Update LfricApps to allow for kernel API changes in Core Science components (Tranche 1)

applications/adjoint_tests/source/algorithm/core_dynamics/adjt_compute_vorticity_alg_mod.x90

@@ -19,6 +19,8 @@ module adjt_compute_vorticity_alg_mod
   use fs_continuity_mod,                   only : W1, W2
   use function_space_collection_mod,       only : function_space_collection
 
+  use config_mod, only: config_type
+
   implicit none
 
   public
@@ -31,15 +33,16 @@ module adjt_compute_vorticity_alg_mod
   !>          Determined by testing the equality of inner products <Mx, Mx> and <AMx, x>,
   !>          where M is the tangent linear and A is the adjoint.
   !> @param[in]  mesh         The model mesh
-  subroutine adjt_compute_vorticity_alg( mesh )
+  subroutine adjt_compute_vorticity_alg(config, mesh)
 
     use compute_vorticity_alg_mod,           only : compute_vorticity_alg
     use adj_compute_vorticity_alg_mod,       only : adj_compute_vorticity_alg
 
     implicit none
 
     ! Arguments
-    type(mesh_type), pointer, intent(in) :: mesh
+    type(config_type), intent(in) :: config
+    type(mesh_type),   intent(in) :: mesh
 
     ! Arguments for tl and adj calls
     type(field_type)            :: xi
@@ -101,7 +104,7 @@ module adjt_compute_vorticity_alg_mod
                  setval_x( u_input, u ) )
 
     ! Tangent linear
-    call compute_vorticity_alg( xi, u, weak_form_u )
+    call compute_vorticity_alg(config, xi, u, weak_form_u)
 
     ! < Mx, Mx >
     call invoke( x_innerproduct_x( xi_inner_prod, xi ), &
@@ -130,7 +133,7 @@ module adjt_compute_vorticity_alg_mod
     u_u_input_inner_prod = 0.0_r_def
 
     ! Adjoint
-    call adj_compute_vorticity_alg( xi, u, weak_form_u )
+    call adj_compute_vorticity_alg(config, xi, u, weak_form_u)
 
     ! < AMx, x >
     call invoke( x_innerproduct_y( xi_xi_input_inner_prod,         &

applications/adjoint_tests/source/algorithm/core_dynamics/atlt_derive_exner_from_eos_alg_mod.x90

@@ -6,6 +6,7 @@
 !> @brief Module containing adjoint test for atl_derive_exner_from_eos_alg
 module atlt_derive_exner_from_eos_alg_mod
 
+  use config_mod,                          only : config_type
   use field_mod,                           only : field_type
   use function_space_mod,                  only : function_space_type
   use constants_mod,                       only : r_def, i_def
@@ -33,16 +34,18 @@ module atlt_derive_exner_from_eos_alg_mod
   !> @details Passes if adjoint is transpose of tangent linear.
   !>          Determined by testing the equality of inner products <Mx, Mx> and <AMx, x>,
   !>          where M is the tangent linear and A is the adjoint.
+  !> @param[in]  config       Application configuration object
   !> @param[in]  mesh         The model mesh
-  subroutine atlt_derive_exner_from_eos_alg( mesh )
+  subroutine atlt_derive_exner_from_eos_alg(config, mesh)
 
     use tl_derive_exner_from_eos_alg_mod,    only : tl_derive_exner_from_eos
     use atl_derive_exner_from_eos_alg_mod,   only : atl_derive_exner_from_eos
 
     implicit none
 
     ! Arguments
-    type(mesh_type), pointer, intent(in) :: mesh
+    type(config_type), intent(in) :: config
+    type(mesh_type),   intent(in) :: mesh
 
     ! Arguments for tl and atl calls
     ! Form of state and rhs is [u,theta,rho,exner]
@@ -111,7 +114,7 @@ module atlt_derive_exner_from_eos_alg_mod
                  setval_random( ls_moist_dyn ) )
 
     ! Tangent linear
-    call tl_derive_exner_from_eos( state, moist_dyn, ls_state, ls_moist_dyn )
+    call tl_derive_exner_from_eos( config, state, moist_dyn, ls_state, ls_moist_dyn )
 
     ! < Mx, Mx >
     call invoke( x_innerproduct_x( state_inner_prod(igh_t), state(igh_t) ),           &
@@ -151,7 +154,7 @@ module atlt_derive_exner_from_eos_alg_mod
     moist_dyn_moist_dyn_input_inner_prod = 0.0_r_def
 
     ! Adjoint
-    call atl_derive_exner_from_eos( state, moist_dyn, ls_state, ls_moist_dyn )
+    call atl_derive_exner_from_eos( config, state, moist_dyn, ls_state, ls_moist_dyn )
 
     ! < AMx, x >
     call invoke( x_innerproduct_y( state_state_input_inner_prod(igh_t),           &

applications/adjoint_tests/source/algorithm/core_dynamics/atlt_rhs_alg_mod.x90

@@ -6,6 +6,7 @@
 !> @brief Module containing adjoint test for atl_rhs_alg
 module atlt_rhs_alg_mod
 
+  use config_mod,                          only : config_type
   use sci_assign_field_random_range_alg_mod, &
                                            only : assign_field_random_range
   use field_mod,                           only : field_type
@@ -41,18 +42,20 @@ module atlt_rhs_alg_mod
   !> @details Passes if adjoint is transpose of tangent linear.
   !>          Determined by testing the equality of inner products <Mx, Mx> and <AMx, x>,
   !>          where M is the tangent linear and A is the adjoint.
+  !> @param[in]  config       Application configuration object
   !> @param[in]  mesh         The model mesh
   !> @param[in]  model_clock  The model clock
-  subroutine atlt_rhs_alg( mesh, model_clock )
+  subroutine atlt_rhs_alg( config, mesh, model_clock )
 
-    use tl_rhs_alg_mod,                      only : tl_rhs_alg
-    use atl_rhs_alg_mod,                     only : atl_rhs_alg
+    use tl_rhs_alg_mod,  only: tl_rhs_alg
+    use atl_rhs_alg_mod, only: atl_rhs_alg
 
     implicit none
 
     ! Arguments
-    type(mesh_type), pointer, intent(in) :: mesh
-    type(model_clock_type),   intent(in) :: model_clock
+    type(config_type),      intent(in) :: config
+    type(mesh_type),        intent(in) :: mesh
+    type(model_clock_type), intent(in) :: model_clock
 
     ! Arguments for tl and atl calls
     ! Form of state and rhs is [u,theta,rho,exner]
@@ -206,8 +209,8 @@ module atlt_rhs_alg_mod
 
 
     ! Tangent linear
-    call tl_rhs_alg( rhs, alpha_dt, base_state, state, moist_dyn,        &
-                     ls_state, ls_moist_dyn, compute_eos,                &
+    call tl_rhs_alg( config, rhs, alpha_dt, base_state, state, moist_dyn, &
+                     ls_state, ls_moist_dyn, compute_eos,                 &
                      dlayer_rhs, model_clock )
 
     ! < Mx, Mx >
@@ -310,8 +313,8 @@ module atlt_rhs_alg_mod
     rhs_rhs_input_inner_prod(:) = 0.0_r_def
 
     ! Adjoint
-    call atl_rhs_alg( rhs, alpha_dt, base_state, state, moist_dyn,        &
-                      ls_state, ls_moist_dyn, compute_eos,                &
+    call atl_rhs_alg( config, rhs, alpha_dt, base_state, state, moist_dyn, &
+                      ls_state, ls_moist_dyn, compute_eos,                 &
                       dlayer_rhs, model_clock )
 
     ! < AMx, x >

applications/adjoint_tests/source/algorithm/lookup/transport/mol/adjt_w3h_adv_upd_lookup_alg_mod.x90

@@ -6,7 +6,9 @@
 !> @brief Module containing adjoint test for adj_w3h_adv_upd_lookup_lookup_kernel
 module adjt_w3h_adv_upd_lookup_alg_mod
 
+
   use adj_trans_lookup_cache_mod,      only : adj_trans_lookup_cache_type
+  use config_mod,                      only : config_type
   use integer_field_mod,               only : integer_field_type
   use r_tran_field_mod,                only : r_tran_field_type
   use fs_continuity_mod,               only : W3, W2
@@ -36,17 +38,19 @@ module adjt_w3h_adv_upd_lookup_alg_mod
   !> @details Passes if adjoint is transpose of tangent linear.
   !>          Determined by testing the equality of inner products <Mx, Mx> and <AMx, x>,
   !>          where M is the tangent linear and A is the adjoint.
+  !> @param[in]  config                  Application configuration object
   !> @param[in]  mesh                    The model mesh
   !> @param[in]  adj_lookup_table_cache  The lookup table cache
-  subroutine adjt_w3h_adv_upd_lookup_alg( mesh, adj_lookup_table_cache )
+  subroutine adjt_w3h_adv_upd_lookup_alg( config, mesh, adj_lookup_table_cache )
 
     use w3h_advective_update_kernel_mod,     only : w3h_advective_update_kernel_type
     use invoke_adj_w3h_adv_upd_lookup_mod,   only : invoke_adj_w3h_adv_upd_lookup_kernel_type
 
     implicit none
 
     ! Arguments
-    type(mesh_type),          pointer, intent(in) :: mesh
+    type(config_type),                 intent(in) :: config
+    type(mesh_type),                   intent(in) :: mesh
     type(adj_trans_lookup_cache_type), intent(in) :: adj_lookup_table_cache
 
     ! Internal arguments for kernels
@@ -84,8 +88,9 @@ module adjt_w3h_adv_upd_lookup_alg_mod
     real(kind=r_tran)            :: machine_tol
     real(kind=r_tran)            :: relative_diff
 
-    nullify(m3_inv, lookup_w3h_adv_upd, lookup_w3h_adv_upd_field, set_count_w3h_adv_upd_field, &
-            vector_space_w3_md_ptr, vector_space_w3_ptr, vector_space_w2_ptr)
+    nullify(m3_inv, lookup_w3h_adv_upd, lookup_w3h_adv_upd_field, &
+            set_count_w3h_adv_upd_field, vector_space_w3_md_ptr,  &
+            vector_space_w3_ptr, vector_space_w2_ptr)
 
     vector_space_w3_md_ptr => function_space_collection%get_fs(                &
         mesh, element_order_h, element_order_v, W3, ndata, ndata_first=.false. &
@@ -101,7 +106,7 @@ module adjt_w3h_adv_upd_lookup_alg_mod
     call wind%initialise( vector_space=vector_space_w2_ptr, name='wind' )
     call advective_increment_input%initialise( vector_space=vector_space_w3_ptr, name='advective_increment_input' )
     call tracer_input%initialise( vector_space=vector_space_w3_md_ptr, name='tracer_input' )
-    m3_inv => get_inverse_mass_matrix_fe( W3, mesh%get_id() )
+    m3_inv => get_inverse_mass_matrix_fe( config, mesh, W3 )
     advective_increment_inner_prod = 0.0_r_def
     tracer_inner_prod = 0.0_r_def
 

applications/adjoint_tests/source/algorithm/solver/adjt_mixed_operator_alg_mod.x90

@@ -148,7 +148,7 @@ contains
 
     call vector_mx%set_scalar(0.0_r_def)
     call vector_amx%set_scalar(0.0_r_def)
-    call mixed_op%apply( vector_x, vector_mx )
+    call mixed_op%apply( config, vector_x, vector_mx )
 
     ! --------------------------------------------------------------------------
     ! Compute <Mx,Mx>
@@ -186,7 +186,7 @@ contains
 
     adj_mixed_op = adj_mixed_operator_type()
 
-    call adj_mixed_op%apply( vector_mx, vector_amx )
+    call adj_mixed_op%apply( config, vector_mx, vector_amx )
 
     ! --------------------------------------------------------------------------
     ! Compute <AMx,x>

applications/adjoint_tests/source/algorithm/solver/adjt_mixed_schur_preconditioner_alg_mod.x90

@@ -163,11 +163,11 @@ contains
     call compute_si_operators( modeldb%config, ls_theta, ls_rho, ls_exner, &
                                model_clock, ls_moist_dyn )
 
-    call create_pressure_preconditioner( rhs, pressure_operator, pressure_preconditioner )
+    call create_pressure_preconditioner( modeldb%config, rhs, pressure_operator, pressure_preconditioner )
     call create_pressure_solver( pressure_operator, pressure_preconditioner, pressure_solver )
     call create_mixed_preconditioner( rhs, pressure_solver, mixed_preconditioner )
 
-    call create_adj_pressure_preconditioner( rhs, adj_lookup_table_cache, &
+    call create_adj_pressure_preconditioner( modeldb%config, rhs, adj_lookup_table_cache, &
                                              adj_pressure_operator, adj_pressure_preconditioner )
     call create_adj_pressure_solver( adj_pressure_operator, adj_pressure_preconditioner, adj_pressure_solver )
     call create_adj_mixed_preconditioner( rhs, adj_pressure_solver, adj_mixed_preconditioner )
@@ -183,7 +183,7 @@ contains
     ! Apply the preconditioner (i.e., forward code)
     ! --------------------------------------------------------------------------
 
-    call mixed_preconditioner%apply( vector_x, vector_mx )
+    call mixed_preconditioner%apply( modeldb%config, vector_x, vector_mx )
 
     ! --------------------------------------------------------------------------
     ! Compute <Mx,Mx>
@@ -219,7 +219,7 @@ contains
     ! Adjoint code
     ! --------------------------------------------------------------------------
 
-    call adj_mixed_preconditioner%apply( vector_mx, vector_amx )
+    call adj_mixed_preconditioner%apply( modeldb%config, vector_mx, vector_amx )
 
     ! --------------------------------------------------------------------------
     ! Compute <AMx,x>

applications/adjoint_tests/source/algorithm/solver/adjt_mixed_solver_alg_mod.x90

@@ -152,8 +152,8 @@ contains
     ! Input fields are r_def fields so preliminary work uses field_types
 
     ! Normalise theta & u residual
-    t_normalisation => get_normalisation( Wtheta, rhs(igh_p)%get_mesh_id() )
-    u_normalisation => get_normalisation( W2, rhs(igh_p)%get_mesh_id() )
+    t_normalisation => get_normalisation( modeldb%config, rhs(igh_p)%get_mesh(), Wtheta )
+    u_normalisation => get_normalisation( modeldb%config, rhs(igh_p)%get_mesh(), W2 )
     call invoke(inc_X_times_Y( rhs(igh_u), u_normalisation ))
 
     if (eliminate_variables == eliminate_variables_analytic) then
@@ -192,12 +192,12 @@ contains
     call compute_si_operators( modeldb%config, ls_theta, ls_rho, ls_exner, &
                                model_clock, ls_moist_dyn )
 
-    call create_pressure_preconditioner( rhs, pressure_operator, pressure_preconditioner )
+    call create_pressure_preconditioner( modeldb%config, rhs, pressure_operator, pressure_preconditioner )
     call create_pressure_solver( pressure_operator, pressure_preconditioner, pressure_solver )
     call create_mixed_preconditioner( rhs, pressure_solver, mixed_preconditioner )
     call create_mixed_solver( mixed_preconditioner, mixed_operator, mixed_solver )
 
-    call create_adj_pressure_preconditioner( rhs, adj_lookup_table_cache, &
+    call create_adj_pressure_preconditioner( modeldb%config, rhs, adj_lookup_table_cache, &
                                              adj_pressure_operator, adj_pressure_preconditioner )
     call create_adj_pressure_solver( adj_pressure_operator, adj_pressure_preconditioner, adj_pressure_solver )
     call create_adj_mixed_preconditioner( rhs, adj_pressure_solver, adj_mixed_preconditioner )
@@ -214,7 +214,7 @@ contains
     ! Apply the mixed_solver (i.e., forward code)
     ! --------------------------------------------------------------------------
 
-    call mixed_solver%apply( vector_mx, vector_x )
+    call mixed_solver%apply( modeldb%config, vector_mx, vector_x )
 
     ! --------------------------------------------------------------------------
     ! Compute <Mx,Mx>
@@ -251,7 +251,7 @@ contains
     ! Adjoint code
     ! --------------------------------------------------------------------------
 
-    call adj_mixed_solver%apply( vector_amx, vector_mx )
+    call adj_mixed_solver%apply( modeldb%config, vector_amx, vector_mx )
 
     ! --------------------------------------------------------------------------
     ! Compute <AMx,x>

applications/adjoint_tests/source/algorithm/solver/adjt_pressure_precon_alg_mod.x90

@@ -152,9 +152,9 @@ contains
     call compute_si_operators( modeldb%config, ls_theta, ls_rho, ls_exner, &
                                model_clock, ls_moist_dyn )
 
-    call create_pressure_preconditioner( rhs, pressure_operator, pressure_preconditioner )
+    call create_pressure_preconditioner( modeldb%config, rhs, pressure_operator, pressure_preconditioner )
 
-    call create_adj_pressure_preconditioner( rhs,                    &
+    call create_adj_pressure_preconditioner( modeldb%config, rhs,    &
                                              adj_lookup_table_cache, &
                                              adj_pressure_operator,  &
                                              adj_pressure_preconditioner )
@@ -175,7 +175,7 @@ contains
     ! Apply the preconditioner (i.e., forward code)
     ! --------------------------------------------------------------------------
 
-    call pressure_preconditioner%apply( vector_x, vector_mx )
+    call pressure_preconditioner%apply( modeldb%config, vector_x, vector_mx )
 
     ! --------------------------------------------------------------------------
     ! Compute <Mx,Mx>
@@ -199,7 +199,7 @@ contains
     ! Adjoint code
     ! --------------------------------------------------------------------------
 
-    call adj_pressure_preconditioner%apply( vector_mx, vector_amx )
+    call adj_pressure_preconditioner%apply(modeldb%config, vector_mx, vector_amx )
 
     ! --------------------------------------------------------------------------
     ! Compute <AMx,x>