Clean up stella: kxky grids, namelists, debug flags, including full_f…

…lux_surface automatic numerical tests (#156)

Continuation of clean up of stella. The kxky grids have been cleaned up, and separated out into different modules. There not exists a <parameters_kxky_grids.f90> file which is the overarching module that reads the parameters for the kxky grids. This then uses either <parameters_kxky_grids_box.f90> or <parameters_kxky_grids_range.f90> depending on which grid type is chosen in the input file. Two additional modules have been added as a result of this split up called <calculations_kxky.f90> and <write_radial_grid.f90>.

There is a new folder called <grids_kxky.f90> file that initialised the kxky grids and fills the arrays for the kxky grids.

The parameter namelist have also been changed, and placed into different modules. The new files are <parameters_numerical.f90> <parameters_physics.f90>, and have replaced the previous modules <run_parameters.f90>, <physics_flags.f90>, <physics_paramters.f90>. These have been named in preparation for organising stella into sub directories.

A new debug feature has also been added to allow the debug flags to be turned on/off in the input file, rather than requiring the code to be re-compiled. This is found in <debug_flags.f90>.

CMakeLists.txt

@@ -42,36 +42,41 @@ option(STELLA_UPDATE_GIT_SUBMODULES "Check submodules are up-to-date during buil
 
 # Sources that don't need preprocessing
 set(STELLA_SOURCES_f90
+  arrays_dist_fn.f90
+  arrays_fields.f90
+  calculations_kxky.f90
   common_types.f90
+  debug_flags.f90
   define.inc
   dist_fn.f90
-  dist_fn_arrays.f90
   dist_redistribute.f90
   euterpe_interface.f90
   extended_zgrid.f90
   ffs_solve.f90
-  fields_arrays.f90
   finite_differences.f90
   flow_shear.f90
   g_tofrom_h.f90
+  grids_kxky.f90
   gyro_averages.f90
   implicit_solve.f90
   init_g.f90
-  kt_grids.f90
   mirror_terms.f90
   multibox.f90
   neoclassical_terms.f90
   parallel_streaming.f90
-  physics_flags.f90
-  physics_parameters.f90
-  run_parameters.f90
+  parameters_kxky_grids.f90
+  parameters_kxky_grids_box.f90
+  parameters_kxky_grids_range.f90
+  parameters_numerical.f90
+  parameters_physics.f90
   species.f90
   stella_layouts.f90
   stella_time.f90
   stella_transforms.f90
   time_advance.f90
   volume_averages.f90
   vpamu_grids.f90
+  write_radial_grid.f90
   zgrid.f90
   diagnostics/parameters_diagnostics.f90
   diagnostics/diagnostics.f90