Purge Intermediate Api access to configuration object from in favor of new config_type object

applications/coupled/source/coupled.f90

@@ -41,27 +41,23 @@ program coupled
   call parse_command_line( filename, component_name=cpl_component_name )
 
   call modeldb%values%initialise( 'values', 5 )
-
-  call modeldb%configuration%initialise( program_name, table_len=10 )
   call modeldb%config%initialise( program_name )
-
-  write(log_scratch_space,'(A)')                          &
-      'Application built with '// trim(precision_real) // &
-      '-bit real numbers.'
-  call log_event( log_scratch_space, log_level_trace )
+  call modeldb%values%add_key_value('cpl_name', cpl_component_name)
 
   modeldb%mpi => global_mpi
 
-  call modeldb%values%add_key_value('cpl_name', cpl_component_name)
   call init_comm( "coupled", modeldb )
-
-  call init_config( filename,                            &
-                    coupled_required_namelists,          &
-                    configuration=modeldb%configuration, &
+  call init_config( filename, coupled_required_namelists, &
                     config=modeldb%config )
 
   call init_logger( modeldb%mpi%get_comm(), &
                     program_name//"_"//cpl_component_name )
+
+  write(log_scratch_space,'(A)')                          &
+      'Application built with '// trim(precision_real) // &
+      '-bit real numbers.'
+  call log_event( log_scratch_space, log_level_trace )
+
   call init_collections()
   call init_time( modeldb )
   deallocate( filename )

applications/coupled/source/driver/coupled_driver_mod.f90

@@ -120,7 +120,7 @@ subroutine initialise( program_name, modeldb, calendar )
     ! Create the required meshes
     stencil_depth = 1
     apply_partition_check = .false.
-    call init_mesh( modeldb%configuration,       &
+    call init_mesh( modeldb%config,              &
                     modeldb%mpi%get_comm_rank(), &
                     modeldb%mpi%get_comm_size(), &
                     base_mesh_names, extrusion,  &

applications/io_demo/source/algorithm/io_demo_constants_mod.x90

@@ -17,7 +17,6 @@ module io_demo_constants_mod
   ! Infrastructure
   use constants_mod,                      only: i_def, r_def, l_def, &
                                                 str_def, str_short
-  use driver_modeldb_mod,                 only: modeldb_type
   use field_collection_mod,               only: field_collection_type
   use field_mod,                          only: field_type
   use fs_continuity_mod,                  only: W2
@@ -49,16 +48,14 @@ module io_demo_constants_mod
 contains
 
   !> @brief Subroutine to create the finite element constants
-  !> @param[in] modeldb   Application state object
   !> @param[in] mesh      The prime model mesh
   !> @param[in] chi       Coordinate fields
   !> @param[in] panel_id  Panel_id field
-  subroutine create_io_demo_constants(modeldb, mesh, chi, panel_id)
+  subroutine create_io_demo_constants(mesh, chi, panel_id)
 
     implicit none
 
     ! Arguments
-    type(modeldb_type),       intent(in) :: modeldb
     type(mesh_type), pointer, intent(in) :: mesh
     type(field_type), target, intent(in) :: chi(:)
     type(field_type), target, intent(in) :: panel_id

applications/io_demo/source/driver/init_io_demo_mod.F90

@@ -106,7 +106,7 @@ subroutine init_io_demo(modeldb, mesh, chi, panel_id)
     ! Create io_demo runtime constants. This creates various things
     ! needed by the fem algorithms such as mass matrix operators, mass
     ! matrix diagonal fields and the geopotential field
-    call create_io_demo_constants(modeldb, mesh, chi, panel_id)
+    call create_io_demo_constants(mesh, chi, panel_id)
 
     call log_event( 'io_demo: Miniapp initialised', LOG_LEVEL_TRACE )
 

applications/io_demo/source/driver/io_demo_driver_mod.f90

@@ -155,7 +155,7 @@ subroutine initialise(program_name, modeldb)
     ! ---------------------------------------------------------
     stencil_depth = 1
     check_partitions = .false.
-    call init_mesh( modeldb%configuration,       &
+    call init_mesh( modeldb%config,              &
                     modeldb%mpi%get_comm_rank(), &
                     modeldb%mpi%get_comm_size(), &
                     base_mesh_names, extrusion,  &

applications/io_demo/source/io_demo.f90

@@ -10,7 +10,8 @@ program io_demo
 
   use cli_mod,                     only : parse_command_line
   use driver_collections_mod,      only : init_collections, final_collections
-  use constants_mod,               only : precision_real
+  use constants_mod,               only : precision_real,l_def, &
+                                          str_max_filename
   use driver_comm_mod,             only : init_comm, final_comm
   use driver_config_mod,           only : init_config, final_config
   use driver_log_mod,              only : init_logger, final_logger
@@ -25,46 +26,45 @@ program io_demo
   use io_demo_mod,        only: io_demo_required_namelists
   use io_demo_driver_mod, only: initialise, step, finalise
   use timing_mod,         only: init_timing, final_timing
-  use io_config_mod,      only: timer_output_path
-  use namelist_mod,       only: namelist_type
 
   implicit none
 
   ! The technical and scientific state
-  type(modeldb_type)           :: modeldb
-  character(*), parameter      :: program_name = "io_demo"
-  character(:), allocatable    :: filename
-  type(namelist_type), pointer :: io_nml
-  logical                      :: lsubroutine_timers
-  integer, parameter           :: default_seed = 123456789
+  type(modeldb_type)        :: modeldb
+  character(*), parameter   :: program_name = "io_demo"
+  character(:), allocatable :: filename
+  integer, parameter        :: default_seed = 123456789
+
   type(random_number_generator_type), pointer :: rng
 
+  character(str_max_filename) :: timer_output_path
+  logical(l_def)              :: subroutine_timers
+
   call parse_command_line( filename )
-  call modeldb%values%initialise()
-  call modeldb%configuration%initialise( program_name, table_len=10 )
   call modeldb%config%initialise(program_name)
+  call modeldb%values%initialise()
+
+  modeldb%mpi => global_mpi
+
+  call init_comm(program_name, modeldb)
+  call init_config(filename, io_demo_required_namelists, &
+                   config=modeldb%config)
+
+  call init_logger( modeldb%mpi%get_comm(), program_name )
 
   write(log_scratch_space,&
         '("Application built with ", A, "-bit real numbers")') &
         trim(precision_real)
   call log_event( log_scratch_space, log_level_trace )
-  modeldb%mpi => global_mpi
-  call init_comm(program_name, modeldb)
 
-  call init_config(filename,                            &
-                   io_demo_required_namelists,          &
-                   configuration=modeldb%configuration, &
-                   config=modeldb%config)
+  subroutine_timers = modeldb%config%io%subroutine_timers()
+  timer_output_path = modeldb%config%io%timer_output_path()
+  call init_timing( modeldb%mpi%get_comm(), subroutine_timers, &
+                    program_name, timer_output_path )
 
-  deallocate( filename )
-
-  call init_logger( modeldb%mpi%get_comm(), program_name )
-  io_nml => modeldb%configuration%get_namelist('io')
-  call io_nml%get_value('subroutine_timers', lsubroutine_timers)
-  call init_timing( modeldb%mpi%get_comm(), lsubroutine_timers, program_name, timer_output_path )
-  nullify( io_nml )
   call init_collections()
   call init_time(modeldb)
+  deallocate( filename )
 
   allocate(rng, source=random_number_generator_type(default_seed))
   call modeldb%values%add_key_value("rng", rng)

applications/lbc_demo/source/driver/lbc_demo_driver_mod.f90

@@ -186,7 +186,7 @@ subroutine initialise( program_name, modeldb)
   stencil_depth = 1
   check_partitions = .false.
 
-  call init_mesh( modeldb%configuration,       &
+  call init_mesh( modeldb%config,              &
                   modeldb%mpi%get_comm_rank(), &
                   modeldb%mpi%get_comm_size(), &
                   base_mesh_names, extrusion,  &

applications/lbc_demo/source/lbc_demo.f90

@@ -37,22 +37,16 @@ program lbc_demo
   integer :: geometry, topology
 
   call parse_command_line( filename )
+  call modeldb%config%initialise( program_name )
 
-  write(log_scratch_space, '(A)') &
-      'Application built with ' // trim(precision_real) // '-bit real numbers'
-  call log_event( log_scratch_space, log_level_trace )
-
-  ! The technical and scientific state
   modeldb%mpi => global_mpi
-  call modeldb%configuration%initialise( program_name, table_len=10 )
-  call modeldb%config%initialise( program_name )
 
   call init_comm(program_name, modeldb)
-
-  call init_config(filename, required_namelists,        &
-                   configuration=modeldb%configuration, &
+  call init_config(filename, required_namelists, &
                    config=modeldb%config)
 
+  call init_logger( modeldb%mpi%get_comm(), program_name )
+
   ! Before anything else, test that the mesh provided was a regional domain.
   ! This application is not intended for cubed-sphere meshes.
   geometry = modeldb%config%base_mesh%geometry()
@@ -64,10 +58,12 @@ program lbc_demo
     call log_event( 'Cubed-Sphere mesh is not supported.', log_level_error)
   end if
 
-  call init_logger( modeldb%mpi%get_comm(), program_name )
+  write(log_scratch_space, '(A)') &
+      'Application built with ' // trim(precision_real) // '-bit real numbers'
+  call log_event( log_scratch_space, log_level_trace )
+
   call init_collections()
   call init_time(modeldb)
-
   deallocate( filename )
 
   ! Create the depository field collection and place it in modeldb

applications/simple_diffusion/source/algorithm/simple_diffusion_constants_mod.x90

@@ -17,7 +17,6 @@ module simple_diffusion_constants_mod
   ! Infrastructure
   use constants_mod,                      only: i_def, r_def, l_def, &
                                                 str_def, str_short
-  use driver_modeldb_mod,                 only: modeldb_type
   use field_collection_mod,               only: field_collection_type
   use field_mod,                          only: field_type
   use fs_continuity_mod,                  only: W2
@@ -49,19 +48,16 @@ module simple_diffusion_constants_mod
 contains
 
   !> @brief Subroutine to create the finite element constants
-  !> @param[in] modeldb   Application state object
   !> @param[in] mesh      The prime model mesh
   !> @param[in] chi       Coordinate fields
   !> @param[in] panel_id  Panel_id field
-  subroutine create_simple_diffusion_constants( modeldb, &
-                                                mesh,    &
+  subroutine create_simple_diffusion_constants( mesh,    &
                                                 chi,     &
                                                 panel_id )
 
     implicit none
 
     ! Arguments
-    type(modeldb_type),       intent(in) :: modeldb
     type(mesh_type), pointer, intent(in) :: mesh
     type(field_type), target, intent(in) :: chi(:)
     type(field_type), target, intent(in) :: panel_id

applications/simple_diffusion/source/driver/init_simple_diffusion_mod.F90

@@ -21,8 +21,7 @@ module init_simple_diffusion_mod
   use function_space_collection_mod,  only : function_space_collection
   use function_space_mod,             only : function_space_type
   use fs_continuity_mod,              only : Wtheta
-  use log_mod,                        only : log_event,      &
-                                             LOG_LEVEL_TRACE
+  use log_mod,                        only : log_event, log_level_trace
   use mesh_mod,                       only : mesh_type
   use lfric_xios_write_mod,           only : write_field_generic
   use simple_diffusion_constants_mod, only : create_simple_diffusion_constants
@@ -64,7 +63,8 @@ subroutine init_simple_diffusion(mesh, chi, panel_id, modeldb)
 
     fs => function_space_collection%get_fs(mesh, order_h, order_v, Wtheta)
 
-    call log_event( 'simple_diffusion: Initialising miniapp ...', LOG_LEVEL_TRACE )
+    call log_event( 'simple_diffusion: Initialising miniapp ...', &
+                    log_level_trace )
 
     ! Create prognostic fields
     ! Creates a field in the Wtheta function space
@@ -87,9 +87,9 @@ subroutine init_simple_diffusion(mesh, chi, panel_id, modeldb)
     ! Create simple_diffusion runtime constants. This creates various things
     ! needed by the fem algorithms such as mass matrix operators, mass
     ! matrix diagonal fields and the geopotential field
-    call create_simple_diffusion_constants(modeldb, mesh, chi, panel_id)
+    call create_simple_diffusion_constants(mesh, chi, panel_id)
 
-    call log_event( 'simple_diffusion: Miniapp initialised', LOG_LEVEL_TRACE )
+    call log_event( 'simple_diffusion: Miniapp initialised', log_level_trace )
 
   end subroutine init_simple_diffusion
 

applications/simple_diffusion/source/driver/simple_diffusion_driver_mod.f90

@@ -149,7 +149,7 @@ subroutine initialise( program_name, modeldb)
     ! ---------------------------------------------------------
     stencil_depth = 1
     check_partitions = .false.
-    call init_mesh( modeldb%configuration,       &
+    call init_mesh( modeldb%config,              &
                     modeldb%mpi%get_comm_rank(), &
                     modeldb%mpi%get_comm_size(), &
                     base_mesh_names, extrusion,  &

applications/simple_diffusion/source/simple_diffusion.f90

@@ -36,25 +36,25 @@ program simple_diffusion
 
   call parse_command_line( filename )
   call modeldb%values%initialise()
-  call modeldb%configuration%initialise( program_name, table_len=10 )
   call modeldb%config%initialise( program_name )
 
-  write(log_scratch_space,&
-        '("Application built with ", A, "-bit real numbers")') &
-        trim(precision_real)
-  call log_event( log_scratch_space, log_level_trace )
   modeldb%mpi => global_mpi
-  call init_comm(program_name, modeldb)
 
-  call init_config( filename, simple_diffusion_required_namelists, &
-                    configuration=modeldb%configuration,           &
+  call init_comm(program_name, modeldb)
+  call init_config( filename,                            &
+                    simple_diffusion_required_namelists, &
                     config=modeldb%config )
 
-  deallocate( filename )
-
   call init_logger( modeldb%mpi%get_comm(), program_name )
+
+  write(log_scratch_space,&
+        '("Application built with ", A, "-bit real numbers")') &
+        trim(precision_real)
+  call log_event( log_scratch_space, log_level_trace )
+
   call init_collections()
   call init_time( modeldb )
+  deallocate( filename )
 
   allocate(rng, source=random_number_generator_type(default_seed))
   call modeldb%values%add_key_value("rng", rng)

applications/skeleton/source/algorithm/skeleton_constants_mod.x90

@@ -113,6 +113,7 @@ contains
     integer(tik) :: id
 
     if ( LPROF ) call start_timing( id, 'skeleton_constants_alg' )
+
     call log_event( "Skeleton: creating runtime constants", LOG_LEVEL_INFO )
 
     order_h     = modeldb%config%finite_element%element_order_h()

applications/skeleton/source/driver/skeleton_driver_mod.f90

@@ -141,7 +141,7 @@ subroutine initialise(program_name, modeldb)
     !-----------------------------------------------------------------------
     stencil_depth = 1
     apply_partition_check = .false.
-    call init_mesh( modeldb%configuration,       &
+    call init_mesh( modeldb%config,              &
                     modeldb%mpi%get_comm_rank(), &
                     modeldb%mpi%get_comm_size(), &
                     base_mesh_names, extrusion,  &

applications/skeleton/source/skeleton.f90

@@ -37,22 +37,21 @@ program skeleton
   character(:), allocatable :: filename
 
   call parse_command_line( filename )
-  call modeldb%configuration%initialise( program_name, table_len=10 )
   call modeldb%config%initialise(program_name)
 
-  write(log_scratch_space,'(A)')                          &
-      'Application built with '// trim(precision_real) // &
-      '-bit real numbers.'
-  call log_event( log_scratch_space, log_level_trace )
-
   modeldb%mpi => global_mpi
 
   call init_comm( "skeleton", modeldb )
   call init_config( filename, skeleton_required_namelists, &
-                    configuration=modeldb%configuration,   &
                     config=modeldb%config )
 
   call init_logger( modeldb%mpi%get_comm(), program_name )
+
+  write(log_scratch_space,'(A)')                          &
+      'Application built with '// trim(precision_real) // &
+      '-bit real numbers.'
+  call log_event( log_scratch_space, log_level_trace )
+
   call init_collections()
   call init_time( modeldb )
   deallocate( filename )

components/driver/source/driver_coordinates_mod.F90

@@ -167,7 +167,18 @@ subroutine assign_coordinate_field(chi, panel_id, mesh)
         'stretching factor is not 1 and mesh is not cubed-sphere',             &
         log_level_error                                                        &
       )
-    end if
+   end if
+
+
+!   if ( geometry == geometry_spherical .and. &
+!        topology == topology_fully_periodic) then
+!      stretch_factor = get_stretch_factor()
+!   else
+!      stretch_factor = 1.0_r_def
+!   end if
+
+!   inverse_rot_matrix = get_inverse_mesh_rotation_matrix()
+!   to_rotate = get_to_rotate()
 
     panel_id_proxy%data = 1.0_r_def