Reorganize JPEC module for IPEC calculations

CLAUDE.md

@@ -78,8 +78,8 @@ JPEC consists of four main modules, each organized in `src/`:
    - `Vacuum_math.jl` - Mathematical utilities
    - `fortran/` - Legacy Fortran code compiled to shared library
 
-4. **DCON** (`src/DCON/`) - Stability analysis
-   - `DconStructs.jl` - Core data structures
+4. **ForceFreeStates** (`src/ForceFreeStates/`) - Stability analysis
+   - `ForceFreeStatesStructs.jl` - Core data structures
    - `Main.jl` - Main entry points
    - `Ode.jl` - ODE solver for stability equations
    - `Sing.jl` - Singular point handling
@@ -126,13 +126,13 @@ CODE - TAG - Detailed message
 ```
 
 Where:
-- CODE: Module name (EQUIL, DCON, VAC, VACUUM, etc.)
+- CODE: Module name (EQUIL, ForceFreeStates, VAC, VACUUM, etc.)
 - TAG: Type descriptor (WIP, MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc.)
 
 Examples:
 - `VAC - WIP - Converting vaccal wall code to Julia`
 - `EQUIL - BUG FIX - Fixed separatrix finding for high kappa`
-- `DCON - NEW FEATURE - Added Mercier criterion calculation`
+- `ForceFreeStates - NEW FEATURE - Added Mercier criterion calculation`
 
 This format is used for compiling release notes, so tags should be human-readable and descriptive.
 

README.md

@@ -30,7 +30,7 @@ To assist with the process of compiling release notes, please confirm to the com
 ```
 CODE - TAG - Detailed message
 ```
-where CODE is EQUIL, DCON, VAC, etc. and TAGs are short descriptors of the type of commit. Example tags might be WIP (work in progress), MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc. Look through old commits for examples of what tags are commonly used.
+where CODE is EQUIL, ForceFreeStates, VAC, etc. and TAGs are short descriptors of the type of commit. Example tags might be WIP (work in progress), MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc. Look through old commits for examples of what tags are commonly used.
 
 Again, this is currently used for the by-hand compilation of release notes. The tags thus need to be human readable but are not strictly inforced to be within some limited set. The objective is to allow a lead developer to skim through commits and pick out only the key new features / bug fixes / improvements to note in the release while not having to read all the work-in-progress or minor changes.
 

benchmarks/DIIID_ideal_example/dcon.toml → benchmarks/DIIID_ideal_example/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

benchmarks/DIIID_ideal_example/euler_fortran_julia_comparison.ipynb

@@ -328,7 +328,7 @@
     "# 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"
+    "JPEC.ForceFreeStates.Main(\"./\") # \"./\" tells us to obtain inputs and direct outputs to our current folder"
    ]
   },
   {

benchmarks/DIIID_ideal_example/vacuum_accuracy_benchmark.jl

@@ -44,7 +44,7 @@ if benchmark_n
         println("Testing n = $n_test")
 
         # Compute Fortran solution
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
                                     n_test, vac_inputs.qa, vac_inputs.r,
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -53,7 +53,7 @@ if benchmark_n
                           complex_flag, kernelsign, wall_flag,
                           farwall_flag, grri, xzpts)
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Compute Julia solution
         vac_inputs_test = deepcopy(vac_inputs)
@@ -123,15 +123,15 @@ if benchmark_m
 
     # Fortran reference
     mpert_ref = mhigh_reference - vac_inputs.mlow
-    JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, mhigh_reference,
+    JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, mhigh_reference,
                                 1, vac_inputs.qa, vac_inputs.r,
                                 vac_inputs.z, vac_inputs.delta)
     wv_block_ref_fortran_m = zeros(ComplexF64, mpert_ref, mpert_ref)
     grri_ref = zeros(Float64, 2 * (mthvac + 5), 2 * mpert_ref)
     JPEC.Vacuum.mscvac(wv_block_ref_fortran_m, mpert_ref, mtheta_eq, mthvac,
                        complex_flag, kernelsign, wall_flag,
                        farwall_flag, grri_ref, xzpts, ahg_file, "$(@__DIR__)/../../examples/DIIID-like_ideal_example")
-    JPEC.Vacuum.unset_dcon_params()
+    JPEC.Vacuum.unset_surface_params()
 
     println("Reference solutions computed.\n")
 
@@ -142,7 +142,7 @@ if benchmark_m
         mpert_test = mhigh_test - vac_inputs.mlow
 
         # Compute Fortran solution
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, mhigh_test,
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, mhigh_test,
                                     1, vac_inputs.qa, vac_inputs.r,
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -152,7 +152,7 @@ if benchmark_m
                           complex_flag, kernelsign, wall_flag,
                           farwall_flag, grri_test, xzpts, ahg_file, "$(@__DIR__)/../../examples/DIIID-like_ideal_example")
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Compute Julia solution
         vac_inputs_test_m = deepcopy(vac_inputs)

benchmarks/DIIID_ideal_example/vacuum_speed_benchmark.jl

@@ -36,7 +36,7 @@ if benchmark_n
         println("Benchmarking n = $n_test")
 
         # Benchmark Fortran version
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh, 
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh, 
                                     n_test, vac_inputs.qa, vac_inputs.r, 
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -49,7 +49,7 @@ if benchmark_n
         push!(fortran_allocs, median(b_fortran).allocs)
         push!(fortran_memory, median(b_fortran).memory / 1e6)
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Benchmark Julia version
         vac_inputs_test = deepcopy(vac_inputs)
@@ -106,7 +106,7 @@ if benchmark_m
         mpert_test = mhigh_test - vac_inputs.mlow
 
         # Benchmark Fortran version
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, mhigh_test, 
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, mhigh_test, 
                                     1, vac_inputs.qa, vac_inputs.r, 
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -119,7 +119,7 @@ if benchmark_m
         push!(fortran_mhigh_allocs, median(b_fortran).allocs)
         push!(fortran_mhigh_memory, median(b_fortran).memory / 1e6)
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Benchmark Julia version
         vac_inputs_test = deepcopy(vac_inputs)

benchmarks/Solovev_ideal_example/vacuum_accuracy_benchmark.jl

@@ -48,7 +48,7 @@ if benchmark_n
         println("Testing n = $n_test")
 
         # Compute Fortran solution
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
                                     n_test, vac_inputs.qa, vac_inputs.r,
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -57,7 +57,7 @@ if benchmark_n
                           complex_flag, kernelsign, wall_flag,
                           farwall_flag, grri, xzpts)
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Compute Julia solution
         vac_inputs_test = deepcopy(vac_inputs)
@@ -122,7 +122,7 @@ if benchmark_a
         println("Testing a = $a_test")
 
         # Compute Fortran solution
-        JPEC.Vacuum.set_dcon_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
+        JPEC.Vacuum.set_surface_params(mtheta_eq, vac_inputs.mlow, vac_inputs.mhigh,
                                     vac_inputs.n, vac_inputs.qa, vac_inputs.r,
                                     vac_inputs.z, vac_inputs.delta)
 
@@ -136,7 +136,7 @@ if benchmark_a
                           complex_flag, kernelsign, wall_flag,
                           farwall_flag, grri, xzpts)
 
-        JPEC.Vacuum.unset_dcon_params()
+        JPEC.Vacuum.unset_surface_params()
 
         # Compute Julia solution
         new_wall = JPEC.Vacuum.WallShapeSettings(

docs/src/equilibrium.md

@@ -19,7 +19,7 @@ Key responsibilities of the module:
 	(global parameters, q-profile finding, separatrix finding, GSE checks).
 
 The module exposes a small public API that covers setup, configuration,
-and common analyses used by other JPEC components (e.g. `DCON`, vacuum
+and common analyses used by other JPEC components (e.g. `ForceFreeStates`, vacuum
 interfaces).
 
 ## API Reference
@@ -65,7 +65,7 @@ Basic example: read a TOML config and build an equilibrium
 using JPEC
 
 # Build from a TOML file (searches relative paths if needed)
-pe = JPEC.Equilibrium.setup_equilibrium("docs/examples/dcon.toml")
+pe = JPEC.Equilibrium.setup_equilibrium("docs/examples/ForceFreeStates.toml")
 
 println("Magnetic axis: ", pe.params.r0, ", ", pe.params.z0)
 println("q(0) = ", pe.params.q0)

docs/src/examples/vacuum.md

@@ -4,14 +4,14 @@ This page demonstrates the usage of the Vacuum module for magnetostatic calculat
 
 ## Basic Vacuum Field Calculation
 
-### Setting up DCON Parameters
+### Setting up Surface Parameters
 
-The vacuum module requires initialization with DCON (Displacement CONtinuum) parameters:
+The vacuum module requires initialization with surface parameters:
 
 ```julia
 using JPEC
 
-# Define DCON parameters
+# Define surface parameters
 mthin = Int32(4)     # Number of theta points
 lmin = Int32(1)      # Minimum poloidal mode number
 lmax = Int32(4)      # Maximum poloidal mode number
@@ -24,8 +24,8 @@ xin = rand(Float64, n_modes)      # Radial coordinates
 zin = rand(Float64, n_modes)      # Vertical coordinates
 deltain = rand(Float64, n_modes)  # Displacement data
 
-# Initialize DCON interface
-JPEC.VacuumMod.set_dcon_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)
+# Initialize surface parameters interface
+JPEC.VacuumMod.set_surface_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)
 ```
 
 ### Vacuum Matrix Calculation
@@ -137,7 +137,7 @@ println("Most unstable eigenvalue: ", eigenvals[max_growth_idx])
 # xin, zin, deltain = process_boundary_data(boundary_data)
 
 # 4. Perform vacuum calculation
-# JPEC.VacuumMod.set_dcon_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)
+# JPEC.VacuumMod.set_surface_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)
 # ... vacuum calculation ...
 
 # 5. Analyze stability
@@ -148,7 +148,7 @@ println("Most unstable eigenvalue: ", eigenvals[max_growth_idx])
 
 ### Common Issues
 
-1. **Initialization Error**: Ensure `set_dcon_params` is called before `mscvac`
+1. **Initialization Error**: Ensure `set_surface_params` is called before `mscvac`
 2. **Memory Issues**: Large `mtheta`/`mthvac` values require significant memory
 3. **Convergence**: Check that geometry arrays are properly normalized
 4. **Complex Arithmetic**: Ensure `complex_flag=true` for stability analysis

docs/src/index.md

@@ -46,7 +46,7 @@ To assist with release note compilation, please follow the commit message format
 ```
 CODE - TAG - Detailed message
 ```
-where CODE is EQUIL, DCON, VAC, etc. and TAGs are descriptors like WIP, MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc.
+where CODE is Equil, ForceFreeStates, Vacuum, etc. and TAGs are descriptors like WIP, MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc.
 
 Additionally, please see [this](https://docs.google.com/document/d/1XAOTz1IV8ErZAAk-iSuEuddNOLB5XcoVZsAbPKRUUuA) google doc for more details on using the GitHub.
 

docs/src/vacuum.md

@@ -7,7 +7,7 @@ Refactored/interfaced from/with VACUUM by M.S. Chance.
 
 The module includes:
 
-- Interface to Fortran vacuum field calculations (`mscvac`, `set_dcon_params`)
+- Interface to Fortran vacuum field calculations (`mscvac`, `set_surface_params`)
 - Pure Julia implementation of vacuum response calculations (`compute_vacuum_response`, `compute_vacuum_field`)
 - Support for various wall geometries and configurations
 
@@ -35,9 +35,9 @@ Modules = [JPEC.Vacuum]
 
 ## Functions
 
-### set_dcon_params
+### set_surface_params
 ```@docs
-JPEC.Vacuum.set_dcon_params
+JPEC.Vacuum.set_surface_params
 ```
 
 ### mscvac
@@ -62,15 +62,15 @@ JPEC.Vacuum.compute_vacuum_field
 ```julia
 using JPEC
 
-# Set DCON parameters
+# Set surface parameters
 mtheta, lmin, lmax, nnin = Int32(4), Int32(1), Int32(4), Int32(2)
 qa1in = 1.23
 xin = rand(Float64, lmax - lmin + 1)
 zin = rand(Float64, lmax - lmin + 1)
 deltain = rand(Float64, lmax - lmin + 1)
 
-# Initialize DCON interface
-JPEC.Vacuum.set_dcon_params(mtheta, lmin, lmax, nnin, qa1in, xin, zin, deltain)
+# Initialize surface parameters interface
+JPEC.Vacuum.set_surface_params(mtheta, lmin, lmax, nnin, qa1in, xin, zin, deltain)
 
 # Set up vacuum calculation parameters
 mpert = 5
@@ -127,7 +127,7 @@ wv, grri, xzpts = JPEC.Vacuum.compute_vacuum_response(inputs, wall_settings)
 
 ## Notes
 
-- Requires proper initialization of DCON parameters before using the Fortran interface
+- Requires proper initialization of surface parameters before using the Fortran interface
 - The pure Julia implementation (`compute_vacuum_response`) provides equivalent functionality
 - For n=0 modes with closed walls, automatic regularization is applied
 

examples/DIIID-like_ideal_example/dcon.toml → examples/DIIID-like_ideal_example/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

examples/DIIID-like_ideal_example/run_and_analyze.ipynb

@@ -43,7 +43,7 @@
     "# 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"
+    "JPEC.ForceFreeStates.Main(\"./\") # \"./\" tells us to obtain inputs and direct outputs to our current folder"
    ]
   },
   {

examples/Solovev_ideal_example/dcon.toml → examples/Solovev_ideal_example/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

examples/Solovev_ideal_example/run_and_analyze.ipynb

@@ -43,7 +43,7 @@
     "# 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"
+    "JPEC.ForceFreeStates.Main(\"./\") # \"./\" tells us to obtain inputs and direct outputs to our current folder"
    ]
   },
   {

examples/Solovev_ideal_example/vacuum_wall_debug.jl

@@ -32,15 +32,15 @@ if !use_wall_arg
 end
 
 
-JPEC.Vacuum.set_dcon_params(mtheta_eq, mlow, mhigh, 
+JPEC.Vacuum.set_surface_params(mtheta_eq, mlow, mhigh, 
                                     n, vac_inputs.qa, vac_inputs.r, 
                                     vac_inputs.z, vac_inputs.delta)
 
 wv_fortran = JPEC.Vacuum.mscvac(wv_block, mpert, mtheta_eq, mthvac, 
                          complex_flag, kernelsign, wall_flag, 
                          farwall_flag, grri, xzpts, ahg_file, "$(@__DIR__)")
 
-JPEC.Vacuum.unset_dcon_params()
+JPEC.Vacuum.unset_surface_params()
 
 # Now deepcopy the julia vac_inputs and set the new ms
 vac_inputs = deepcopy(vac_inputs)

examples/Solovev_ideal_example_multi_n/dcon.toml → examples/Solovev_ideal_example_multi_n/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

examples/Solovev_ideal_example_multi_n/run_and_analyze.ipynb

@@ -42,9 +42,9 @@
     "# 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\n",
-    "JPEC.DCON.Main(\"single_n_1\")\n",
-    "JPEC.DCON.Main(\"single_n_2\")"
+    "JPEC.ForceFreeStates.Main(\"./\") # \"./\" tells us to obtain inputs and direct outputs to our current folder\n",
+    "JPEC.ForceFreeStates.Main(\"single_n_1\")\n",
+    "JPEC.ForceFreeStates.Main(\"single_n_2\")"
    ]
   },
   {

examples/Solovev_ideal_example_multi_n/single_n_1/dcon.toml → examples/Solovev_ideal_example_multi_n/single_n_1/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

examples/Solovev_ideal_example_multi_n/single_n_2/dcon.toml → examples/Solovev_ideal_example_multi_n/single_n_2/ForceFreeStates.toml

@@ -1,4 +1,4 @@
-[DCON_CONTROL]
+[ForceFreeStates_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)

notebooks/vacuum_fortran_example.ipynb

@@ -32,9 +32,9 @@
     "zin = rand(Float64, lmax - lmin + 1)\n",
     "deltain = rand(Float64, lmax - lmin + 1)\n",
     "\n",
-    "println(\"Testing set_dcon_params…\")\n",
-    "JPEC.VacuumMod.set_dcon_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)\n",
-    "println(\"set_dcon_params OK!\")"
+    "println(\"Testing set_surface_params…\")\n",
+    "JPEC.VacuumMod.set_surface_params(mthin, lmin, lmax, nnin, qa1in, xin, zin, deltain)\n",
+    "println(\"set_surface_params OK!\")"
    ]
   },
   {