add example for particle/depth_integrated_predator

.github/workflows/fabm.yml

@@ -125,7 +125,7 @@ jobs:
         env:
           FFLAGS: ${{ env.FFLAGS }} -fp-model precise -fp-model source
   ifx:
-    # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
+    # for available versions, see https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/intel_oneapi_compilers/package.py
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     strategy:
       matrix:
@@ -221,7 +221,7 @@ jobs:
       - name: Run all test cases with pyfabm
         run: python util/developers/run_all_testcases.py pyfabm --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
   aocc:
-    # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/aocc/package.py
+    # for available versions, see https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/aocc/package.py
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     strategy:
       matrix:

src/fabm_types.F90

@@ -520,7 +520,8 @@ module fabm_types
       procedure :: request_coupling_ll
       procedure :: request_coupling_il
       procedure :: request_coupling_lt
-      generic   :: request_coupling => request_coupling_ln, request_coupling_in, request_coupling_nn, &
+      procedure :: request_coupling_nn_   ! Workaround aocc/nvfortran bug that breaks generic when procedure is overridden
+      generic   :: request_coupling => request_coupling_ln, request_coupling_in, request_coupling_nn_, &
                                        request_coupling_ls, request_coupling_is, &
                                        request_coupling_ll, request_coupling_il, &
                                        request_coupling_lt
@@ -1446,6 +1447,12 @@ subroutine request_coupling_ln(self, link, target_name)
       task%target_name = target_name
    end subroutine request_coupling_ln
 
+   subroutine request_coupling_nn_(self, name, target_name)
+      class (type_base_model), intent(inout), target :: self
+      character(len=*),        intent(in)            :: name, target_name
+      call self%request_coupling_nn(name, target_name)
+   end subroutine
+
    recursive subroutine request_coupling_nn(self, name, target_name)
       class (type_base_model), intent(inout), target :: self
       character(len=*),        intent(in)            :: name, target_name

src/models/examples/particle/examples_particle_model_library.F90

@@ -25,7 +25,9 @@ subroutine create(self, name, model)
       class (type_base_model), pointer :: model
 
       select case (name)
-      case ('particle'); allocate(type_passive_particle::model)
+      case ('particle');    allocate(type_passive_particle_cs::model)
+      case ('particle_cs'); allocate(type_passive_particle_cs::model)
+      case ('particle_vs'); allocate(type_passive_particle_vs::model)
       !case ('migration'); allocate(type_templates_migration::model)
       case ('depth_integrated_predator'); allocate(type_depth_integrated_predator::model)
       case default

src/models/examples/particle/passive_particle.F90

@@ -2,26 +2,64 @@
 
 module examples_particle_passive_particle
 
+   ! A passive particle
+
+   ! Two types are provided:
+   ! * type_passive_particle_cs has constant C:N:P stoichoiometry.
+   !   Its concentration is expressed in carbon units.
+   !   Elemental ratios N:C and  P:C are configurable and default to Redfield.
+   ! * type_passive_particle_vs has variable C:N:P stoichoiometry.
+
    use fabm_particle
    use fabm_types
 
    implicit none
 
    private
 
-   type, extends(type_particle_model), public :: type_passive_particle
+   type, extends(type_particle_model), public :: type_passive_particle_cs
+      type (type_state_variable_id) :: id_c
+   contains
+      procedure :: initialize => initialize_cs
+   end type
+
+   type, extends(type_particle_model), public :: type_passive_particle_vs
       type (type_state_variable_id) :: id_c
+      type (type_state_variable_id) :: id_n
+      type (type_state_variable_id) :: id_p
    contains
-      procedure :: initialize
+      procedure :: initialize => initialize_vs
    end type
 
 contains
 
-   subroutine initialize(self, configunit)
-      class (type_passive_particle), intent(inout), target :: self
-      integer,                       intent(in)            :: configunit
+   subroutine initialize_cs(self, configunit)
+      class (type_passive_particle_cs), intent(inout), target :: self
+      integer,                          intent(in)            :: configunit
+
+      real(rk) :: NC, PC
+
+      call self%register_state_variable(self%id_c, 'c', 'mmol C m-3', 'concentration')
+
+      call self%get_parameter(NC, 'NC', 'mol N mol C-1', 'nitrogen : carbon ratio', default=16.0_rk/ 106.0_rk)
+      call self%get_parameter(PC, 'PC', 'mol P mol C-1', 'phosphorus : carbon ratio', default=1.0_rk/ 106.0_rk)
+
+      call self%add_to_aggregate_variable(standard_variables%total_carbon, self%id_c)
+      call self%add_to_aggregate_variable(standard_variables%total_nitrogen, self%id_c, scale_factor=NC)
+      call self%add_to_aggregate_variable(standard_variables%total_phosphorus, self%id_c, scale_factor=PC)
+   end subroutine
+
+   subroutine initialize_vs(self, configunit)
+      class (type_passive_particle_vs), intent(inout), target :: self
+      integer,                          intent(in)            :: configunit
+
+      call self%register_state_variable(self%id_c, 'c', 'mmol C m-3', 'carbon')
+      call self%register_state_variable(self%id_n, 'n', 'mmol N m-3', 'nitrogen')
+      call self%register_state_variable(self%id_p, 'p', 'mmol P m-3', 'phosphorus')
 
-      call self%register_state_variable(self%id_c, 'c', 'mmol m-3', 'concentration')
+      call self%add_to_aggregate_variable(standard_variables%total_carbon, self%id_c)
+      call self%add_to_aggregate_variable(standard_variables%total_nitrogen, self%id_n)
+      call self%add_to_aggregate_variable(standard_variables%total_phosphorus, self%id_p)
    end subroutine
 
 end module

testcases/fabm-examples-particle.yaml

@@ -0,0 +1,17 @@
+instances:
+   plankton:
+      model: examples/particle/particle_cs
+      initialization:
+         c: 1.0                                             # concentration [mmol C m-3; default=0.0]
+   detritus:
+      model: examples/particle/particle_vs
+   predator:
+      model: examples/particle/depth_integrated_predator
+      parameters:
+         clearance_rate: 0.1                                # clearance rate [m3 d-1 mmol-1]
+         mortality: 0.02                                    # mortality [d-1]
+      initialization:
+         c: 0.001                                           # density [mmol C m-2; default=0.0]
+      coupling:
+         prey: plankton
+         waste: detritus