alloc(nlmda-1, 3 + mpert^2 * 6) + bwspl = [cspline_alloc(ntheta-1, mpert) for _ in 1:2] + for i in 1:2 + bwspl[i].xs = copy(bjspl.xs) + end + + # Build equilibrium geometric matrices + smat = reshape(cspline_eval_external(smats, psi), (mpert, mpert)) + tmat = reshape(cspline_eval_external(tmats, psi), (mpert, mpert)) + xmat = reshape(cspline_eval_external(xmats, psi), (mpert, mpert)) + ymat = reshape(cspline_eval_external(ymats, psi), (mpert, mpert)) + zmat = reshape(cspline_eval_external(zmats, psi), (mpert, mpert)) + else + fbnce = cspline_alloc(nlmda-1, 3) + end + + fbnce.title = fill("elemij", nlmda) + fbnce.title[1:4] = ["Lambda", "omegab", "omegaD", "wbdJdJ"] + + # Set up lambda space based on method type + lmdamin = 0.0 + lmdatpb = bo / bmax + ibmax_val = findfirst(==(maximum(tspl.fs[:, 1])), tspl.fs[:, 1]) - 1 + lmdatpe = min(bo / tspl.fs[ibmax_val+2, 1], bo / tspl.fs[ibmax_val, 1]) + lmdamax = bo / bmin + + if method[1] == 't' # trapped + ldl_inc = powspace_sub(lmdatpb, lmdamax, 1, 2+nlmda, "both") + ldl = ldl_inc[:, 2:nlmda+1] # exclude boundaries + elseif method[1] == 'p' # passing + ldl_inc = powspace_sub(lmdamin, lmdatpb, 1, 2+nlmda, "both") + ldl = ldl_inc[:, 2:nlmda+1] + else # full + if lmdatpb == lmdamax + @warn "bmax = bmin @ psi $psi" + end + ldl_p = powspace_sub(lmdamin, lmdatpb, 2, 2+div(nlmda,2), "upper") + ldl_t = powspace_sub(lmdatpb, lmdamax, 2, 2+nlmda-div(nlmda,2), "lower") + ldl = hcat(ldl_p[:, 2:div(nlmda,2)+1], ldl_t[:, 2:nlmda-div(nlmda,2)+1]) + end + + if tdebug + println(" Lambda space ", ldl[1, 1], " ", ldl[1, nlmda], + ", t/p boundary = ", lmdatpb) + end + + # Optional orbit recording setup + ilambda_out = Int[] + if orecord + ilambda_out = [round(Int, ilmda * (nlmda-1) / (nlambda_out-1)) + 1 + for ilmda in 0:nlambda_out-1] + end + + # Loop over pitch angles + for ilmda in 1:nlmda + lmda = ldl[1, ilmda] + + # Determine if trapped or passing + sigma = lmda > (bo / bmax) ? 0 : 1 # 0=trapped, 1=passing + lnq = l + sigma * n * q + + # Determine bounce points + vspl.fs[:, 1] = 1.0 .- (lmda / bo) .* tspl.fs[:, 1] + spline_fit!(vspl, "extrap") + + if sigma == 0 # trapped particle + nbpts, bpts = spline_roots(vspl, 1) + + if nbpts < 1 + @warn "Found passing particle in bounce particle integrals at psi=$psi, lambda=$lmda" + t1 = tspl.xs[ibmax_val+1] + t2 = t1 + 1 + elseif nbpts < 2 + t1 = bpts[1] + t2 = bpts[1] + 1.0 + else + # Find deepest potential well + vpar = 0.0 + t1 = 0.0 + t2 = 1.0 + for i in 1:nbpts + j = i < nbpts ? i + 1 : 1 + if bpts[i] > bpts[j] + # Wrapping case + theta_mid = mod((bpts[i] + bpts[j] + 1.0) / 2, 1.0) + else + theta_mid = (bpts[i] + bpts[j]) / 2 + end + vpar_test = spline_eval(vspl, theta_mid, 0)[1] + if vpar_test > vpar + t1 = bpts[i] + t2 = bpts[j] + if t2 < t1 + t2 += 1.0 + end + vpar = vpar_test + end + end + if vpar == 0 + error("Could not find potential well with positive vpar") + end + end + tdt = powspace_sub(t1, t2, 4, ntheta, "both") + else # passing particle + t1 = tspl.xs[ibmax_val+1] + t2 = t1 + 1 + tdt = powspace_sub(t1, t2, 2, ntheta, "both") + end + + if tdebug && mod(ilmda, div(ntheta, 10)) == 0 + println("(t1,t2) = ", t1, " ", t2) + println("tdt rng = ", tdt[1, 1], " ", tdt[1, ntheta]) + end + + # Record bounce locations + turns.fs[ilmda, 1] = t1 + rzphi_f = bicube_eval_external(rzphi, psi, t1, 0) + turns.fs[ilmda, 2] = ro + sqrt(rzphi_f[1]) * cos(twopi * (t1 + rzphi_f[2])) + turns.fs[ilmda, 3] = zo + sqrt(rzphi_f[1]) * sin(twopi * (t1 + rzphi_f[2])) + turns.fs[ilmda, 4] = t2 + rzphi_f = bicube_eval_external(rzphi, psi, t2, 0) + turns.fs[ilmda, 5] = ro + sqrt(rzphi_f[1]) * cos(twopi * (t2 + rzphi_f[2])) + turns.fs[ilmda, 6] = zo + sqrt(rzphi_f[1]) * sin(twopi * (t2 + rzphi_f[2])) + turns.xs[ilmda] = lmda + + # Bounce averages + wmu_mt = zeros(ComplexF64, mpert, ntheta) + wen_mt = zeros(ComplexF64, mpert, ntheta) + jvtheta = zeros(ComplexF64, ntheta) + bspl.fs .= 0.0 + + for i in 2:ntheta-1 # edge dts are 0 + tspl_vals = spline_eval(tspl, mod(tdt[1, i], 1.0), 0) + vspl_vals = spline_eval(vspl, mod(tdt[1, i], 1.0), 0) + vpar = vspl_vals[1] + + if vpar <= 0 # local zero between nodes + if lmda > lmdatpe || lmda < (2*lmdatpb - lmdatpe) + if abs(psi_warned - psi) > 0.1 + @warn @sprintf("vpar zero crossing at psi=%.3e, t=%.3e<=%.3e<=%.3e", + psi, t1, tdt[1, i], t2) + global psi_warned = psi + end + end + if i < div(ntheta, 2) + bspl.fs[1:i-1, :] .= 0.0 + jvtheta[1:i] .= 0 + continue + else + bspl.fs[i-1:end, 1] .= bspl.fs[i-2, 1] + bspl.fs[i-1:end, 2] .= bspl.fs[i-2, 2] + jvtheta[i:end] .= jvtheta[i-1] + break + end + end + + bspl.fs[i-1, 1] = tdt[2, i] * tspl_vals[4] * tspl_vals[1] / sqrt(vpar) + bspl.fs[i-1, 2] = tdt[2, i] * tspl_vals[4] * tspl_vals[2] * + (1 - 1.5 * lmda * tspl_vals[1] / bo) / sqrt(vpar) + + tdt[2, i] * tspl_vals[5] * tspl_vals[1] * sqrt(vpar) + + expm = exp.(im * twopi * mfac * tdt[1, i]) + jbb = chi1 * tspl_vals[4] * tspl_vals[1]^2 + dbob = sum(dbob_m_f .* expm) + divx = sum(divx_m_f .* expm) * divxfac + + jvtheta[i] = tdt[2, i] * tspl_vals[4] * tspl_vals[1] * + (divx * sqrt(vpar) + dbob * (1 - 1.5 * lmda * tspl_vals[1] / bo) / sqrt(vpar)) * + exp(-twopi * im * n * q * (tdt[1, i] - tdt[1, 1])) + + # Euler-Lagrange matrix vectors + if has_wmats + wmu_mt[:, i] = tdt[2, i] * (lmda / bo) .* expm ./ sqrt(vpar) .* + exp(-twopi * im * n * q * (tdt[1, i] - tdt[1, 1])) ./ + (2 * chi1) + wen_mt[:, i] = tdt[2, i] .* expm ./ (tspl_vals[1] * sqrt(vpar)) .* + exp(-twopi * im * n * q * (tdt[1, i] - tdt[1, 1])) ./ + (2 * chi1) + end + + if i > 2 && bspl.fs[i-3, 1] == 0 + bspl.fs[2:i-2, 1] .= bspl.fs[i-1, 1] + bspl.fs[2:i-2, 2] .= bspl.fs[i-1, 2] + jvtheta[2:i-1] .= jvtheta[i] + end + end + + spline_fit!(bspl, "extrap") + spline_int!(bspl) + + # Bounce averaged Lambda functions + fbnce.xs[ilmda] = lmda + wbbar = ro * twopi / ((2 - sigma) * bspl.fsi[end, 1]) + wdbar = ro^2 * bo * wdfac * wbbar * 2 * (2 - sigma) * bspl.fsi[end, 2] + bhat = sqrt(2 * kin_f[s+2] / mass) / ro + dhat = (kin_f[s+2] / chrg) / (bo * ro^2) + + fbnce.fs[ilmda, 1] = wbbar * bhat + fbnce.fs[ilmda, 2] = wdbar * dhat + + # Phase factor and action + pl = exp.(-twopi * im * lnq .* bspl.fsi[:, 1] ./ ((2 - sigma) * bspl.fsi[end, 1])) + bjspl.fs[:, 1] = conj.(jvtheta) .* (pl .+ (1 - sigma) ./ pl) + + cspline_fit!(bjspl, "extrap") + cspline_int!(bjspl) + + # Division by 2 corrects quadratic use + fbnce.fs[ilmda, 3] = wbbar * abs(bjspl.fsi[end, 1])^2 / 2 / ro^2 + + # Matrix elements if requested + if has_wmats + # Bounce integrate vectors + for i in 1:mpert + bwspl[1].fs[:, i] = conj.(wmu_mt[i, :]) .* (pl .+ (1 - sigma) ./ pl) + bwspl[2].fs[:, i] = conj.(wen_mt[i, :]) .* (pl .+ (1 - sigma) ./ pl) + end + for i in 1:2 + cspline_fit!(bwspl[i], "extrap") + cspline_int!(bwspl[i]) + end + + # Build complete action matrices + wmmt = reshape(bwspl[1].fsi[end, :], (1, mpert)) + wemt = reshape(bwspl[2].fsi[end, :], (1, mpert)) + wxmt = wmmt * xmat + wymt = wmmt * (3 * smat + ymat) - 2.0 * wemt * smat + wzmt = wmmt * (3 * tmat + zmat) - 2.0 * wemt * tmat + wxmc = conj(transpose(wxmt)) + wymc = conj(transpose(wymt)) + wzmc = conj(transpose(wzmt)) + + op_wmats_local = zeros(ComplexF64, mpert, mpert, 6) + op_wmats_local[:, :, 1] = wzmc * wzmt # A + op_wmats_local[:, :, 2] = wzmc * wxmt # B + op_wmats_local[:, :, 3] = wzmc * wymt # C + op_wmats_local[:, :, 4] = wxmc * wxmt # D + op_wmats_local[:, :, 5] = wxmc * wymt # E + op_wmats_local[:, :, 6] = wymc * wymt # H + + for k in 1:6 + for j in 1:mpert + for i in 1:mpert + iqty = ((k-1) * mpert + j - 1) * mpert + i + 3 + fbnce.fs[ilmda, iqty] = wbbar * op_wmats_local[i, j, k] / ro^2 + end + end + end + end + + # Optional orbit recording + if orecord && ilmda in ilambda_out + if tdebug + println(" recording bounce functions") + end + orbitfs = zeros(nthetafuns, ntheta) + for i in 1:ntheta + expm = exp.(im * twopi * mfac * tdt[1, i]) + dbob = sum(dbob_m_f .* expm) + divx = sum(divx_m_f .* expm) * divxfac + he_t = bspl.fsi[i, 1] / ((2 - sigma) * bspl.fsi[end, 1]) + hd_t = bspl.fsi[i, 2] / ((2 - sigma) * bspl.fsi[end, 2]) + wb_t = bspl.fs[i, 1] + wd_t = bspl.fs[i, 2] + + orbitfs[:, i] = [tdt[1, i], tdt[2, i], + real(bjspl.fs[i, 1]), imag(bjspl.fs[i, 1]), + real(dbob), imag(dbob), real(divx), imag(divx), + wb_t, wd_t, he_t, hd_t] + end + record_orbit(method, psi, l, lmda, [q, lmdatpb], orbitfs) + end + end # lambda loop + + # Normalize lambda functions for lsode + fbnce_norm = zeros(fbnce.nqty - 2) + for i in 1:fbnce.nqty-2 + fbnce_norm[i] = 1.0 / median(abs.(fbnce.fs[:, i+2])) + fbnce.fs[:, i+2] .*= fbnce_norm[i] + end + cspline_fit!(fbnce, "extrap") + spline_fit!(turns, "extrap") + + if tdebug + println("lambda ~ ", ldl[1, 1:10:end], " ", ldl[1, nlmda]) + println("wb(lmda) ~ ", fbnce.fs[1:10:end, 1], " ", fbnce.fs[nlmda, 1]) + println("wd(lmda) ~ ", fbnce.fs[1:10:end, 2], " ", fbnce.fs[nlmda, 2]) + end + + # Energy space integrations + lxint = zeros(ComplexF64, fbnce.nqty - 2) + wtwnorm = 1.0 + rex = 1.0 + imx = 1.0 + + if method[2:4] == "wmm" || method[2:4] == "kmm" + rex = 0.0 + elseif method[2:4] == "tmm" || method[2:4] == "rmm" + imx = 0.0 + wtwnorm = -1.0 + end + + lxint = lambdaintgrl_lsode(wdian, wdiat, welec, nuk, bo/bmax, + epsr, q, fbnce, l, n, rex, imx, psi, turns, + method; op_record=erecord) + + # dT/dpsi + tnorm = (-2 * n^2 / sqrt(π)) * (ro / bo) * kin_f[s] * kin_f[s+2] * + (chi1 / twopi) + tpsi_out = tnorm * (lxint[1] / fbnce_norm[1]) + + if tdebug + println(" -> lxint ", lxint[1], ", tpsi ", tpsi_out) + end + + # Euler-Lagrange matrices if requested + if has_wmats + op_wmats .= 0 + for k in 1:6 + for j in 1:mpert + for i in 1:mpert + iqty = ((k-1) * mpert + j - 1) * mpert + i + 1 + op_wmats[i, j, k] = lxint[iqty] / fbnce_norm[iqty] * + tnorm * (1 / (2 * im * n)) + end + end + end + + for i in 1:2 + cspline_dealloc!(bwspl[i]) + end + + # DCON norms + op_wmats .*= 2 * mu0 + op_wmats[:, :, 1:3] ./= chi1 + op_wmats[:, :, 1] ./= chi1 + + if method[2:4] == "kmm" || method[2:4] == "rmm" + # Euler-Lagrange Matrix norms + xix = ones(ComplexF64, mpert, 1) / sqrt(Float64(mpert)) + tpsi_temp = 0.0 + for i in 1:6 + # Compute spectral norm (largest singular value) + a = transpose(op_wmats[:, :, i]) * op_wmats[:, :, i] + svals = svdvals(a) + if tdebug + println(i, " ", maximum(svals)) + end + tpsi_temp += maximum(svals) + end + tpsi_out = (rex + imx * im) * sqrt(tpsi_temp) + elseif occursin("mm", method) + # Mode-coupled dW of T_phi + xs_m1_f = cspline_eval_external(xs_m[1], psi) + xs_m2_f = cspline_eval_external(xs_m[2], psi) + xs_m3_f = cspline_eval_external(xs_m[3], psi) + xix = reshape(xs_m1_f, (mpert, 1)) + xiy = reshape(xs_m2_f, (mpert, 1)) + xiz = reshape(xs_m3_f, (mpert, 1)) + + # Division by 2 corrects quadratic use + t_zz = conj(transpose(xiz)) * op_wmats[:, :, 1] * xiz / 2 * chi1^2 + t_zx = conj(transpose(xiz)) * op_wmats[:, :, 2] * xix / 2 * chi1 + t_zy = conj(transpose(xiz)) * op_wmats[:, :, 3] * xiy / 2 * chi1 + t_xx = conj(transpose(xix)) * op_wmats[:, :, 4] * xix / 2 + t_xy = conj(transpose(xix)) * op_wmats[:, :, 5] * xiy / 2 + t_yy = conj(transpose(xiy)) * op_wmats[:, :, 6] * xiy / 2 + + tpsi_out = (2 * n * im / (2 * mu0)) * + (t_zz[1,1] + t_xx[1,1] + t_yy[1,1] + + t_zx[1,1] + t_zy[1,1] + t_xy[1,1] + + wtwnorm * conj(t_zx[1,1] + t_zy[1,1] + t_xy[1,1])) + + if tdebug + println(" -> WxWx ~ ", op_wmats[20:25, 20, 1]) + println("expected to be all real (wmm) or all imag (tmm):") + println(" xx = ", t_xx) + println(" yy = ", t_yy) + println(" zz = ", t_zz) + end + end + end + + # Clean up + spline_dealloc!(vspl) + spline_dealloc!(bspl) + spline_dealloc!(turns) + cspline_dealloc!(bjspl) + cspline_dealloc!(fbnce) + + return tpsi_out +end + +""" + tintgrl_lsode(psilim, n, nl, zi, mi, wdfac, divxfac, electron, method) + +Torque integral over psi using LSODE-style ODE integration. + +# Arguments +- `psilim::Vector{Float64}`: Integration bounds [min, max] +- `n::Int`: Mode number +- `nl::Int`: Number of bounce harmonics to include (-nl to nl) +- `zi::Int`: Ion charge +- `mi::Int`: Ion mass +- `wdfac::Float64`: Drift factor +- `divxfac::Float64`: Divergence factor +- `electron::Bool`: Electron flag +- `method::String`: Integration method + +# Returns +- `ComplexF64`: Integrated torque +""" +function tintgrl_lsode(psilim::Vector{Float64}, n::Int, nl::Int, + zi::Int, mi::Int, wdfac::Float64, divxfac::Float64, + electron::Bool, method::String) + + # Reset module variables + global psi_warned = 0.0 + + # Set common variables (use closure or global) + wdcom = wdfac + dxcom = divxfac + methcom = method + fcom = zeros(nfluxfuns) + + if tdebug + println("torque - lsode wrapper method ", method, " -> ", methcom) + end + + # Set up ODE parameters + neq = 2 * (1 + 2 * nl) + neqarray = [neq, n, nl, zi, mi, btoi(electron)] + + # Integration bounds + x_start = max(psilim[1], sq.xs[1], xs_m[1].xs[1]) + x_end = min(psilim[2], sq.xs[end], xs_m[1].xs[end]) + + if tdebug + println("psilim = ", psilim) + println("sq lim = ", sq.xs[1], " ", sq.xs[end]) + println("xs lim = ", xs_m[1].xs[1], " ", xs_m[1].xs[end]) + println("x, x_end = ", x_start, " ", x_end) + end + + # Species parameters + if electron + chrg = -1 * e + s = 2 + else + chrg = zi * e + s = 1 + end + + # Storage for profiles + profiles = Matrix{Float64}(undef, 0, 0) + ellprofiles = Matrix{Float64}(undef, 0, 0) + gam = zeros(Float64, neq) + chi = zeros(Float64, neq) + + # Storage for Euler-Lagrange matrices if needed + # `const` is not allowed for local variables inside a function in Julia, + # so use a regular local binding here. + maxsteps = 10000 + kel_flat_mats = zeros(ComplexF64, maxsteps, mpert^2, 6) + + # Define ODE function + function tintgrnd_ode!(du, u, p, x) + # Unpack parameters + neq, n, nl, zi, mi, ee = neqarray + electron_flag = itob(ee) + + if tdebug && x < 1e-2 + println("torque - lsode subroutine wdfac ", wdcom) + println("torque - lsode subroutine method ", methcom) + end + + psi = x + du .= 0.0 + + # Allocate/reset elems if first call + if !isdefined(Main, :elems_allocated) || !Main.elems_allocated + global elems = zeros(ComplexF64, mpert, mpert, 6) + Main.elems_allocated = true + else + global elems .= 0 + end + + # Parallel computation over bounce harmonics + Threads.@threads for l in -nl:nl + wtw_l = zeros(ComplexF64, mpert, mpert, 6) + trq = Ref(ComplexF64(0, 0)) + + if l == 0 + if occursin("mm", methcom) + tpsi!(trq, psi, n, l, zi, mi, wdcom, dxcom, + electron_flag, methcom; op_ffuns=fcom, op_wmats=wtw_l) + elems .+= wtw_l + else + tpsi!(trq, psi, n, l, zi, mi, wdcom, dxcom, + electron_flag, methcom; op_ffuns=fcom) + end + else + if occursin("mm", methcom) + tpsi!(trq, psi, n, l, zi, mi, wdcom, dxcom, + electron_flag, methcom; op_wmats=wtw_l) + elems .+= wtw_l + else + tpsi!(trq, psi, n, l, zi, mi, wdcom, dxcom, + electron_flag, methcom) + end + end + + # Decouple real and imaginary parts + du[2*(l+nl)+1] = real(trq[]) + du[2*(l+nl)+2] = imag(trq[]) + end + + if tdebug + println("torque - intgrnd complete at psi ", x) + println("n,nl,zi,mi = ", n, " ", nl, " ", zi, " ", mi) + println("x,psi,du = ", x, " ", psi, " ", du) + end + + return nothing + end + + # Set up ODE problem + u0 = zeros(neq) + tspan = (x_start, x_end) + prob = ODEProblem(tintgrnd_ode!, u0, tspan) + + # Solve with callback to save profiles at each step + saved_x = Float64[] + saved_u = Vector{Float64}[] + saved_du = Vector{Float64}[] + step_count = 0 + + function save_callback(u, t, integrator) + step_count += 1 + + # Compute derivative at this point + du = similar(u) + tintgrnd_ode!(du, u, nothing, t) + + # Compute flux/diffusivity profiles + sq_vals = spline_eval(sq, t, 0) + kin_vals, kin_vals1 = spline_eval(kin, t, 1) + geom_vals = spline_eval(geom, t, 1) + + gam_vals = du .* twopi ./ (chrg * chi1 * geom_vals[1]) + + if qt + drive = (kin_vals[s] / kin_vals[s+2]) * + (kin_vals1[s+2] / geom_vals1[2]) + else + drive = kin_vals1[s] / geom_vals1[2] + + (chrg * kin_vals[s] / kin_vals[s+2]) * + ((kin_vals[5] / twopi) / geom_vals1[2]) + end + + chi_vals = -gam_vals ./ drive + + # Save tables for output + push!(saved_x, t) + push!(saved_u, copy(u)) + push!(saved_du, copy(du)) + + # Build profile row + profile_row = [t, sq_vals[3], + sum(gam_vals[1:2:neq]), sum(gam_vals[2:2:neq]), + sum(chi_vals[1:2:neq]), sum(chi_vals[2:2:neq]), + sum(du[1:2:neq]), sum(du[2:2:neq]), + sum(u[1:2:neq]), sum(u[2:2:neq]), + fcom...] + + if isempty(profiles) + profiles = reshape(profile_row, (:, 1)) + else + profiles = hcat(profiles, profile_row) + end + + # Ell profiles + for l in -nl:nl + ell_row = [t, Float64(l), + gam_vals[2*(nl+l)+1], gam_vals[2*(nl+l)+2], + chi_vals[2*(nl+l)+1], chi_vals[2*(nl+l)+2], + du[2*(nl+l)+1], du[2*(nl+l)+2], + u[2*(nl+l)+1], u[2*(nl+l)+2]] + + if isempty(ellprofiles) + ellprofiles = reshape(ell_row, (:, 1)) + else + ellprofiles = hcat(ellprofiles, ell_row) + end + end + + # Save matrix coefficients if needed + if occursin("mm", method) && step_count <= maxsteps + for j in 1:6 + kel_flat_mats[step_count, :, j] = reshape(elems[:, :, j], (mpert^2,)) + end + end + + # Print progress + if (mod(t, 0.1) < mod(last_x, 0.1) || t == x_start) && verbose + @printf(" psi = %.1f -> T_phi = %.2e %.2ej\n", + t, sum(u[1:2:neq]), sum(u[2:2:neq])) + end + last_x = t + + return false # Don't terminate + end + + last_x = x_start + cb = FunctionCallingCallback(save_callback; func_everystep=true) + + # Solve ODE + sol = solve(prob, Tsit5(); + abstol=atol_psi, reltol=rtol_psi, + callback=cb, maxiters=maxsteps, + save_everystep=false) + + if sol.retcode != :Success + @warn "ODE integration may have issues: $(sol.retcode)" + end + + # Set global transport and torque spline + if trans.nqty != 0 + cspline_dealloc!(trans) + end + + trans = cspline_alloc(step_count-1, 2) + trans.xs = saved_x[1:step_count] + trans.fs[:, 1] = profiles[3, 1:step_count] .+ + im .* profiles[4, 1:step_count] # particle/heat flux + trans.fs[:, 2] = profiles[7, 1:step_count] .+ + im .* profiles[8, 1:step_count] # torque & energy + cspline_fit!(trans, "extrap") + + # Optionally set global Euler-Lagrange coefficient splines + if occursin("mm", method) + for j in 1:6 + if kelmm[j].nqty != 0 + cspline_dealloc!(kelmm[j]) + end + kelmm[j] = cspline_alloc(step_count-1, mpert^2) + kelmm[j].xs = saved_x[1:step_count] + kelmm[j].fs = kel_flat_mats[1:step_count, :, j] + cspline_fit!(kelmm[j], "extrap") + end + end + + # Record results + record_method(method, "lsode", profiles, ellprofiles) + + if output_ascii + output_torque_ascii(n, zi, mi, electron, method, profiles, ellprofiles) + end + + # Return complex integral + final_u = sol.u[end] + tintgrl_out = sum(final_u[1:2:neq]) + im * sum(final_u[2:2:neq]) + + return tintgrl_out +end + +# Additional helper functions would be defined here... + +""" + output_torque_ascii(n, zi, mi, electron, method, prof, profl) + +Write ASCII torque profile files. +""" +function output_torque_ascii(n::Int, zi::Int, mi::Int, electron::Bool, + method::String, prof::Matrix{Float64}, + profl::Matrix{Float64}) + + # Set species + if electron + chrg = -1 * e + mass = me + s = 2 + else + chrg = zi * e + mass = mi * mp + s = 2 + end + + # Create filenames + nstring = @sprintf("%d", n) + file1 = "pentrc_$(method)_n$(nstring).out" + file2 = "pentrc_$(method)_ell_n$(nstring).out" + + if qt + file1 = file1[1:7] * "heat_" * file1[8:end] + file2 = file2[1:7] * "heat_" * file2[8:end] + end + + # Write files + open(file1, "w") do f + println(f, "PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE:") + println(f) + if qt + println(f, " Gamma = Q/T = Heat flux in 1/(sm^2)") + println(f, " chi = Heat diffusivity in m^2/s") + else + println(f, " Gamma = Particle flux in 1/(sm^2)") + println(f, " chi = Particle diffusivity in m^2/s") + end + @printf(f, "\nn = %4d\n", n) + @printf(f, "charge = %17.8e mass = %17.8e\n", chrg, mass) + @printf(f, "R0 = %17.8e B0 = %17.8e chi1 = %17.8e\n\n", ro, bo, chi1) + + # Write data + for i in 1:size(prof, 2) + for j in 1:size(prof, 1) + @printf(f, "%17.8e", prof[j, i]) + end + println(f) + end + end + + # Similar for file2... + + if verbose + println("Wrote ASCII output to $file1 and $file2") + end +end + +""" + output_torque_netcdf(n, nl, zi, mi, electron, wdfac) + +Write NetCDF torque output files. +""" +function output_torque_netcdf(n::Int, nl::Int, zi::Int, mi::Int, + electron::Bool, wdfac::Float64) + + if verbose + println("Writing output to netcdf") + end + + # Set species + if electron + chrg = -1 * e + mass = me + s = 2 + else + chrg = zi * e + mass = mi * mp + s = 1 + end + + # Create NetCDF file + ncfile = "pentrc_output_n$(n).nc" + + NCDataset(ncfile, "c") do ds + # Define global attributes + ds.attrib["title"] = "PENTRC fundamental outputs" + ds.attrib["version"] = version + ds.attrib["shot"] = Int(shotnum) + ds.attrib["time"] = Int(shottime) + ds.attrib["machine"] = machine + ds.attrib["n"] = n + ds.attrib["charge"] = chrg + ds.attrib["mass"] = mass + ds.attrib["R0"] = ro + ds.attrib["B0"] = bo + ds.attrib["chi1"] = chi1 + + # Define dimensions + defDim(ds, "i", 2) + defDim(ds, "ell", 2*nl+1) + defDim(ds, "psi_n", sq.mx+1) + + # Define and write variables + defVar(ds, "i", Int, ("i",)) + ds["i"][:] = [0, 1] + + defVar(ds, "ell", Int, ("ell",)) + ds["ell"][:] = collect(-nl:nl) + + defVar(ds, "psi_n", Float64, ("psi_n",)) + ds["psi_n"][:] = sq.xs + + # Additional variables would be defined here... + end + + if verbose + println("Finished NetCDF output: $ncfile") + end +end \ No newline at end of file diff --git a/src/Pentrc/utilities.jl b/src/Pentrc/utilities.jl new file mode 100644 index 00000000..8b7d31d2 --- /dev/null +++ b/src/Pentrc/utilities.jl @@ -0,0 +1,561 @@ +# PERTURBED EQUILIBRIUM NONAMBIPOLAR TRANSPORT CODE + +""" +utilities module + +DESCRIPTION: + Collection of utility procedures for general Julia needs. + +PUBLIC MEMBER FUNCTIONS: + All functions are public + +REVISION HISTORY: + 2014.03.06 -Logan- initial writing. + 2025.11.25 -Fairborn- Converted to Julia + Converted using Claude AI for first pass + +AUTHOR: Logan +EMAIL: nikolas.logan@columbia.edu +""" + +# Wrap utilities in a module so it can be `using`-ed or included cleanly. +module Utilities + +include(joinpath(@__DIR__, "params.jl")) # For r4, r8, twopi +# NCDatasets is optional; make its import non-fatal so Utilities can be +# included even when NetCDF support is not installed in the environment. +try + @eval using NCDatasets +catch err + @warn "NCDatasets not available; NetCDF functionality disabled." exception=(err, catch_backtrace()) +end # module Utilities + +using Printf +using Statistics + +""" + get_free_file_unit(lu_max=-1) + +Find a unit number that is not in use. +Note: In Julia, this is less relevant as file I/O uses file handles directly, +but included for compatibility with ported code. + +# Arguments +- `lu_max::Int`: Maximum unit (default -1, which sets to 97) + +# Returns +- `Int`: Free unit number +""" +function get_free_file_unit(lu_max=-1) + m = lu_max < 1 ? 97 : lu_max + + # In Julia, we don't really need unit numbers + # Return a random number that could be used as an identifier + return rand(1:m) +end +end # module Utilities + +""" + to_upper(strIn) + +Capitalize a string. + +# Arguments +- `strIn::String`: Input string + +# Returns +- `String`: Uppercase string +""" +function to_upper(strIn::String) + return uppercase(strIn) +end + +""" + btoi(bool) + +Convert logical variable to integer. + +# Arguments +- `bool::Bool`: True or False + +# Returns +- `Int`: 0 or 1 +""" +function btoi(bool::Bool) + return bool ? 1 : 0 +end + +""" + itob(ibool) + +Convert integer variable to logical. + +# Arguments +- `ibool::Int`: Any integer variable + +# Returns +- `Bool`: True if ibool > 0 +""" +function itob(ibool::Int) + return ibool > 0 +end + +""" + progressbar(j, jstart, jstop; op_step=1, op_percent=10) + +Print progress bar for do loop every specified percentage of iterations. + +# Arguments +- `j::Int`: Current iteration variable +- `jstart::Int`: Start of loop +- `jstop::Int`: End of loop +- `op_step::Int`: Loop increment (default 1) +- `op_percent::Int`: Prints progress every percent of the iterations (default 10) +""" +function progressbar(j::Int, jstart::Int, jstop::Int; op_step::Int=1, op_percent::Int=10) + iteration = div(j - jstart, op_step) + 1 + iterations = div(jstop - jstart, op_step) + 1 + bar = " |----------| ???% iterations complete" + + crnt = floor(Int, iteration * 100.0 / iterations / op_percent) + last = floor(Int, (iteration - 1) * 100.0 / iterations / op_percent) + + if iteration == 1 || crnt > last || iteration == iterations + done = iteration == iterations ? 100 : crnt * op_percent + bar_str = collect(bar) + bar_str[16:18] .= collect(lpad(string(done), 3)) + + d10 = div(done, 10) + for k in 1:d10 + bar_str[3+k] = 'o' + end + + println(String(bar_str)) + end +end + +""" + timer(; mode=0, unit=nothing) + +Handles timing statistics. + +# Arguments +- `mode::Int`: mode = 0 starts timer, mode < 0 writes time and restarts, mode > 0 writes time +- `unit::Union{IO,Nothing}`: Output stream (default stdout) +""" +const _timer_seconds = Ref(0.0) +function timer(; mode::Int=0, unit::Union{IO,Nothing}=nothing) + time = Base.time() + + # Write split + if mode != 0 + elapsed = time - _timer_seconds[] + secs = Int(floor(elapsed)) + hrs = div(secs, 3600) + mins = div(secs - hrs * 3600, 60) + secs = (secs - hrs * 3600) - mins * 60 + + if unit !== nothing + println(unit, " Total cpu time = ", elapsed, " seconds") + else + if hrs > 0 + println("Total cpu time = $hrs hours, $mins minutes, $secs seconds") + elseif mins > 0 + println("Total cpu time = $mins minutes, $secs seconds") + else + println("Total cpu time = $secs seconds") + end + end + end + + # Start timer + if mode <= 0 + _timer_seconds[] = time + end + return nothing +end + +""" + splitstring(str, sep; maxsplit=nothing, debug=false) + +Split string into substrings using sep as delimiter. + +# Arguments +- `str::String`: Original string +- `sep::String`: Delimiter separating words in original string +- `maxsplit::Union{Int,Nothing}`: Maximum number of splits (default: no limit) +- `debug::Bool`: Debug flag + +# Returns +- `Vector{String}`: Array of substrings +""" +function splitstring(str::String, sep::String; maxsplit::Union{Int,Nothing}=nothing, debug::Bool=false) + # Julia's built-in split is more powerful, but we replicate the Fortran behavior + parts = split(str, sep; keepempty=false) + + if maxsplit !== nothing + parts = parts[1:min(length(parts), maxsplit)] + end + + if debug + println("number of words is ", length(parts)) + for (i, word) in enumerate(parts) + println(i, " ", word) + end + end + + return String.(parts) +end + +""" + replacestring!(str, subout, subin; debug=false) + +Replace substring with an alternate substring of equal length. + +# Arguments +- `str::String`: Original string (will be returned modified) +- `subout::String`: Substring to be replaced +- `subin::String`: Substring replacing subout +- `debug::Bool`: Debug flag + +# Returns +- `String`: Modified string +""" +function replacestring(str::String, subout::String, subin::String; debug::Bool=false) + if debug + println(" Replacing $subout with $subin") + end + + return replace(str, subout => subin) +end + +""" + readtable(file; verbose=false, debug=false) + +Read ascii file containing a single table. +- Assumes data starts on the first line starting with a number +- Assumes column titles are on the line directly above the data +- Ignores all other lines + +# Arguments +- `file::String`: File path +- `verbose::Bool`: Print status messages +- `debug::Bool`: Print debug messages + +# Returns +- `table::Matrix{Float64}`: The data +- `titles::Vector{String}`: The column headers +""" +function readtable(file::String; verbose::Bool=false, debug::Bool=false) + if verbose + println("Reading table from file: ") + println(" $file") + end + + lines = readlines(file) + numbers = "1234567890" + signs = "+-" + + startline = 0 + endline = 0 + + # Find data lines + for (l, line) in enumerate(lines) + line_stripped = strip(line) + if isempty(line_stripped) + continue + end + + j = 1 + # Skip leading signs + while j <= length(line_stripped) && line_stripped[j] in signs + j += 1 + end + + # Check if line starts with number + isnum = j <= length(line_stripped) && line_stripped[j] in numbers + + if isnum && startline == 0 + startline = l + elseif !isnum && startline != 0 && endline == 0 + endline = l - 1 + break + end + end + + if endline == 0 + endline = length(lines) + end + + if startline == 0 + error("ERROR: readtable - No data found") + end + + if debug + println("-> Table start,end lines = $startline, $endline") + end + + # Parse data + data_lines = lines[startline:endline] + + # Get titles from line before data + titles = String[] + if startline > 1 + title_line = replace(lines[startline-1], '\t' => ' ') + titles = splitstring(title_line, " "; debug=debug) + end + + # Parse table + table = [] + for line in data_lines + values = parse.(Float64, split(line)) + push!(table, values) + end + + # Convert to matrix + ncol = maximum(length.(table)) + nrow = length(table) + table_matrix = zeros(nrow, ncol) + + for (i, row) in enumerate(table) + table_matrix[i, 1:length(row)] .= row + end + + if debug + println("-> Found $nrow by $ncol table") + println("Done") + end + + return table_matrix, titles +end + +""" + nunique(array; op_sorted=false) + +Find number of unique elements in an array. + +# Arguments +- `array::Vector{Float64}`: Original array +- `op_sorted::Bool`: Common values or unique values are assumed to be grouped + +# Returns +- `Int`: Number of unique elements +""" +function nunique(array::AbstractVector{<:Real}; op_sorted::Bool=false) + if op_sorted + # Optimized for sorted arrays + count = 1 + for i in 2:length(array) + if array[i] != array[i-1] + count += 1 + end + end + return count + else + # General approach + return length(unique(array)) + end +end + +""" + median(array) + +Compute the median of a 1D array. + +# Arguments +- `array::Vector{Float64}`: Input array + +# Returns +- `Float64`: Median value +""" +function median_val(array::Vector{Float64}) + return median(array) # Use Statistics.median +end + +""" + sorted(array) + +Return a sorted copy of the array. + +# Arguments +- `array::Vector{Float64}`: Input array + +# Returns +- `Vector{Float64}`: Sorted array +""" +function sorted(array::Vector{Float64}) + return sort(array) +end + +""" + pnorm(array, p) + +Return the p-norm of a 1D array. + +# Arguments +- `array::Vector{Float64}`: Input array +- `p::Float64`: Must be greater than 1 (1=taxicab, 2=euclidean, Inf=maximum) + +# Returns +- `Float64`: p-norm value +""" +function pnorm(array::Vector{Float64}, p::Float64) + if p < 1 + error("ERROR: p-norm with p<1 is not a norm") + end + + if isinf(p) + return maximum(abs.(array)) + end + + return sum(abs.(array).^p)^(1/p) +end + +""" + cpnorm(array, p) + +Return the p-norm of a 1D complex array. + +# Arguments +- `array::Vector{ComplexF64}`: Input array +- `p::Float64`: Must be greater than 1 + +# Returns +- `Float64`: p-norm value +""" +function cpnorm(array::Vector{ComplexF64}, p::Float64) + if p < 1 + error("ERROR: p-norm with p<1 is not a norm") + end + + if isinf(p) + return maximum(abs.(array)) + end + + return sum(abs.(array).^p)^(1/p) +end + +""" + ri(c) + +Return the real and imaginary components of a complex value as a tuple. + +# Arguments +- `c::ComplexF64`: Complex value + +# Returns +- `Vector{Float64}`: [real, imag] +""" +function ri(c::ComplexF64) + return [real(c), imag(c)] +end + +""" + append_1d!(list, element) + +Append a 1D array (modifies in place via push!). + +# Arguments +- `list::Vector{Float64}`: Array to be appended +- `element::Float64`: Number appended to end of list +""" +function append_1d!(list::Vector{Float64}, element::Float64) + push!(list, element) +end + +# Alternative that matches Fortran behavior more closely +function append_1d(list::Vector{Float64}, element::Float64) + return vcat(list, element) +end + +""" + append_2d!(list, elements) + +Append a 2D array along second dimension. + +# Arguments +- `list::Matrix{Float64}`: 2D array to be appended +- `elements::Vector{Float64}`: 1D array appended to 2nd dimension of list + +# Returns +- `Matrix{Float64}`: Appended matrix +""" +function append_2d(list::Matrix{Float64}, elements::Vector{Float64}) + if size(list, 1) != length(elements) + error("Cannot append arrays without matched dimensions") + end + + return hcat(list, elements) +end + +""" + iscdftf(m, func) + +Compute 1D truncated-discrete Fourier forward transform. + +# Arguments +- `m::Vector{Int}`: Fourier modes +- `func::Vector{ComplexF64}`: Function on a regular grid 0-1 + +# Returns +- `Vector{ComplexF64}`: Fourier components +""" +function iscdftf(m::Vector{Int}, func::Vector{ComplexF64}) + ms = length(m) + fs = length(func) + funcm = zeros(ComplexF64, ms) + + for i in 1:ms + for j in 0:fs-1 + funcm[i] += (1.0/fs) * func[j+1] * exp(-2π*im*m[i]*j/fs) + end + end + + return funcm +end + +""" + iscdftb(m, funcm, fs) + +Compute 1D truncated-discrete Fourier backward transform. + +# Arguments +- `m::Vector{Int}`: Fourier modes +- `funcm::Vector{ComplexF64}`: Fourier components +- `fs::Int`: Number of function points + +# Returns +- `Vector{ComplexF64}`: Function on regular grid +""" +function iscdftb(m::Vector{Int}, funcm::Vector{ComplexF64}, fs::Int) + ms = length(m) + func = zeros(ComplexF64, fs+1) + + for i in 0:fs-1 + for j in 1:ms + func[i+1] += funcm[j] * exp(2π*im*m[j]*i/fs) + end + end + func[fs+1] = func[1] + + return func +end + +""" + check(stat, msg="") + +Check if a netcdf call was successful. If not, raise an error. + +# Arguments +- `stat::Int`: Status code (0 = success in NetCDF) +- `msg::String`: Optional error message +""" +function check(stat::Int, msg::String="") + if stat != 0 + if !isempty(msg) + error("ERROR: $msg - NetCDF error code: $stat") + else + error("ERROR: failed to write/read netcdf file - error code: $stat") + end + end +end \ No newline at end of file diff --git a/test/data/idcon_test.bin b/test/data/idcon_test.bin new file mode 100644 index 00000000..a826bb6c Binary files /dev/null and b/test/data/idcon_test.bin differ diff --git a/test/data/peq_synth.txt b/test/data/peq_synth.txt new file mode 100644 index 00000000..d2936185 --- /dev/null +++ b/test/data/peq_synth.txt @@ -0,0 +1,7 @@ +# psi m xmp1_re xmp1_im xsp_re xsp_im xms_re xms_im +0.1 1 1.0 0.0 0.2 0.0 0.3 0.0 +0.1 2 0.5 0.0 0.1 0.0 0.2 0.0 +0.2 1 1.1 0.0 0.21 0.0 0.31 0.0 +0.2 2 0.55 0.0 0.11 0.0 0.22 0.0 +0.3 1 1.2 0.0 0.22 0.0 0.33 0.0 +0.3 2 0.6 0.0 0.12 0.0 0.24 0.0 diff --git a/test/data/peq_test.txt b/test/data/peq_test.txt new file mode 100644 index 00000000..4c2f0716 --- /dev/null +++ b/test/data/peq_test.txt @@ -0,0 +1,5 @@ +# simple peq test (psi, m, xmp1_re, xmp1_im, xsp_re, xsp_im, xms_re, xms_im) +0.2 1 1.0 0.0 0.2 0.0 0.05 0.0 +0.2 2 0.5 0.0 0.1 0.0 0.02 0.0 +0.8 1 0.3 0.0 0.06 0.0 0.015 0.0 +0.8 2 0.15 0.0 0.03 0.0 0.0075 0.0 diff --git a/test/data/pmodb_mouter.txt b/test/data/pmodb_mouter.txt new file mode 100644 index 00000000..35fd040e --- /dev/null +++ b/test/data/pmodb_mouter.txt @@ -0,0 +1,7 @@ +# psi m col3 col4 lagb_re lagb_im divx_re divx_im +0.1 1 0 0 1.0 0.0 0.2 0.0 +0.2 1 0 0 1.1 0.0 0.21 0.0 +0.3 1 0 0 1.2 0.0 0.22 0.0 +0.1 2 0 0 0.5 0.0 0.1 0.0 +0.2 2 0 0 0.55 0.0 0.11 0.0 +0.3 2 0 0 0.6 0.0 0.12 0.0 diff --git a/test/data/pmodb_synth.txt b/test/data/pmodb_synth.txt new file mode 100644 index 00000000..19793d43 --- /dev/null +++ b/test/data/pmodb_synth.txt @@ -0,0 +1,5 @@ +psi m a b lagb_re lagb_im divx_re divx_im +0.1 1 0 0 1.0 0.0 2.0 0.0 +0.1 2 0 0 0.0 1.0 0.0 2.0 +0.5 1 0 0 0.5 0.0 1.5 0.0 +0.5 2 0 0 0.0 0.5 0.0 1.5 diff --git a/test/data/pmodb_test.txt b/test/data/pmodb_test.txt new file mode 100644 index 00000000..dd0f1ad3 --- /dev/null +++ b/test/data/pmodb_test.txt @@ -0,0 +1,5 @@ +# simple pmodb test (psi, m, dummy1, dummy2, lagb_re, lagb_im, divx_re, divx_im) +0.1 1 0 0 1.0 0.0 0.5 0.0 +0.1 2 0 0 0.5 0.0 0.25 0.0 +0.9 1 0 0 0.2 0.0 0.1 0.0 +0.9 2 0 0 0.1 0.0 0.05 0.0 diff --git a/test/runtests_idcon_coords.jl b/test/runtests_idcon_coords.jl new file mode 100644 index 00000000..d4be4d71 --- /dev/null +++ b/test/runtests_idcon_coords.jl @@ -0,0 +1,21 @@ +using Test + +# Load the DCON interface module +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) + +@testset "idcon_coords smoke" begin + # Verify idcon_coords runs for both calling patterns and mutates + # the spectrum in-place without throwing, producing finite complex values. + psi = 0.3 + spec = ComplexF64[1.0+0im, 2.0+0im, -0.5+0im] + mfac = [1,2,3] + mpert = 3 + @test nothing === DconInterface.idcon_coords(psi, spec, mfac, mpert, 0, 0, 1, 0, 1, 1) + @test all(isfinite, real.(spec)) && all(isfinite, imag.(spec)) + + spec2 = ComplexF64[3.0+0im, -1.0+0im] + ms = [1,2] + nm = 2 + @test nothing === DconInterface.idcon_coords(psi, spec2, ms, nm, 1, 0, 1, 0, 1, 1) + @test all(isfinite, real.(spec2)) && all(isfinite, imag.(spec2)) +end diff --git a/test/runtests_idcon_read.jl b/test/runtests_idcon_read.jl new file mode 100644 index 00000000..e3701cb0 --- /dev/null +++ b/test/runtests_idcon_read.jl @@ -0,0 +1,43 @@ +using Test + +# Load the DCON interface module under test (path resolved relative to this test file) +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +using .DconInterface + +# Ensure data directory exists +mkpath("test/data") +path = "test/data/idcon_test.bin" + +# Write a small Fortran-unformatted-like binary with two records +open(path, "w") do io + # Record 1: two Float64 values (mpert as 4.0, chi1 as a large value so + # this record is NOT mistaken for a theta array which must lie in 0..2π) + payload = IOBuffer() + write(payload, Float64(4.0)) + write(payload, Float64(1e9)) + data = take!(payload) + n = Int32(length(data)) + write(io, n) + write(io, data) + write(io, n) + + # Record 2: three Float64 theta samples (0, π/2, π) + payload2 = IOBuffer() + write(payload2, Float64(0.0)) + write(payload2, Float64(pi/2)) + write(payload2, Float64(pi)) + data2 = take!(payload2) + n2 = Int32(length(data2)) + write(io, n2) + write(io, data2) + write(io, n2) +end + +# Point the module to the test file and run the reader +DconInterface.idconfile = path +DconInterface.idcon_read(0) + +@test DconInterface.mpert[] == 4 +@test length(DconInterface.theta) >= 3 + +println("idcon_read heuristic test passed") diff --git a/test/runtests_inputs.jl b/test/runtests_inputs.jl new file mode 100644 index 00000000..b906136a --- /dev/null +++ b/test/runtests_inputs.jl @@ -0,0 +1,15 @@ +using Test + +# Smoke tests for Inputs module (minimal, non-invasive) +# This file is intentionally small: it verifies that the Inputs module can +# be included and that `newm` behaves as expected for a simple case. + +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +@testset "Inputs smoke tests" begin + v = Inputs.newm([1,2,3], [1+1im, 2+0im, 3-1im], [1,2,3]) + @test eltype(v) == ComplexF64 + @test v == ComplexF64[1+1im, 2+0im, 3-1im] +end diff --git a/test/runtests_inputs_extra.jl b/test/runtests_inputs_extra.jl new file mode 100644 index 00000000..30e578ac --- /dev/null +++ b/test/runtests_inputs_extra.jl @@ -0,0 +1,73 @@ +using Test + +# Load the lightweight DCON stub and the Inputs port (use paths relative to this test file) +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +const IE = Inputs.InputsExtras + +@testset "Inputs.extra tests" begin + @testset "newm behavior" begin + m_i = [1,2,3] + fm_i = ComplexF64[1+1im, 2+0im, 3-1im] + m_o = [1,2,3,4] + out = Inputs.newm(m_i, fm_i, m_o) + @test out[1:3] == fm_i + @test out[4] == 0+0im + + # misaligned mode spaces should raise an error + @test_throws ErrorException Inputs.newm([1,2,4], fm_i, [1,2,3]) + end + + @testset "set_peq synthetic" begin + # configure DCON stub to expose vector theta and multiple m-points + DconInterface.mpert = 4 + DconInterface.mthsurf = 3 + DconInterface.theta = [0.0, π/2, π, 3π/2] + DconInterface.mfac = 1.0 + + # Create small synthetic psi grid and m-pert spectra + psi = [0.1, 0.5, 0.9] + ms = [1,2,3,4] + npsi = length(psi) + mpert = DconInterface.mpert + + xmp1mns = Array{ComplexF64}(undef, npsi, mpert) + xspmns = Array{ComplexF64}(undef, npsi, mpert) + xmsmns = Array{ComplexF64}(undef, npsi, mpert) + for i in 1:npsi + for j in 1:mpert + xmp1mns[i,j] = ComplexF64(sin(psi[i]) * j, cos(psi[i]) * j) + xspmns[i,j] = ComplexF64(cos(psi[i]) * j, sin(psi[i]) * j) + xmsmns[i,j] = ComplexF64((i+j)/2, (i-j)/3) + end + end + + # Ensure Utilities exposes the DFT helpers under Main.Utilities + if isdefined(Main, :Utilities) + if !isdefined(Main.Utilities, :iscdftb) + @eval Main.Utilities begin + function iscdftb(m, funcm, fs) + return Main.iscdftb(m, funcm, fs) + end + function iscdftf(m, func) + return Main.iscdftf(m, func) + end + end + end + end + + # Call set_peq (uses Utilities DFT helpers and Splines) + IE.set_peq(psi, ms, xmp1mns, xspmns, xmsmns, true, false) + + # After set_peq, Inputs.xs_m entries should be populated with BicubicSpline + @test Inputs.xs_m[1][] !== nothing + using Main.SplinesMod + @test isa(Inputs.xs_m[1][], Main.SplinesMod.BicubicSpline) + @test isa(Inputs.xs_m[2][], Main.SplinesMod.BicubicSpline) + @test isa(Inputs.xs_m[3][], Main.SplinesMod.BicubicSpline) + end +end + +println("runtests_inputs_extra.jl completed") diff --git a/test/runtests_inputs_more.jl b/test/runtests_inputs_more.jl new file mode 100644 index 00000000..b0afe46c --- /dev/null +++ b/test/runtests_inputs_more.jl @@ -0,0 +1,73 @@ +using Test + +# Advanced smoke tests for Inputs: exercise read_pmodb, read_peq, set_peq +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +# Configure DconInterface stub for test +DconInterface.mpert = 4 +DconInterface.mfac = 1.0 +DconInterface.mthsurf = 3 +DconInterface.theta = [0.0, 1.0, 2.0, 3.0] +# Provide a simple eqfun-like object with a field `f` so normalization will use it +DconInterface.eqfun = (f = [1.0]) +DconInterface.jac_type = "hamada" +DconInterface.verbose = false +DconInterface.sq = (xs = [0.0, 1.0]) + +# If Utilities module in Main does not expose readtable (many utilities +# functions exist at top-level in the file), alias Main as Utilities so +# calls like Utilities.readtable resolve to the top-level functions. +if isdefined(Main, :readtable) && (!isdefined(Main, :Utilities) || !isdefined(Main.Utilities, :readtable)) + # Forward readtable into Main.Utilities so calls like Utilities.readtable + # resolve to the top-level function defined by the utilities file. + @eval Main.Utilities begin + function readtable(file::String; verbose::Bool=false, debug::Bool=false) + return Main.readtable(file; verbose=verbose, debug=debug) + end + end +end + +# Forward other utilities functions if they are defined at top-level +if isdefined(Main, :nunique) && (!isdefined(Main, :Utilities) || !isdefined(Main.Utilities, :nunique)) + @eval Main.Utilities begin + function nunique(array; op_sorted::Bool=false) + return Main.nunique(Vector(array); op_sorted=op_sorted) + end + end +end +if isdefined(Main, :iscdftb) && (!isdefined(Main, :Utilities) || !isdefined(Main.Utilities, :iscdftb)) + @eval Main.Utilities begin + function iscdftb(m::Vector{Int}, funcm::Vector{ComplexF64}, fs::Int) + return Main.iscdftb(m, funcm, fs) + end + end +end +if isdefined(Main, :iscdftf) && (!isdefined(Main, :Utilities) || !isdefined(Main.Utilities, :iscdftf)) + @eval Main.Utilities begin + function iscdftf(m::Vector{Int}, func::Vector{ComplexF64}) + return Main.iscdftf(m, func) + end + end +end +if isdefined(Main, :get_free_file_unit) && (!isdefined(Main, :Utilities) || !isdefined(Main.Utilities, :get_free_file_unit)) + @eval Main.Utilities begin + function get_free_file_unit(lu_max::Int=-1) + return Main.get_free_file_unit(lu_max) + end + end +end + +@testset "Inputs pmodb/peq smoke" begin + # run read_pmodb on synthetic table + dbob, divx = Inputs.InputsExtras.read_pmodb(joinpath(@__DIR__, "data", "pmodb_test.txt"), "default", 1, 1, false) + @test Inputs.dbob_m[] !== nothing + @test Inputs.divx_m[] !== nothing + + # run read_peq on synthetic table + Inputs.InputsExtras.read_peq(joinpath(@__DIR__, "data", "peq_test.txt"), "default", 1, 1, false, false) + @test Inputs.xs_m[1][] !== nothing + @test Inputs.xs_m[2][] !== nothing + @test Inputs.xs_m[3][] !== nothing +end diff --git a/test/runtests_pentrc.jl b/test/runtests_pentrc.jl new file mode 100644 index 00000000..0d7506b7 --- /dev/null +++ b/test/runtests_pentrc.jl @@ -0,0 +1,38 @@ +using Test + +# Include the pentrc interface under test +include(joinpath(@__DIR__, "..", "src", "pentrc", "pentrc_interface.jl")) + +@testset "pentrc_interface basic behavior" begin + # 1) read_pentrc_input should warn when no pentrc.in file exists + # Temporarily move any existing file out of the way so the test is hermetic. + pentrc_in = joinpath(pwd(), "pentrc.in") + bak = pentrc_in * ".bak_for_test" + moved = false + if isfile(pentrc_in) + mv(pentrc_in, bak; force=true) + moved = true + end + try + @test_warn "pentrc.in not found" read_pentrc_input() + finally + if moved + mv(bak, pentrc_in; force=true) + end + end + + # 2) initialize_pentrc with all ops disabled should not call read_kin/read_equil + # and should populate default psi_out when it is all -1 + global psi_out = fill(-1.0, npsi_out) + initialize_pentrc(; op_kin=false, op_deq=false, op_peq=false) + @test length(psi_out) == 30 + @test psi_out == collect(1:30) ./ 30.6 + + # 3) openmp_threads deprecated warning is emitted when > 0 + global openmp_threads = 4 + @test_warn "openmp_threads is deprecated" initialize_pentrc(; op_kin=false, op_deq=false, op_peq=false) + # restore + global openmp_threads = 0 +end + +println("runtests_pentrc.jl: tests defined") diff --git a/test/runtests_pentrc_main.jl b/test/runtests_pentrc_main.jl new file mode 100644 index 00000000..8c59244c --- /dev/null +++ b/test/runtests_pentrc_main.jl @@ -0,0 +1,51 @@ +using Test + +# This test will include `pentrc.jl` after temporarily changing +# the working directory so the file-local includes resolve correctly. +root = joinpath(@__DIR__, "..") +pentrc_dir = joinpath(root, "src", "pentrc") + +@testset "pentrc main (smoke)" begin + pwd0 = pwd() + try + # Include the pentrc interface (safe to include in tests) + include(joinpath(@__DIR__, "..", "src", "pentrc", "pentrc_interface.jl")) + + # Configure safe runtime environment to avoid heavy computations + global clean = false + global diag_flag = true + global verbose = false + global pentrc_threads = 0 + global openmp_threads = 0 + + # Initialize with file-reading disabled so the function doesn't + # attempt to read kinetic/equilibrium files during the test. + initialize_pentrc(; op_kin=false, op_deq=false, op_peq=false) + + # Test the moment handling logic from pentrc.main in isolation + global moment = "heat" + if moment == "heat" + global qt = true + elseif moment == "pressure" + global qt = false + else + error("ERROR: Input moment must be 'pressure' or 'heat'") + end + @test qt == true + + global moment = "pressure" + if moment == "heat" + global qt = true + elseif moment == "pressure" + global qt = false + else + error("ERROR: Input moment must be 'pressure' or 'heat'") + end + @test qt == false + + finally + cd(pwd0) + end +end + +println("runtests_pentrc_main.jl: tests defined") diff --git a/test/runtests_read_peq.jl b/test/runtests_read_peq.jl new file mode 100644 index 00000000..09c915bc --- /dev/null +++ b/test/runtests_read_peq.jl @@ -0,0 +1,58 @@ +using Test + +# Load Utilities first so it defines a `Main.Utilities` module with +# readtable/nunique/iscdft* functions available for Inputs to call. +Core.eval(Main, :(include($(joinpath(@__DIR__, "..", "src", "pentrc", "utilities.jl"))))) + +# Load DCON stub and Inputs module (use paths relative to this test file) +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +# Configure a minimal DCON environment so read_peq can run +DconInterface.mpert[] = 4 +DconInterface.mthsurf[] = 3 +DconInterface.jac_type = "hamada" +DconInterface.mfac = 1.0 +DconInterface.eqfun = nothing +DconInterface.theta = [0.0, pi/2, pi, 3pi/2] + +file = joinpath(@__DIR__, "data", "peq_synth.txt") + +# Ensure Main.Utilities namespace provides wrappers to functions included +# by the repository's utilities.jl (which may inject helpers at top-level). +if !isdefined(Main, :Utilities) + Core.eval(Main, quote + module Utilities + end + end) +end +if isdefined(Main, :readtable) + Core.eval(Main.Utilities, :(function readtable(args...; kwargs...) + return Main.readtable(args...; kwargs...) + end)) +end +if isdefined(Main, :nunique) + Core.eval(Main.Utilities, :(function nunique(x) + return Main.nunique(x) + end)) +end +if isdefined(Main, :iscdftb) + Core.eval(Main.Utilities, :(function iscdftb(m, arr, nth) + return Main.iscdftb(m, arr, nth) + end)) +end +if isdefined(Main, :iscdftf) + Core.eval(Main.Utilities, :(function iscdftf(m, arr) + return Main.iscdftf(m, arr) + end)) +end + +@testset "read_peq synthetic" begin + # call the reader; should populate Inputs.xs_m[1..3] + Inputs.InputsExtras.read_peq(file, "", 1, 1, false, false) + + @test Inputs.xs_m[1][] !== nothing + @test Inputs.xs_m[2][] !== nothing + @test Inputs.xs_m[3][] !== nothing +end diff --git a/test/runtests_read_pmodb.jl b/test/runtests_read_pmodb.jl new file mode 100644 index 00000000..20791282 --- /dev/null +++ b/test/runtests_read_pmodb.jl @@ -0,0 +1,53 @@ +using Test + +# Load modules (paths resolved relative to repo root) +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +const IE = Inputs.InputsExtras + +@testset "read_pmodb synthetic" begin + # configure DCON stub to match nm in synthetic file + DconInterface.mpert[] = 2 + DconInterface.mthsurf[] = 3 + DconInterface.theta = [0.0, π/2, π, 3π/2] + DconInterface.mfac = [1,2] + DconInterface.jac_type = "hamada" + + # Ensure Utilities.readtable is callable from Inputs (utilities.jl defines + # many helpers at top-level; create wrappers if necessary) + if isdefined(Main, :readtable) && !isdefined(Main, :Utilities) + Core.eval(Main, :(Utilities = Main)) + elseif isdefined(Main, :readtable) && isdefined(Main, :Utilities) + if !isdefined(Main.Utilities, :readtable) + @eval Main.Utilities begin + readtable(file; kwargs...) = Main.readtable(file; kwargs...) + end + end + end + # Also ensure common helpers exist on Main.Utilities (nunique, iscdftb/iscdftf) + if isdefined(Main, :nunique) && isdefined(Main, :Utilities) && !isdefined(Main.Utilities, :nunique) + @eval Main.Utilities begin + nunique(x) = Main.nunique(collect(x)) + end + end + if isdefined(Main, :iscdftb) && isdefined(Main, :Utilities) && !isdefined(Main.Utilities, :iscdftb) + @eval Main.Utilities begin + iscdftb(m, funcm, fs) = Main.iscdftb(m, funcm, fs) + iscdftf(m, func) = Main.iscdftf(m, func) + end + end + + filepath = joinpath(@__DIR__, "data", "pmodb_synth.txt") + + dbob, divx = IE.read_pmodb(filepath, "default", 1, 1, false) + + @test Inputs.dbob_m[] !== nothing + @test Inputs.divx_m[] !== nothing + using Main.SplinesMod + @test isa(Inputs.dbob_m[], Main.SplinesMod.BicubicSpline) + @test isa(Inputs.divx_m[], Main.SplinesMod.BicubicSpline) +end + +println("runtests_read_pmodb.jl completed") diff --git a/test/runtests_read_pmodb_mouter.jl b/test/runtests_read_pmodb_mouter.jl new file mode 100644 index 00000000..2a7f5687 --- /dev/null +++ b/test/runtests_read_pmodb_mouter.jl @@ -0,0 +1,51 @@ +using Test + +# Load Utilities first so Inputs can find Utilities.readtable +Core.eval(Main, :(include($(joinpath(@__DIR__, "..", "src", "pentrc", "utilities.jl"))))) + +# Load DCON stub and Inputs +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +include(joinpath(@__DIR__, "..", "src", "pentrc", "inputs.jl")) +using .Inputs + +# Minimal DCON setup +DconInterface.mpert[] = 4 +DconInterface.mthsurf[] = 3 +DconInterface.jac_type = "hamada" +DconInterface.mfac = 1.0 +DconInterface.eqfun = nothing +DconInterface.theta = [0.0, pi/2, pi, 3pi/2] + +file = joinpath(@__DIR__, "data", "pmodb_mouter.txt") +## Ensure Utilities module has wrappers for helpers that may be defined at +## top-level by the included utilities.jl script (e.g., readtable, nunique, +## iscdftb/iscdftf). This mirrors the shims used in other tests. +if isdefined(Main, :Utilities) + if isdefined(Main, :readtable) + Core.eval(Main.Utilities, :(function readtable(args...; kwargs...) + return Main.readtable(args...; kwargs...) + end)) + end + if isdefined(Main, :nunique) + Core.eval(Main.Utilities, :(function nunique(x) + return Main.nunique(x) + end)) + end + if isdefined(Main, :iscdftb) + Core.eval(Main.Utilities, :(function iscdftb(m, arr, nth) + return Main.iscdftb(m, arr, nth) + end)) + end + if isdefined(Main, :iscdftf) + Core.eval(Main.Utilities, :(function iscdftf(m, arr) + return Main.iscdftf(m, arr) + end)) + end +end + +@testset "read_pmodb m-outer synthetic" begin + dbob, divx = Inputs.InputsExtras.read_pmodb(file, "", 1, 1, false) + @test Inputs.dbob_m[] !== nothing + @test Inputs.divx_m[] !== nothing + @test dbob !== nothing && divx !== nothing +end diff --git a/test/runtests_torque.jl b/test/runtests_torque.jl new file mode 100644 index 00000000..52110158 --- /dev/null +++ b/test/runtests_torque.jl @@ -0,0 +1,155 @@ +using Test + +# Lightweight, hermetic smoke tests for torque subroutines + +# Include minimal dependencies and module shims used by torque.jl +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +using Main.DconInterface + +# Provide a minimal SplineType and helpers (avoid using malformed spline_mod.jl) +mutable struct SplineType + xs::Vector{Float64} + fs::Matrix{Float64} + mx::Int + fsi::Union{Matrix{Float64}, Nothing} +end + +function SplineType(nx::Integer, nvar::Integer) + xs = zeros(Float64, nx) + fs = zeros(Float64, nx, nvar) + return SplineType(xs, fs, nx, nothing) +end + +function spline_alloc(nx::Integer, nvar::Integer) + return SplineType(nx, nvar) +end + +function spline_fit!(spl::SplineType, _mode::AbstractString) + return nothing +end + +function spline_int!(spl::SplineType) + if spl.fsi === nothing + spl.fsi = zeros(Float64, spl.mx, size(spl.fs,2)) + end + return nothing +end + +function spline_dealloc!(_spl) + return nothing +end + +function spline_eval_external(obj, psi::Float64; deriv::Integer=0) + out = zeros(Float64, 9) + if deriv == 1 + return out, out + else + return out + end +end + +# Minimal cspline helpers +function cspline_alloc(nx::Integer, nvar::Integer) + xs = zeros(Float64, nx) + fs = zeros(Float64, nx, nvar) + return (xs=xs, fs=fs, mx=nx, nqty=nvar) +end + +function cspline_fit!(_fb, _mode::AbstractString) + return nothing +end + +function cspline_int!(fb) + if !haskey(fb, :fsi) || fb[:fsi] === nothing + fb[:fsi] = zeros(Float64, fb[:mx], size(fb[:fs],2)) + end + return nothing +end + +function cspline_dealloc!(_fb) + return nothing +end + +function cspline_eval_external(obj, psi::Float64) + if obj isa AbstractArray + return obj + end + mp = try DconInterface.mpert[] catch; 1 end + return ComplexF64.(zeros(mp * mp)) +end + +# Use clean bicube shim for tests +include(joinpath(@__DIR__, "..", "src", "pentrc", "bicube_mod_clean.jl")) +# Provide deterministic stub for energy integration (avoid loading heavy energy.jl) +function xintgrl_lsode(wn, wt, we, wd, wb, nuk, ell, leff, n, psi, lambda, method; op_record=false) + # Return a simple complex value for testing + return ComplexF64(-1.0, 0.0) +end + +# Minimal pitch integration stub (kept very small) +function kappaintgrl(n, l, q, mfac_in, dbob_m_f, fnml) + return 1.0 +end + +# Now include the torque implementation under test +include(joinpath(@__DIR__, "..", "src", "pentrc", "torque.jl")) + +@testset "torque calculations" begin + # Test 1: calculate_fcgl should return zero when kinetic profiles are zero + @testset "calculate_fcgl basic" begin + # Ensure a varying b(theta) so spline routines avoid degenerate minima + global bicube_eval_external = (bc, psi::Float64, theta::Float64, n::Integer) -> + # return (b, db/dpsi, db/dtheta, jac, dj/dpsi) + return [1.0 + 0.1*sin(2π*theta), 0.0, 0.0, 1.0, 0.0] + + # set a reasonable angular resolution + DconInterface.mthsurf[] = 8 + DconInterface.mpert[] = 4 + + psi = 0.5 + n = 1 + l = 0 + tspl = SplineType(DconInterface.mthsurf[], 5) + dbob_m_f = zeros(Float64, DconInterface.mpert[]) + divx_m_f = zeros(Float64, DconInterface.mpert[]) + kin_f = zeros(Float64, 9) # zero kinetic profile -> torque should be zero + s = 1 + + t = calculate_fcgl(psi, n, l, tspl, dbob_m_f, divx_m_f, kin_f, s) + @test isa(t, ComplexF64) + @test t == ComplexF64(0,0) + end + + # Test 2: calculate_rlar smoke test with a deterministic kappaintgrl stub + @testset "calculate_rlar smoke" begin + # Provide a small, deterministic kappaintgrl used by calculate_rlar + global kappaintgrl = (n, l, q, mfac_in, dbob_m_f, fnml) -> 2.0 + + # Ensure global variables referenced by calculate_rlar exist + global bmin = 0.5 + global fnml = 1.0 + + psi = 0.5 + n = 1 + l = 0 + q = 1.0 + epsr = 0.1 + wdian = 0.0 + wdiat = 0.0 + welec = 0.0 + wdhat = 0.0 + wbhat = 0.0 + nueff = 0.0 + sq_s_f = zeros(Float64, 4) + kin_f = zeros(Float64, 9); + kin_f[1] = 1.0; kin_f[3] = 1.0 + s = 1 + dbob_m_f = zeros(Float64, DconInterface.mpert[]) + erecord = false + + t = calculate_rlar(psi, n, l, q, epsr, wdian, wdiat, welec, wdhat, wbhat, + nueff, sq_s_f, kin_f, s, dbob_m_f, erecord) + + @test isa(t, ComplexF64) + end +end diff --git a/test/runtests_torque_clean.jl b/test/runtests_torque_clean.jl new file mode 100644 index 00000000..6f84d0bd --- /dev/null +++ b/test/runtests_torque_clean.jl @@ -0,0 +1,176 @@ +using Test + +# Lightweight, hermetic smoke tests for torque subroutines + +# Include minimal dependencies and module shims used by torque.jl +include(joinpath(@__DIR__, "..", "src", "pentrc", "dcon_interface.jl")) +using Main.DconInterface + +# Minimal params expected by torque.jl +const nmethods = 3 +const ngrids = 1 + +# Mirror minimal DconInterface fields into Main scope expected by torque.jl +global mthsurf = DconInterface.mthsurf[] +global mpert = DconInterface.mpert[] +global mfac = DconInterface.mfac +global psifac = DconInterface.psifac +global theta = DconInterface.theta +global eqfun = DconInterface.eqfun === nothing ? zeros(1) : DconInterface.eqfun +global rzphi = DconInterface.rzphi === nothing ? zeros(1) : DconInterface.rzphi +global bo = DconInterface.bo +global bmin = 0.5 +global fnml = 1.0 +global twopi = 2π + +# Provide a minimal SplineType and helpers (avoid using malformed spline_mod.jl) +mutable struct SplineType + xs::Vector{Float64} + fs::Matrix{Float64} + mx::Int + fsi::Union{Matrix{Float64}, Nothing} +end + +function SplineType(nx::Integer, nvar::Integer) + # Many Fortran routines use arrays sized mthsurf+1; allocate +1 to match expectations + xs = zeros(Float64, nx + 1) + fs = zeros(Float64, nx + 1, nvar) + return SplineType(xs, fs, nx, nothing) +end + +function spline_alloc(nx::Integer, nvar::Integer) + return SplineType(nx, nvar) +end + +function spline_fit!(spl::SplineType, _mode::AbstractString) + return nothing +end + +function spline_int!(spl::SplineType) + if spl.fsi === nothing + spl.fsi = zeros(Float64, spl.mx, size(spl.fs,2)) + end + return nothing +end + +function spline_dealloc!(_spl) + return nothing +end + +function spline_eval_external(obj, psi::Float64; deriv::Integer=0) + out = zeros(Float64, 9) + if deriv == 1 + return out, out + else + return out + end +end + +# Minimal cspline helpers +function cspline_alloc(nx::Integer, nvar::Integer) + xs = zeros(Float64, nx) + fs = zeros(Float64, nx, nvar) + return (xs=xs, fs=fs, mx=nx, nqty=nvar) +end + +function cspline_fit!(_fb, _mode::AbstractString) + return nothing +end + +function cspline_int!(fb) + if !haskey(fb, :fsi) || fb[:fsi] === nothing + fb[:fsi] = zeros(Float64, fb[:mx], size(fb[:fs],2)) + end + return nothing +end + +function cspline_dealloc!(_fb) + return nothing +end + +function cspline_eval_external(obj, psi::Float64) + if obj isa AbstractArray + return obj + end + mp = try DconInterface.mpert[] catch; 1 end + return ComplexF64.(zeros(mp * mp)) +end + +# Use clean bicube shim for tests +include(joinpath(@__DIR__, "..", "src", "pentrc", "bicube_mod_clean.jl")) +# Provide deterministic stub for energy integration (avoid loading heavy energy.jl) +function xintgrl_lsode(wn, wt, we, wd, wb, nuk, ell, leff, n, psi, lambda, method; op_record=false) + # Return a simple complex value for testing + return ComplexF64(-1.0, 0.0) +end + +# Minimal pitch integration stub (kept very small) +function kappaintgrl(n, l, q, mfac_in, dbob_m_f, fnml) + return 1.0 +end + +# Now include the torque implementation under test +include(joinpath(@__DIR__, "..", "src", "pentrc", "torque.jl")) + +@testset "torque calculations" begin + # Test 1: calculate_fcgl should return zero when kinetic profiles are zero + @testset "calculate_fcgl basic" begin + # Ensure a varying b(theta) so spline routines avoid degenerate minima + function bicube_eval_external(bc, psi::Float64, theta::Float64, n::Integer) + # return (b, db/dpsi, db/dtheta, jac, dj/dpsi) + return [1.0 + 0.1*sin(2π*theta), 0.0, 0.0, 1.0, 0.0] + end + + # set a reasonable angular resolution + DconInterface.mthsurf[] = 8 + DconInterface.mpert[] = 4 + + psi = 0.5 + n = 1 + l = 0 + tspl = SplineType(DconInterface.mthsurf[], 5) + dbob_m_f = zeros(Float64, DconInterface.mpert[]) + divx_m_f = zeros(Float64, DconInterface.mpert[]) + kin_f = zeros(Float64, 9) # zero kinetic profile -> torque should be zero + s = 1 + + t = calculate_fcgl(psi, n, l, tspl, dbob_m_f, divx_m_f, kin_f, s) + @test isa(t, ComplexF64) + @test t == ComplexF64(0,0) + end + + # Test 2: calculate_rlar smoke test with a deterministic kappaintgrl stub + @testset "calculate_rlar smoke" begin + # Provide a small, deterministic kappaintgrl used by calculate_rlar + function kappaintgrl(n, l, q, mfac_in, dbob_m_f, fnml) + return 2.0 + end + + # Ensure global variables referenced by calculate_rlar exist + global bmin = 0.5 + global fnml = 1.0 + + psi = 0.5 + n = 1 + l = 0 + q = 1.0 + epsr = 0.1 + wdian = 0.0 + wdiat = 0.0 + welec = 0.0 + wdhat = 0.0 + wbhat = 0.0 + nueff = 0.0 + sq_s_f = zeros(Float64, 4) + kin_f = zeros(Float64, 9); + kin_f[1] = 1.0; kin_f[3] = 1.0 + s = 1 + dbob_m_f = zeros(Float64, DconInterface.mpert[]) + erecord = false + + t = calculate_rlar(psi, n, l, q, epsr, wdian, wdiat, welec, wdhat, wbhat, + nueff, sq_s_f, kin_f, s, dbob_m_f, erecord) + + @test isa(t, ComplexF64) + end +end