TokaMaker: Add support for grouping coils into coil sets (#38)

* Add X-point candidate filtering with characteristic scale length
* Add support for arbitrary number of coil regularization terms
* Add HBT example and update ITER and fixed-boundary examples
* Update examples and format notes in Jupyter notebook examples

src/bin/tokamaker_gs.F90

@@ -162,9 +162,9 @@ program tokamaker_gs
   CLOSE(io_unit)
   !---Read coil constraint matrix
   IF(.NOT.ASSOCIATED(mygs%coil_reg_mat))THEN
-    ALLOCATE(mygs%coil_reg_mat(mygs%ncoil_regs+1,mygs%ncoil_regs+1))
+    ALLOCATE(mygs%coil_reg_mat(mygs%ncoils+1,mygs%ncoils+1))
     OPEN(NEWUNIT=io_unit,FILE='coil_reg_mat.dat')
-    DO i=1,mygs%ncoil_regs+1
+    DO i=1,mygs%ncoils+1
       READ(io_unit,*)mygs%coil_reg_mat(i,:)
     END DO
     CLOSE(io_unit)

src/bin/tokamaker_wall.F90

@@ -830,8 +830,8 @@ program tokamaker_wall
 IF(TRIM(coil_file)/='none')THEN
   mygs%coil_file=coil_file
   CALL mygs%load_coils(ignore_inmesh=.TRUE.)
-  DO i=1,mygs%ncoils
-    mygs%coils(i)%curr=0.d0 ! Zero all external coils
+  DO i=1,mygs%ncoils_ext
+    mygs%coils_ext(i)%curr=0.d0 ! Zero all external coils
   END DO
   DO i=1,mygs%ncoil_regs
     mygs%coil_regions(i)%curr=0.d0 ! Zero all internal coil regions
@@ -955,20 +955,20 @@ subroutine compute_eddy(self)
           CASE(1)
             IF(grid_3d)THEN
               CALL nonax_indcouple(self%cond_regions(i)%nc_quad,rc,self%cond_regions(i)%extent, &
-              eigs,self%coils(k)%pt,self%coils(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall, &
+              eigs,self%coils_ext(k)%pt,self%coils_ext(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall, &
               rz_grid,rz_correction)
             ELSE 
               CALL nonax_indcouple(self%cond_regions(i)%nc_quad,rc,self%cond_regions(i)%extent, &
-              eigs,self%coils(k)%pt,self%coils(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall)
+              eigs,self%coils_ext(k)%pt,self%coils_ext(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall)
             END IF
           CASE(2)
             IF(grid_3d)THEN
               CALL nonax_rescouple(self%cond_regions(i)%nc_quad,rc,self%cond_regions(i)%extent, &
-              eigs,self%coils(k)%pt,self%coils(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall, &
+              eigs,self%coils_ext(k)%pt,self%coils_ext(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall, &
               eta,rz_grid,rz_correction)
             ELSE 
               CALL nonax_rescouple(self%cond_regions(i)%nc_quad,rc,self%cond_regions(i)%extent, &
-              eigs,self%coils(k)%pt,self%coils(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall,eta)
+              eigs,self%coils_ext(k)%pt,self%coils_ext(k)%ncoils,correction(:,j),sensors,nsensor,mirror_wall,eta)
             END IF
           CASE(3)
             IF(grid_3d)THEN

src/docs/doc_tokamaker_main.md

@@ -16,11 +16,13 @@ Talk about TokaMaker...
 The following examples illustrate usage of TokaMaker to compute different Grad-Shafranov equilibria. 
 
 ### Mesh Generation
- - \subpage doc_tMaker_mesh_ex1
+ - \subpage doc_tMaker_HBT_ex1
+ - \subpage doc_tMaker_ITER_ex1
 
 ### Fixed Boundary Equilibria
- - \subpage doc_tMaker_ex1
- - \subpage doc_tMaker_ex2
+ - \subpage doc_tMaker_fixed_ex1
+ - \subpage doc_tMaker_fixed_ex2
 
 ### Free Boundary Equilibria
- - \subpage doc_tMaker_ex3
+ - \subpage doc_tMaker_HBT_ex2
+ - \subpage doc_tMaker_ITER_ex2

src/examples/TokaMaker/CMakeLists.txt

@@ -3,6 +3,11 @@ install(FILES fixed_boundary/fixed_boundary_ex1.ipynb DESTINATION examples/TokaM
 install(FILES fixed_boundary/fixed_boundary_ex2.ipynb DESTINATION examples/TokaMaker/fixed_boundary COMPONENT examples)
 install(FILES fixed_boundary/gNT_example DESTINATION examples/TokaMaker/fixed_boundary COMPONENT examples)
 #
+install(FILES HBT/HBT_geom.json DESTINATION examples/TokaMaker/HBT COMPONENT examples)
+install(FILES HBT/HBT_mesh_ex.ipynb DESTINATION examples/TokaMaker/HBT COMPONENT examples)
+install(FILES HBT/HBT_eq_ex.ipynb DESTINATION examples/TokaMaker/HBT COMPONENT examples)
+install(FILES HBT/HBT_mesh.h5 DESTINATION examples/TokaMaker/HBT COMPONENT examples)
+#
 install(FILES ITER/ITER_mesh_ex.ipynb DESTINATION examples/TokaMaker/ITER COMPONENT examples)
 install(FILES ITER/ITER_baseline_ex.ipynb DESTINATION examples/TokaMaker/ITER COMPONENT examples)
 install(FILES ITER/ITER_geom.json DESTINATION examples/TokaMaker/ITER COMPONENT examples)