python_fabm.F90 22.2 KB
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#include "fabm_driver.h"
!-----------------------------------------------------------------------
!BOP
!
! !MODULE: Python interface to the Framework for Aquatic Biogeochemical Models (FABM)
!
! !INTERFACE:
   module fabm_python
!
! !DESCRIPTION:
! TODO
!
! !USES:
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   use iso_c_binding, only: c_double, c_int, c_char, C_NULL_CHAR, c_f_pointer, c_loc, c_ptr
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   !DIR$ ATTRIBUTES DLLEXPORT :: STATE_VARIABLE,DIAGNOSTIC_VARIABLE,CONSERVED_QUANTITY

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   use fabm
   use fabm_config
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   use fabm_types, only:rk,attribute_length,type_model_list_node,type_base_model, &
                        factory,type_link,type_link_list,type_internal_variable
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   use fabm_driver, only: type_base_driver, driver
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   use fabm_properties
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   use fabm_python_helper
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   use fabm_c_helper
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   implicit none
!
! !PUBLIC MEMBER FUNCTIONS:
   public

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   integer,parameter :: BULK_STATE_VARIABLE            = 1
   integer,parameter :: SURFACE_STATE_VARIABLE         = 2
   integer,parameter :: BOTTOM_STATE_VARIABLE          = 3
   integer,parameter :: BULK_DIAGNOSTIC_VARIABLE       = 4
   integer,parameter :: HORIZONTAL_DIAGNOSTIC_VARIABLE = 5
   integer,parameter :: CONSERVED_QUANTITY             = 6

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   class (type_model),private,pointer,save :: model => null()
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   real(8),dimension(:),pointer :: state
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   character(len=1024),dimension(:),allocatable :: environment_names,environment_units
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   type (type_link_list),save :: coupling_link_list
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   type (type_property_dictionary),save,private :: forced_parameters,forced_couplings
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   type,extends(type_base_driver) :: type_python_driver
   contains
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      procedure :: fatal_error => python_driver_fatal_error
      procedure :: log_message => python_driver_log_message
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   end type
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!EOP
!-----------------------------------------------------------------------

   contains

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Initialise the model
!
! !INTERFACE:
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   subroutine initialize(path) bind(c)
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!DIR$ ATTRIBUTES DLLEXPORT :: initialize
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      character(kind=c_char),target,intent(in) :: path(*)
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!
! !DESCRIPTION:
!
! !REVISION HISTORY:
!  Original author(s): Jorn Bruggeman
!
!EOP
!
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      character(len=attribute_length),pointer :: ppath
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      class (type_property),          pointer :: property
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!-----------------------------------------------------------------------
!BOC
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      call c_f_pointer(c_loc(path), ppath)

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      if (associated(model)) call finalize()
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      if (.not.associated(driver)) allocate(type_python_driver::driver)

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      ! Build FABM model tree (configuration will be read from fabm.yaml).
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      allocate(model)
      call fabm_create_model_from_yaml_file(model,path=ppath(:index(ppath,C_NULL_CHAR)-1),parameters=forced_parameters)

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      ! Get a list of all parameters that had an explicit value specified.
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      property => model%root%parameters%first
      do while (associated(property))
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         if (.not.model%root%parameters%missing%contains(property%name)) &
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            call forced_parameters%set_property(property)
         property => property%next
      end do
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      ! Get a list of all active couplings.
      property => model%root%couplings%first
      do while (associated(property))
         if (.not.model%root%couplings%missing%contains(property%name)) &
            call forced_couplings%set_property(property)
         property => property%next
      end do

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      ! Send information on spatial domain to FABM (this also allocates memory for diagnostics)
      call fabm_set_domain(model)

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      ! Retrieve arrays to hold values for environmental variables and corresponding metadata.
      call get_environment_metadata(model,environment_names,environment_units)

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      call get_couplings(model,coupling_link_list)
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   end subroutine initialize
!EOC

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   subroutine reinitialize()
      type (type_model),           pointer :: newmodel
      type (type_model_list_node), pointer :: node
      class (type_base_model),     pointer :: childmodel
      class (type_property),       pointer :: property,next

      allocate(newmodel)

      ! Transfer forced parameters to root of the model.
      call newmodel%root%parameters%update(forced_parameters)
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      call newmodel%root%couplings%update(forced_couplings)
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      ! Re-create original models
      node => model%root%children%first
      do while (associated(node))
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         if (node%model%user_created) then
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            call factory%create(node%model%type_name,childmodel)
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            childmodel%user_created = .true.
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            call newmodel%root%add_child(childmodel,node%model%name,node%model%long_name,configunit=-1)
         end if
         node => node%next
      end do

      ! Clean up old model
      call finalize()
      model => newmodel

      ! Initialize new model
      call fabm_initialize(model)

      ! Removed unused forced parameters from root model.
      property => model%root%parameters%first
      do while (associated(property))
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         if (.not. model%root%parameters%retrieved%contains(property%name)) then
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            next => property%next
            call model%root%parameters%delete(property%name)
            property => next
         else
            property => property%next
         end if
      end do

      ! Send information on spatial domain to FABM (this also allocates memory for diagnostics)
      call fabm_set_domain(model)

      ! Retrieve arrays to hold values for environmental variables and corresponding metadata.
      call get_environment_metadata(model,environment_names,environment_units)
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      call get_couplings(model,coupling_link_list)
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   end subroutine reinitialize
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   subroutine check_ready()
      !DIR$ ATTRIBUTES DLLEXPORT :: check_ready
      call fabm_check_ready(model)
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   end subroutine check_ready
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   integer(c_int) function model_count() bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: model_count

      type (type_model_list_node), pointer :: node

      model_count = 0
      node => model%root%children%first
      do while (associated(node))
         model_count = model_count + 1
         node => node%next
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      end do
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   end function model_count
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   subroutine get_counts(nstate_bulk,nstate_surface,nstate_bottom,ndiagnostic_bulk,ndiagnostic_horizontal,nconserved, &
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      ndependencies,nparameters,ncouplings) bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_counts
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      integer(c_int),intent(out) :: nstate_bulk,nstate_surface,nstate_bottom
      integer(c_int),intent(out) :: ndiagnostic_bulk,ndiagnostic_horizontal
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      integer(c_int),intent(out) :: nconserved,ndependencies,nparameters,ncouplings
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      nstate_bulk = size(model%state_variables)
      nstate_surface = size(model%surface_state_variables)
      nstate_bottom = size(model%bottom_state_variables)
      ndiagnostic_bulk = size(model%diagnostic_variables)
      ndiagnostic_horizontal = size(model%horizontal_diagnostic_variables)
      nconserved = size(model%conserved_quantities)
      ndependencies = size(environment_names)
      nparameters = model%root%parameters%size()
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      ncouplings = coupling_link_list%count()
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   end subroutine get_counts
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   subroutine get_variable_metadata(category,index,length,name,units,long_name,path) bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_variable_metadata
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      integer(c_int),        intent(in), value             :: category,index,length
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      character(kind=c_char),intent(out),dimension(length) :: name,units,long_name,path
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      class (type_external_variable),pointer :: variable

      ! Get a pointer to the target variable
      select case (category)
      case (BULK_STATE_VARIABLE)
         variable => model%state_variables(index)
      case (SURFACE_STATE_VARIABLE)
         variable => model%surface_state_variables(index)
      case (BOTTOM_STATE_VARIABLE)
         variable => model%bottom_state_variables(index)
      case (BULK_DIAGNOSTIC_VARIABLE)
         variable => model%diagnostic_variables(index)
      case (HORIZONTAL_DIAGNOSTIC_VARIABLE)
         variable => model%horizontal_diagnostic_variables(index)
      case (CONSERVED_QUANTITY)
         variable => model%conserved_quantities(index)
      end select
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      call copy_to_c_string(variable%name,           name)
      call copy_to_c_string(variable%units,          units)
      call copy_to_c_string(variable%local_long_name,long_name)
      call copy_to_c_string(variable%path,           path)
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   end subroutine get_variable_metadata
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   function get_variable(category,index) bind(c) result(pvariable)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_variable
      integer(c_int),intent(in), value :: category,index
      type (c_ptr)                     :: pvariable
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      type (type_internal_variable),pointer :: variable

      ! Get a pointer to the target variable
      select case (category)
      case (BULK_STATE_VARIABLE)
         variable => model%state_variables(index)%target
      case (SURFACE_STATE_VARIABLE)
         variable => model%surface_state_variables(index)%target
      case (BOTTOM_STATE_VARIABLE)
         variable => model%bottom_state_variables(index)%target
      case (BULK_DIAGNOSTIC_VARIABLE)
         variable => model%diagnostic_variables(index)%target
      case (HORIZONTAL_DIAGNOSTIC_VARIABLE)
         variable => model%horizontal_diagnostic_variables(index)%target
      case (CONSERVED_QUANTITY)
         variable => model%conserved_quantities(index)%target
      end select
      pvariable = c_loc(variable)
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   end function get_variable
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   subroutine get_parameter_metadata(index,length,name,units,long_name,typecode,has_default) bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_parameter_metadata
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      integer(c_int),        intent(in), value             :: index,length
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      character(kind=c_char),intent(out),dimension(length) :: name,units,long_name
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      integer(c_int),        intent(out)                   :: typecode,has_default
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      integer                       :: i
      class (type_property),pointer :: property

      i = 1
      property => model%root%parameters%first
      do while (associated(property))
         if (index==i) exit
         property => property%next
         i = i + 1
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      end do

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      call copy_to_c_string(property%name,     name)
      call copy_to_c_string(property%units,    units)
      call copy_to_c_string(property%long_name,long_name)
      typecode = property%typecode()
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      has_default = logical2int(property%has_default)
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   end subroutine get_parameter_metadata
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   subroutine get_dependency_metadata(index,length,name,units) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_dependency_metadata
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      integer(c_int),        intent(in), value             :: index,length
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      character(kind=c_char),intent(out),dimension(length) :: name,units
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      call copy_to_c_string(environment_names(index),name)
      call copy_to_c_string(environment_units(index),units)
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   end subroutine get_dependency_metadata
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   subroutine get_coupling(index,slave,master) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_coupling
      integer(c_int),        intent(in), value :: index
      type (c_ptr),          intent(out)       :: slave,master

      type (type_link),pointer :: link_slave
      integer                  :: i
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      link_slave => coupling_link_list%first
      do i=2,index
         link_slave => link_slave%next
      end do
      slave = c_loc(link_slave%original)
      master = c_loc(link_slave%target)
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   end subroutine get_coupling
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   function variable_get_suitable_masters(pvariable) result(plist) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: variable_get_suitable_masters
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      type (c_ptr), intent(in), value :: pvariable
      type (c_ptr)                    :: plist
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      type (type_internal_variable),pointer :: variable
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      type (type_link_list),        pointer :: list
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      call c_f_pointer(pvariable, variable)
      list => get_suitable_masters(model,variable)
      plist = c_loc(list)
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   end function variable_get_suitable_masters
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   subroutine get_model_metadata(name,length,long_name,user_created) bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_model_metadata
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      character(kind=c_char),intent(in), target :: name(*)
      integer(c_int),        intent(in), value  :: length
      character(kind=c_char),intent(out)        :: long_name(length)
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      integer(c_int),        intent(out)        :: user_created
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      character(len=attribute_length),pointer   :: pname
      class (type_base_model),        pointer   :: found_model
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      call c_f_pointer(c_loc(name), pname)
      found_model => model%root%find_model(pname(:index(pname,C_NULL_CHAR)-1))
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      if (.not.associated(found_model)) call driver%fatal_error('get_model_metadata', &
         'model "'//pname(:index(pname,C_NULL_CHAR)-1)//'" not found.')
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      call copy_to_c_string(found_model%long_name,long_name)
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      user_created = logical2int(found_model%user_created)
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   end subroutine get_model_metadata
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   subroutine link_dependency_data(index,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: link_dependency_data
      integer(c_int),intent(in),value  :: index
      real(c_double),intent(in),target :: value

      call fabm_link_bulk_data(model,environment_names(index),value)
      call fabm_link_horizontal_data(model,environment_names(index),value)
      call fabm_link_scalar_data(model,environment_names(index),value)
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   end subroutine link_dependency_data
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   subroutine link_bulk_state_data(index,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: link_bulk_state_data
      integer(c_int),intent(in),   value  :: index
      real(c_double),intent(inout),target :: value
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      value = model%state_variables(index)%initial_value
      call fabm_link_bulk_state_data(model,index,value)
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   end subroutine link_bulk_state_data
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   subroutine link_surface_state_data(index,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: link_surface_state_data
      integer(c_int),intent(in),   value  :: index
      real(c_double),intent(inout),target :: value
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      value = model%surface_state_variables(index)%initial_value
      call fabm_link_surface_state_data(model,index,value)
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   end subroutine link_surface_state_data
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   subroutine link_bottom_state_data(index,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: link_bottom_state_data
      integer(c_int),intent(in),   value  :: index
      real(c_double),intent(inout),target :: value

      value = model%bottom_state_variables(index)%initial_value
      call fabm_link_bottom_state_data(model,index,value)
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   end subroutine link_bottom_state_data
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   subroutine get_rates(pelagic_rates_) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_rates
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      real(c_double),target,intent(in) :: pelagic_rates_(*)
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      real(c_double),pointer :: pelagic_rates(:)
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      real(rk)               :: ext
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      call fabm_get_light_extinction(model,ext)
      call fabm_get_light(model)
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      call c_f_pointer(c_loc(pelagic_rates_),pelagic_rates, &
        (/size(model%state_variables)+size(model%surface_state_variables)+size(model%bottom_state_variables)/))
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      pelagic_rates = 0.0_rk
      call fabm_do(model,pelagic_rates)

      ! Compute rate of change in conserved quantities
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      !call fabm_state_to_conserved_quantities(model,pelagic_rates,conserved_rates)
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      ! Normalize rate of change in conserved quantities to sum of absolute rates of change.
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      !call fabm_state_to_conserved_quantities(model,abs(pelagic_rates),abs_conserved_rates)
      !where (abs_conserved_rates>0.0_rk) conserved_rates = conserved_rates/abs_conserved_rates
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   end subroutine get_rates
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   subroutine get_bulk_diagnostic_data(index,ptr) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_bulk_diagnostic_data
      integer(c_int),intent(in),value :: index
      type(c_ptr),   intent(out)      :: ptr
      ptr = c_loc(fabm_get_bulk_diagnostic_data(model,index))
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   end subroutine get_bulk_diagnostic_data
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   subroutine get_horizontal_diagnostic_data(index,ptr) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_horizontal_diagnostic_data
      integer(c_int),intent(in),value :: index
      type(c_ptr),   intent(out)      :: ptr
      ptr = c_loc(fabm_get_horizontal_diagnostic_data(model,index))
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   end subroutine get_horizontal_diagnostic_data
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   subroutine finalize() bind(c)
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      call fabm_finalize(model)
      if (allocated(environment_names)) deallocate(environment_names)
      if (allocated(environment_units)) deallocate(environment_units)
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   end subroutine finalize
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   subroutine reset_parameter(index) bind(c)
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      !DIR$ ATTRIBUTES DLLEXPORT :: reset_parameter
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      integer(c_int),value,intent(in) :: index
      class (type_property),pointer   :: property
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      property => model%root%parameters%get_property(index)
      if (.not.associated(property)) return
      call forced_parameters%delete(property%name)
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      ! Re-initialize the model using updated parameter values
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      call reinitialize()
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   end subroutine reset_parameter
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   subroutine set_real_parameter(name,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: set_real_parameter
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      character(kind=c_char),target,intent(in) :: name(*)
      real(c_double),value,         intent(in) :: value
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      character(len=attribute_length),pointer :: pname

      call c_f_pointer(c_loc(name), pname)
      call forced_parameters%set_real(pname(:index(pname,C_NULL_CHAR)-1),value)
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      ! Re-initialize the model using updated parameter values
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      call reinitialize()
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   end subroutine set_real_parameter
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   function get_real_parameter(index,default) bind(c) result(value)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_real_parameter
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      integer(c_int),value,intent(in) :: index,default
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      real(c_double)                  :: value
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      class (type_property),pointer   :: property

      property => model%root%parameters%get_property(index)
      select type (property)
      class is (type_real_property)
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         if (int2logical(default)) then
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            value = property%default
         else
            value = property%value
         end if
      class default
         call driver%fatal_error('get_real_parameter','not a real variable')
      end select
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   end function get_real_parameter
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   subroutine set_integer_parameter(name,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: set_integer_parameter
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      character(kind=c_char),target,intent(in) :: name(*)
      integer(c_int),value,         intent(in) :: value
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      character(len=attribute_length),pointer :: pname

      call c_f_pointer(c_loc(name), pname)
      call forced_parameters%set_integer(pname(:index(pname,C_NULL_CHAR)-1),value)
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      ! Re-initialize the model using updated parameter values
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      call reinitialize()
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   end subroutine set_integer_parameter
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   function get_integer_parameter(index,default) bind(c) result(value)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_integer_parameter
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      integer(c_int),value,intent(in) :: index,default
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      integer(c_int)                  :: value
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      class (type_property),pointer   :: property

      property => model%root%parameters%get_property(index)
      select type (property)
      class is (type_integer_property)
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         if (int2logical(default)) then
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            value = property%default
         else
            value = property%value
         end if
      class default
         call driver%fatal_error('get_integer_parameter','not an integer variable')
      end select
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   end function get_integer_parameter
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   subroutine set_logical_parameter(name,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: set_logical_parameter
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      character(kind=c_char),target,    intent(in) :: name(*)
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      integer(c_int),value,intent(in) :: value

      character(len=attribute_length),pointer :: pname

      call c_f_pointer(c_loc(name), pname)
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      call forced_parameters%set_logical(pname(:index(pname,C_NULL_CHAR)-1),int2logical(value))
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      ! Re-initialize the model using updated parameter values
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      call reinitialize()
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   end subroutine set_logical_parameter
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   function get_logical_parameter(index,default) bind(c) result(value)
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      !DIR$ ATTRIBUTES DLLEXPORT :: get_logical_parameter
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      integer(c_int),value,intent(in) :: index,default
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      integer(c_int)                  :: value
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      class (type_property),pointer   :: property

      property => model%root%parameters%get_property(index)
      select type (property)
      class is (type_logical_property)
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         if (int2logical(default)) then
            value = logical2int(property%default)
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         else
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            value = logical2int(property%value)
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         end if
      class default
         call driver%fatal_error('get_logical_parameter','not a logical variable')
      end select
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   end function get_logical_parameter
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   subroutine set_string_parameter(name,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: set_string_parameter
      character(kind=c_char),target,intent(in) :: name(*),value(*)

      character(len=attribute_length),pointer :: pname,pvalue
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      call c_f_pointer(c_loc(name),  pname)
      call c_f_pointer(c_loc(value), pvalue)
      call forced_parameters%set_string(pname(:index(pname,C_NULL_CHAR)-1),pvalue(:index(pname,C_NULL_CHAR)-1))
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      ! Re-initialize the model using updated parameter values
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      call reinitialize()
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   end subroutine set_string_parameter
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   subroutine get_string_parameter(index,default,length,value) bind(c)
      !DIR$ ATTRIBUTES DLLEXPORT :: get_string_parameter
      integer(c_int),value,intent(in) :: index,default,length
      character(kind=c_char)          :: value(length)

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      class (type_property),pointer   :: property

      property => model%root%parameters%get_property(index)
      select type (property)
      class is (type_string_property)
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         if (int2logical(default)) then
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            call copy_to_c_string(property%default, value)
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         else
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            call copy_to_c_string(property%value, value)
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         end if
      class default
         call driver%fatal_error('get_string_parameter','not a string variable')
      end select
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   end subroutine get_string_parameter
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   subroutine python_driver_fatal_error(self,location,message)
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      class (type_python_driver),intent(inout) :: self
      character(len=*),          intent(in)    :: location,message

      write (*,*) trim(location)//': '//trim(message)
      stop 1
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   end subroutine python_driver_fatal_error
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   subroutine python_driver_log_message(self,message)
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      class (type_python_driver),intent(inout) :: self
      character(len=*),          intent(in)    :: message

      !write (*,*) trim(message)
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   end subroutine python_driver_log_message
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   end module fabm_python

!-----------------------------------------------------------------------
! Copyright by the GOTM-team under the GNU Public License - www.gnu.org
!-----------------------------------------------------------------------