DCON - NEW FEATURE - Adds kinetic damping matrix infrastructure

.JuliaFormatter.toml

@@ -9,4 +9,4 @@ remove_extra_newlines = false
 trailing_comma = false
 join_lines_based_on_source = true
 separate_kwargs_with_semicolon = true
-whitespace_ops_in_indices = false
+whitespace_ops_in_indices = false

.github/workflows/claude-code-review.yml

@@ -55,4 +55,3 @@ jobs:
           # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
           # or https://code.claude.com/docs/en/cli-reference for available options
           claude_args: '--allowed-tools "Bash(gh issue view:*),Bash(gh search:*),Bash(gh issue list:*),Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*)"'
-

.github/workflows/claude.yml

@@ -47,4 +47,3 @@ jobs:
           # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
           # or https://code.claude.com/docs/en/cli-reference for available options
           # claude_args: '--allowed-tools Bash(gh pr:*)'
-

.github/workflows/copilot-setup-steps.yaml

@@ -3,47 +3,47 @@ name: "Copilot Setup Steps"
 # Automatically run the setup steps when they are changed to allow for easy validation,
 # and allow manual testing through the repository's "Actions" tab
 on:
-  workflow_dispatch: 
+  workflow_dispatch:
   push:
-    paths:  
+    paths:
       - .github/workflows/copilot-setup-steps.yml
   pull_request:
     paths:
       - . github/workflows/copilot-setup-steps.yml
 
 jobs:
   # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot
-  copilot-setup-steps: 
+  copilot-setup-steps:
     runs-on: ubuntu-latest
-    
+
     # Set the permissions to the lowest permissions possible needed for your steps
     permissions:
       contents: read
-    
+
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
-      
+
       - name: Set up Julia
         uses: julia-actions/setup-julia@v2
         with:
           version:  '1.11'
-      
+
       - name: Cache Julia packages
         uses: julia-actions/cache@v2
         with:
           cache-name: julia-cache
           cache-packages: true
           cache-artifacts: true
           cache-registries: true
-      
+
       - name: Install Fortran compiler (for Fortran dependencies)
         run: |
           sudo apt-get update
           sudo apt-get install -y gfortran libopenblas-dev
-      
+
       - name: Build Julia project
         run: julia --project="." -e "using Pkg; Pkg.build()"
-      
+
       - name:  Instantiate Julia environment
         run: julia --project="." -e "using Pkg; Pkg.instantiate()"

.github/workflows/make_docs.yaml

@@ -53,4 +53,4 @@ jobs:
       - name: Build and deploy documentation
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia --project=docs docs/make.jl
+        run: julia --project=docs docs/make.jl

.pre-commit-config.yaml

@@ -19,7 +19,6 @@ repos:
             metadata.kernelspec metadata.language_info.version
             cell.metadata.executionInfo cell.metadata.colab
             cell.metadata.id cell.metadata.scrolled
-
   # General file cleanup
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0

PENTRCconverstionTODO.md

@@ -0,0 +1,42 @@
+# JPEC – Kinetic Version Porting Plan
+
+## Porting Map (GPEC → JPEC)
+| Module | GPEC (Fortran) Dir | Function / Routine | JPEC Dir | Function | Notes | Status |
+| --- | --- | --- | --- | --- | --- | --- |
+| DCON | `dcon/forfit.F` | `fourfit_action_matrix()` | `src/DCON/Fourfit.jl` | `make_metric` | `fourfit_action_matrix()` Renamed `action_matrices()`. Isn't this different than `make_metric` | In progress |
+|  |  | `fourfit_kinetic_matrix()` |  |  `make_kinetic_matrix`  | conneted with pentrc | In progress - mostly coded by Claude so far |
+| PENTRC | `pentrc/torque.F90` |`tpsi()` | src/ | | | TODO |
+| PENTRC | `pentrc/torque.F90` |`tintgrl_grid` | src/ | | | TODO |
+| PENTRC | `pentrc/torque.F90` |`tintgrl_lsode` | src/ | | | TODO |
+| DCON | `dcon/sing.f` | `ksing_find()` | `src/DCON/Sing.jl` | Option 1) `sing_find!`<br>Option 2) `sing_king_fing!` |  | first pass done and kinda tested|
+|  |  | `sing_get_f_det()` | `src/DCON/Sing.jl` | `sing_get_f_det()` | Maybe include inside `ksing_find()` | first pass done and kinda tested |
+|  |  | `sing_der()` | `src/DCON/Sing.jl` | `sing_der!` |  | TODO |
+| DCON | `dcon/ode.f` | `ode_kin_cross()` | `src/DCON/Ode.jl` | `ode_kin_cross()` | for `ode_run()` | TODO |
+|  |  | `ode_axis_init()` |  | `ode_axis_init()` |  | TODO |
+|  |  | `ode_step()` |  | `compute_tols()` | Kinetic part needed only in `ode_step` | TODO |
+| PENTRC | `pentrc/pentrc_interface.f90` | `initialize_pentrc()` |  |  |  | TODO |
+| PENTRC | `pentrc/dcon_interface.f` | `set_eq()` |  |  |  | TODO |
+|  |  | `set_geom()` |  |  | used in `set_eq()` | TODO |
+| PENTRC | `pentrc/inputs.f90` | `read_kin()` |  |  |  | TODO |
+|  |  | `read_equil()` |  |  |  | TODO |
+|  |  | `set_peq()` |  |  |  | TODO |
+| PENTRC | `pentrc/utilities` | `*` |  |  |  | TODO |
+| PENTRC | `pentrc/*` | some more things |  |  | esp parmas.f90/ㅣlsode.f90 | TODO |
+
+More things to change :
+- use pitch_integration, only : lambdaintgrl_lsode,kappaintgrl,kappadjsum
+- use energy_integration, only : xintgrl_lsode,qt
+- use special, only : ellipk,ellipe
+- use grid_mod, only : powspace_sub,linspace_sub
+- I added `fourfit.F` to this repo in `src/dcon/fortran` right now. We will need to remove this later, but I wanted GitHub Copilot to have access to it.
+
+---
+
+## Additional TODOs
+
+* [ ] Replace `OMP_SET_NUM_THREADS(dcon_kin_threads)`
+  → Julia multithreading
+  → [https://docs.julialang.org/en/v1/manual/multi-threading/](https://docs.julialang.org/en/v1/manual/multi-threading/)
+
+* [ ] Remove unused or duplicated Julia files
+  (e.g., `idcon_read`, `idcon_build`, …)

Project.toml

@@ -11,6 +11,7 @@ FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
@@ -28,6 +29,7 @@ FFTW = "1.9.0"
 HDF5 = "0.17.2"
 Interpolations = "0.16.1"
 JLD2 = "0.6.3"
+LaTeXStrings = "1.4.0"
 LinearAlgebra = "1.11.0"
 OrdinaryDiffEq = "6.102.0"
 Pkg = "1.11.0"

README.md

@@ -46,4 +46,4 @@ Code
     julia> ]
     pkg> add Revise
 
-Now, in the top of each Jupyter notebook, you can call `using Revise` at the top of any Jupyter notebook to speed up compile times as you develop and test. Better yet, set up your environement to [use Revise by default](https://timholy.github.io/Revise.jl/stable/config/#Using-Revise-by-default)
+Now, in the top of each Jupyter notebook, you can call `using Revise` at the top of any Jupyter notebook to speed up compile times as you develop and test. Better yet, set up your environement to [use Revise by default](https://timholy.github.io/Revise.jl/stable/config/#Using-Revise-by-default)

benchmarks/DIIID_ideal_example/dcon.toml

@@ -49,4 +49,5 @@ equal_arc_wall = 0
 a = 0.2415
 
 [DEBUG]
-output_benchmark_data = true      # Output benchmark data for comparison between codes
+output_benchmark_data = true      # Output benchmark data for comparison between codes
+make_plots = true                 # Makes another hdf5 file that can be used for plotting things like |F| vs psi

benchmarks/DIIID_ideal_example/euler_fortran_julia_comparison.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "2cc3c9a9",
+   "id": "0",
    "metadata": {},
    "source": [
     "## Overview\n",
@@ -12,7 +12,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "db314816",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2b21eeae",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Load in Fortran data\n",
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7fec1fab",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -137,7 +137,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "59f1ad09",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -311,7 +311,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "74226ac8",
+   "id": "5",
    "metadata": {},
    "source": [
     "## Load in Julia data\n",
@@ -321,7 +321,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c76aa60a",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -334,7 +334,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac491233",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -356,7 +356,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bcf321ba",
+   "id": "8",
    "metadata": {},
    "source": [
     "# Compare Outputs\n",
@@ -366,7 +366,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d2ee9066",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -389,15 +389,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b3e56821",
+   "id": "10",
    "metadata": {},
    "source": [
     "## Plots"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "1834dfce",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Plot comparison of xi_psi for a few poloidal mode numbers"
@@ -406,7 +406,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "54b41c30",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -424,7 +424,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b641e050",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Plot comparison of psifac integration\n",
@@ -434,7 +434,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b778938c",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -451,7 +451,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bf6483a8",
+   "id": "15",
    "metadata": {},
    "source": [
     "### Compare the eigenvectors of each DCON energy matrix eigenmode"
@@ -460,7 +460,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "89839f1e",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -520,16 +520,10 @@
   }
  ],
  "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"
+   "name": "julia"
   }
  },
  "nbformat": 4,