add part_of_state flag

CMakeLists.txt

@@ -5,7 +5,7 @@
 cmake_minimum_required(VERSION 3.13)
 
 project(fabm
-  VERSION 2.1.6
+  VERSION 3.0.0
   DESCRIPTION "Framework for Aquatic Biogeochemical Models"
   HOMEPAGE_URL https://fabm.net
   LANGUAGES Fortran

include/fabm.h

@@ -107,9 +107,9 @@
 #else
 !  Interior procedures operate in 0D
 !  Interior slices may be 0D scalars or 1D arrays [the latter if the model has a vertical dimension]
-#  define _LOOP_BEGIN_EX_(cache)
-#  define _CONCURRENT_LOOP_BEGIN_EX_(cache)
-#  define _LOOP_END_
+#  define _LOOP_BEGIN_EX_(cache) if (cache%n /= 0) then
+#  define _CONCURRENT_LOOP_BEGIN_EX_(cache) if (cache%n /= 0) then
+#  define _LOOP_END_ end if
 #  ifdef _INTERIOR_IS_VECTORIZED_
 !    Interior slices are 1D arrays - we will operate on their first element (_I_=1)
 #    define _DECLARE_INTERIOR_INDICES_ integer,parameter :: _I_=1
@@ -134,9 +134,9 @@
 #else
 !  Horizontal procedures operate in 0D
 !  Horizontal slices MUST be scalars; interior slices can be scalars or 1D arrays
-#  define _HORIZONTAL_LOOP_BEGIN_EX_(cache)
-#  define _CONCURRENT_HORIZONTAL_LOOP_BEGIN_EX_(cache)
-#  define _HORIZONTAL_LOOP_END_
+#  define _HORIZONTAL_LOOP_BEGIN_EX_(cache) if (cache%n /= 0) then
+#  define _CONCURRENT_HORIZONTAL_LOOP_BEGIN_EX_(cache) if (cache%n /= 0) then
+#  define _HORIZONTAL_LOOP_END_ end if
 #  ifdef _INTERIOR_IS_VECTORIZED_
 !    Interior slices are 1D arrays - we will operate on their first element (_I_=1)
 #    define _DECLARE_HORIZONTAL_INDICES_ integer,parameter :: _I_=1
@@ -186,11 +186,11 @@
 !  Vertical procedures operate in 0D
 !  Interior slices may scalars or 1D arrays [the latter if the model is vectorized over a horizontal dimension]
 !  Applies to all models without depth dimension; for instance, 0D box or model with i,j or i
-#  define _CONCURRENT_VERTICAL_LOOP_BEGIN_EX_(cache)
-#  define _VERTICAL_LOOP_END_
+#  define _CONCURRENT_VERTICAL_LOOP_BEGIN_EX_(cache) if (cache%n /= 0) then
+#  define _VERTICAL_LOOP_END_ end if
 #  define _VERTICAL_LOOP_EXIT_
-#  define _DOWNWARD_LOOP_BEGIN_
-#  define _UPWARD_LOOP_BEGIN_
+#  define _DOWNWARD_LOOP_BEGIN_ if (cache%n /= 0) then
+#  define _UPWARD_LOOP_BEGIN_ if (cache%n /= 0) then
 #  define _MOVE_TO_SURFACE_
 #  define _MOVE_TO_BOTTOM_
 #  ifdef _INTERIOR_IS_VECTORIZED_

include/fabm_private.h

@@ -269,12 +269,18 @@
 #  define _IS_UNMASKED_(maskvalue) .true.
 #endif
 
-#if defined(_FABM_CONTIGUOUS_)&&!defined(_FABM_NO_CONTIGUOUS_)
+#ifndef _FABM_NO_CONTIGUOUS_
 #  define _CONTIGUOUS_ ,contiguous
 #else
 #  define _CONTIGUOUS_
 #endif
 
+#ifdef _FABM_CONTIGUOUS_
+#  define _HOST_CONTIGUOUS_ _CONTIGUOUS_
+#else
+#  define _HOST_CONTIGUOUS_
+#endif
+
 #ifndef _BEGIN_OUTER_HORIZONTAL_LOOP_
 #  define _BEGIN_OUTER_HORIZONTAL_LOOP_
 #  define _END_OUTER_HORIZONTAL_LOOP_
@@ -326,7 +332,8 @@
 #if _HORIZONTAL_DIMENSION_COUNT_>0
 #  define _INDEX_HORIZONTAL_LOCATION_ (_HORIZONTAL_LOCATION_)
 #  define _DIMENSION_GLOBAL_HORIZONTAL_ ,dimension(_HORIZONTAL_LOCATION_DIMENSIONS_)
-#  define _ATTRIBUTES_GLOBAL_HORIZONTAL_ _DIMENSION_GLOBAL_HORIZONTAL_ _CONTIGUOUS_
+#  define _ATTRIBUTES_GLOBAL_HORIZONTAL_ _DIMENSION_GLOBAL_HORIZONTAL_ _HOST_CONTIGUOUS_
+#  define _ATTRIBUTES_GLOBAL_HORIZONTAL_CONTIGUOUS_ _DIMENSION_GLOBAL_HORIZONTAL_ _CONTIGUOUS_
 #  define _ARG_HORIZONTAL_LOCATION_ _HORIZONTAL_LOCATION_
 #  define _POSTARG_HORIZONTAL_LOCATION_ ,_ARG_HORIZONTAL_LOCATION_
 #  define _POSTARG_HORIZONTAL_LOCATION_RANGE_ ,_HORIZONTAL_LOCATION_RANGE_
@@ -339,6 +346,7 @@
 #  define _INDEX_HORIZONTAL_LOCATION_
 #  define _DIMENSION_GLOBAL_HORIZONTAL_
 #  define _ATTRIBUTES_GLOBAL_HORIZONTAL_
+#  define _ATTRIBUTES_GLOBAL_HORIZONTAL_CONTIGUOUS_
 #  define _ARG_HORIZONTAL_LOCATION_
 #  define _POSTARG_HORIZONTAL_LOCATION_
 #  define _POSTARG_HORIZONTAL_LOCATION_RANGE_
@@ -356,7 +364,8 @@
 #if _FABM_DIMENSION_COUNT_>0
 #  define _INDEX_LOCATION_ (_LOCATION_)
 #  define _DIMENSION_GLOBAL_ ,dimension(_LOCATION_DIMENSIONS_)
-#  define _ATTRIBUTES_GLOBAL_ _DIMENSION_GLOBAL_ _CONTIGUOUS_
+#  define _ATTRIBUTES_GLOBAL_ _DIMENSION_GLOBAL_ _HOST_CONTIGUOUS_
+#  define _ATTRIBUTES_GLOBAL_CONTIGUOUS_ _DIMENSION_GLOBAL_ _CONTIGUOUS_
 #  define _POSTARG_LOCATION_ ,_LOCATION_
 #  define _POSTARG_LOCATION_RANGE_ ,_LOCATION_RANGE_
 #  define _PREARG_LOCATION_ _LOCATION_,
@@ -368,6 +377,7 @@
 #  define _INDEX_LOCATION_
 #  define _DIMENSION_GLOBAL_
 #  define _ATTRIBUTES_GLOBAL_
+#  define _ATTRIBUTES_GLOBAL_CONTIGUOUS_
 #  define _POSTARG_LOCATION_
 #  define _POSTARG_LOCATION_RANGE_
 #  define _PREARG_LOCATION_

include/fabm_version.h

@@ -1 +1 @@
-#define _FABM_API_VERSION_ 2
+#define _FABM_API_VERSION_ 3

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyfabm"
-version = "2.1.6"
+version = "3.0.0"
 authors = [
   {name = "Jorn Bruggeman", email = "[email protected]"},
   {name = "Karsten Bolding", email = "[email protected]"}

src/CMakeLists.txt

@@ -115,6 +115,7 @@ add_library(fabm_base OBJECT
             ${CMAKE_CURRENT_LIST_DIR}/fabm_standard_variables.F90
             ${CMAKE_CURRENT_LIST_DIR}/fabm_properties.F90
             ${CMAKE_CURRENT_LIST_DIR}/fabm_types.F90
+            ${CMAKE_CURRENT_LIST_DIR}/fabm_global_types.F90
             ${CMAKE_CURRENT_LIST_DIR}/fabm_particle.F90
             ${CMAKE_CURRENT_LIST_DIR}/fabm_expressions.F90
             ${CMAKE_CURRENT_LIST_DIR}/builtin/tracer.F90

src/builtin/constant.F90

@@ -45,7 +45,6 @@ subroutine interior_constant_initialize(self, configunit)
       real(rk)                               :: value
       type (type_interior_standard_variable) :: standard_variable
 
-      call self%register_implemented_routines()
       call self%get_parameter(standard_variable%name, 'standard_name', '', 'standard name', default='')
       call self%get_parameter(value, 'value', '', 'value')
       if (standard_variable%name /= '') then
@@ -66,7 +65,6 @@ subroutine horizontal_constant_initialize(self, configunit)
       real(rk)                                 :: value
       type (type_horizontal_standard_variable) :: standard_variable
 
-      call self%register_implemented_routines()
       call self%get_parameter(standard_variable%name, 'standard_name', '', 'standard name', default='')
       call self%get_parameter(value, 'value', '', 'value')
       if (standard_variable%name /= '') then
@@ -87,7 +85,6 @@ subroutine surface_constant_initialize(self, configunit)
       real(rk)                              :: value
       type (type_surface_standard_variable) :: standard_variable
 
-      call self%register_implemented_routines()
       call self%get_parameter(standard_variable%name, 'standard_name', '', 'standard name', default='')
       call self%get_parameter(value, 'value', '', 'value')
       if (standard_variable%name /= '') then
@@ -108,7 +105,6 @@ subroutine bottom_constant_initialize(self, configunit)
       real(rk)                             :: value
       type (type_bottom_standard_variable) :: standard_variable
 
-      call self%register_implemented_routines()
       call self%get_parameter(standard_variable%name, 'standard_name', '', 'standard name', default='')
       call self%get_parameter(value, 'value', '', 'value')
       if (standard_variable%name /= '') then
@@ -129,7 +125,6 @@ subroutine global_constant_initialize(self, configunit)
       real(rk)                             :: value
       type (type_global_standard_variable) :: standard_variable
 
-      call self%register_implemented_routines()
       call self%get_parameter(standard_variable%name, 'standard_name', '', 'standard name', default='')
       call self%get_parameter(value, 'value', '', 'value')
       if (standard_variable%name /= '') then

src/builtin/depth_integral.F90

@@ -34,7 +34,6 @@ subroutine depth_integral_initialize(self, configunit)
       class (type_depth_integral), intent(inout), target :: self
       integer,                     intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do_column/))
       call self%get_parameter(self%average, 'average', '', 'compute average by dividing integral by total height', default=self%average)
       call self%register_dependency(self%id_input, 'source', '', 'source')
       call self%register_dependency(self%id_thickness, standard_variables%cell_thickness)

src/builtin/depth_mapping.F90

@@ -153,7 +153,6 @@ subroutine vertical_depth_range_initialize(self, configunit)
       class (type_vertical_depth_range), intent(inout), target :: self
       integer,                           intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do/))
       call self%get_parameter(self%minimum_depth, 'minimum_depth', 'm', 'minimum depth (distance from surface)', &
          default=self%minimum_depth)
       call self%get_parameter(self%maximum_depth, 'maximum_depth', 'm', 'maximum depth (distance from surface)', &
@@ -258,8 +257,6 @@ subroutine weighted_depth_integral_initialize(self, configunit)
 
       class (type_absolute_rate_distributor), pointer :: rate_distributor
 
-      call self%register_implemented_routines((/source_do_column/))
-
       call self%get_parameter(self%average, 'average', '', 'average', default=self%average)
       call self%get_parameter(self%act_as_state_variable, 'act_as_state_variable', '', 'act as state variable', &
          default=self%act_as_state_variable)
@@ -324,8 +321,6 @@ subroutine projector_initialize(self, configunit)
 
       class (type_projected_rate_distributor), pointer :: rate_distributor
 
-      call self%register_implemented_routines((/source_do/))
-
       call self%get_parameter(self%act_as_state_variable, 'act_as_state_variable', '', 'act as state variable', &
          default=self%act_as_state_variable)
 
@@ -365,7 +360,6 @@ subroutine absolute_rate_distributor_initialize(self, configunit)
       class (type_absolute_rate_distributor), intent(inout), target :: self
       integer,                                intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do/))
       call self%register_state_dependency(self%id_target, 'target', '', 'variable to apply sources and sinks to')
       call self%register_dependency(self%id_w, 'w', '1', 'weights for vertical distribution')
       call self%register_dependency(self%id_w_int, 'w_int', 'm', 'depth-integrated weights for vertical distribution')
@@ -416,7 +410,6 @@ subroutine projected_rate_distributor_initialize(self, configunit)
       class (type_projected_rate_distributor), intent(inout), target :: self
       integer,                                 intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do_column/))
       call self%register_state_dependency(self%id_target, 'target', '', 'variable to apply sources and sinks to')
       call self%register_dependency(self%id_h, standard_variables%cell_thickness)
       call self%register_dependency(self%id_sms, 'sms', '', 'sources-sinks')

src/builtin/model_library.F90

@@ -86,9 +86,9 @@ subroutine create(self,name,model)
          case ('vertical_integral');        allocate(type_depth_integral::model)
          case ('bounded_vertical_integral');allocate(type_bounded_depth_integral::model)
          case ('interior_temporal_mean');   allocate(type_interior_temporal_mean::model)
-         case ('surface_temporal_mean');    allocate(type_surface_temporal_mean::model)
-         case ('bottom_temporal_mean');     allocate(type_bottom_temporal_mean::model)
-         case ('surface_temporal_maximum'); allocate(type_surface_temporal_maximum::model)
+         case ('surface_temporal_mean');    allocate(type_horizontal_temporal_mean::model)
+         case ('bottom_temporal_mean');     allocate(type_horizontal_temporal_mean::model)
+         case ('surface_temporal_maximum'); allocate(type_horizontal_temporal_maximum::model)
          case ('depth_integrated_particle_override'); allocate(type_depth_integrated_particle_override::model)
          case ('vertical_depth_range');     allocate(type_vertical_depth_range::model)
          ! Add new examples models here
@@ -106,7 +106,6 @@ subroutine bottom_field_initialize(self,configunit)
       class (type_bottom_field), intent(inout), target :: self
       integer,                   intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do_bottom/))
       call self%register_diagnostic_variable(self%id_result, 'result', '', 'bottom values', source=source_do_bottom)
       call self%register_dependency(self%id_source, 'source', '', 'interior values')
    end subroutine bottom_field_initialize
@@ -127,7 +126,6 @@ subroutine surface_field_initialize(self,configunit)
       class (type_surface_field), intent(inout), target :: self
       integer,                    intent(in)            :: configunit
 
-      call self%register_implemented_routines((/source_do_surface/))
       call self%register_diagnostic_variable(self%id_result, 'result', '', 'surface values', source=source_do_surface)
       call self%register_dependency(self%id_source, 'source', '', 'interior values')
    end subroutine surface_field_initialize
@@ -148,7 +146,6 @@ subroutine column_projection_initialize(self,configunit)
       class (type_column_projection),intent(inout),target :: self
       integer,                       intent(in)           :: configunit
 
-      call self%register_implemented_routines((/source_do/))
       call self%register_dependency(self%id_source,'source', '', 'horizontal source')
       call self%register_diagnostic_variable(self%id_result,'result', '', 'interior result')
    end subroutine column_projection_initialize

src/builtin/relaxation.F90

@@ -26,7 +26,6 @@ subroutine interior_relaxation_initialize(self,configunit)
       class (type_interior_relaxation),intent(inout),target :: self
       integer,                         intent(in)           :: configunit
 
-      call self%register_implemented_routines((/source_do/))
       call self%register_state_dependency(self%id_original, 'original', '', 'variable that is to be relaxed')
       call self%register_dependency(self%id_target, 'target', '', 'target to relax towards')
       call self%get_parameter(self%rate_is_variable, 'rate_is_variable', '', 'use variable relaxation rate', default=.false.)

src/builtin/scale.F90

@@ -2,31 +2,37 @@
 
 module fabm_builtin_scale
    use fabm_types
+   use fabm_builtin_source, only: copy_fluxes, copy_horizontal_fluxes
 
    implicit none
 
    private
 
    public type_scaled_interior_variable, type_scaled_horizontal_variable
 
-   type, extends(type_base_model) :: type_scaled_interior_variable
+   type, extends(type_base_model) :: type_scaled_variable
+      real(rk)                        :: weight = 1.0_rk
+      real(rk)                        :: offset = 0.0_rk
+      character(len=attribute_length) :: units         = ''
+      real(rk)                        :: missing_value = -2.e20_rk
+      logical                         :: act_as_state_variable = .false.
+      logical                         :: include_background = .false.
+      integer                         :: result_output = output_instantaneous
+   end type
+
+   type, extends(type_scaled_variable) :: type_scaled_interior_variable
       type (type_dependency_id)          :: id_source
       type (type_diagnostic_variable_id) :: id_result
-      real(rk)                           :: weight = 1.0_rk
-      real(rk)                           :: offset = 0.0_rk
-      logical                            :: include_background = .false.
    contains
       procedure :: initialize     => scaled_interior_variable_initialize
       procedure :: do             => scaled_interior_variable_do
       procedure :: after_coupling => scaled_interior_variable_after_coupling
    end type
 
-   type, extends(type_base_model) :: type_scaled_horizontal_variable
+   type, extends(type_scaled_variable) :: type_scaled_horizontal_variable
       type (type_horizontal_dependency_id)          :: id_source
       type (type_horizontal_diagnostic_variable_id) :: id_result
-      real(rk)                                      :: weight = 1.0_rk
-      real(rk)                                      :: offset = 0.0_rk
-      logical                                       :: include_background = .false.
+      integer                                       :: domain = domain_horizontal
    contains
       procedure :: initialize     => scaled_horizontal_variable_initialize
       procedure :: do_horizontal  => scaled_horizontal_variable_do_horizontal
@@ -38,7 +44,11 @@ module fabm_builtin_scale
    subroutine scaled_interior_variable_initialize(self, configunit)
       class (type_scaled_interior_variable), intent(inout), target :: self
       integer,                               intent(in)            :: configunit
-      call self%register_implemented_routines((/source_do/))
+
+      call self%register_dependency(self%id_source, 'source', '', 'source variable')
+      call self%register_diagnostic_variable(self%id_result, 'result', self%units, 'result', &
+         missing_value=self%missing_value, output=self%result_output, act_as_state_variable=self%act_as_state_variable)
+      if (self%act_as_state_variable) call copy_fluxes(self, self%id_result, self%id_source%link%target%name, scale_factor=1.0_rk / self%weight)
    end subroutine
 
    subroutine scaled_interior_variable_do(self, _ARGUMENTS_DO_)
@@ -66,7 +76,12 @@ end subroutine scaled_interior_variable_after_coupling
    subroutine scaled_horizontal_variable_initialize(self, configunit)
       class (type_scaled_horizontal_variable), intent(inout), target :: self
       integer,                                 intent(in)            :: configunit
-      call self%register_implemented_routines((/source_do_horizontal/))
+
+      call self%register_dependency(self%id_source, 'source', '', 'source variable')
+      call self%register_diagnostic_variable(self%id_result, 'result', self%units, 'result', &
+         missing_value=self%missing_value, output=self%result_output, act_as_state_variable= &
+         self%act_as_state_variable, source=source_do_horizontal, domain=self%domain)
+      if (self%act_as_state_variable) call copy_horizontal_fluxes(self, self%id_result, self%id_source%link%target%name, scale_factor=1.0_rk / self%weight)
    end subroutine
 
    subroutine scaled_horizontal_variable_do_horizontal(self, _ARGUMENTS_HORIZONTAL_)