Merge branch 'master' into 95-code-breaks-if-iswcal=0

github-actions/fabm0d-gotm-ersem/aquarium-tut-config-setup.sh

@@ -6,4 +6,4 @@ git clone https://github.com/pmlmodelling/ersem-setups.git
 cd ersem-setups/0d-aquarium
 
 echo "Running FABM with repo configuration"
-~/local/fabm/0d/bin/fabm0d -y ../L4/fabm.yaml
+~/local/fabm/0d/bin/fabm0d -y ../../ersem/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop.yaml

github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-dep-debian.sh

@@ -2,4 +2,4 @@
 
 echo "Installing netCDF"
 sudo apt update
-sudo apt install libnetcdff-dev
+sudo apt install libnetcdff-dev cmake

github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh

@@ -3,6 +3,7 @@
 echo "Cloning config repo"
 git clone https://github.com/pmlmodelling/ersem-setups.git
 
+cp ersem/testcases/fabm-ersem-15.06-L4-ben-docdyn-iop.yaml ersem-setups/L4/fabm.yaml
 cd ersem-setups/L4
 
 echo "Running GOTM with repo configuration"

github-actions/gotm-fabm-ersem/test_profiling.py

@@ -126,7 +126,7 @@ def test_ersem_func_names(self):
         name = self.ersem["name"].tolist()
         name_expected = self.ersem_expected["name"].tolist()
         self.assertListEqual(sorted(name_expected), sorted(name))
-        
+
     @pytest.mark.skip()
     def test_gotm_func_names(self):
         """
@@ -154,6 +154,7 @@ def test_netcdf_func_names(self):
         name_expected = self.netcdf_expected["name"].tolist()
         self.assertListEqual(sorted(name_expected), sorted(name))
 
+    @pytest.mark.skip()
     def test_ersem_func_calls(self):
         """
         Check the number of func calls for ERSEM modules stays the same
@@ -169,6 +170,7 @@ def test_ersem_func_calls(self):
                 self.ersem["name"], self.ersem['self calls'])}
         assert calls == calls_expected
 
+    @pytest.mark.skip()
     def test_gotm_func_calls(self):
         """
         Check the number of func calls for GOTM modules stays the same
@@ -182,6 +184,7 @@ def test_gotm_func_calls(self):
             {n: c for n, c in zip(self.gotm["name"], self.gotm['self calls'])}
         assert calls == calls_expected
 
+    @pytest.mark.skip()
     def test_fabm_func_calls(self):
         """
         Check the number of func calls for FABM modules stays the same
@@ -195,6 +198,7 @@ def test_fabm_func_calls(self):
             {n: c for n, c in zip(self.fabm["name"], self.fabm['self calls'])}
         assert calls == calls_expected
 
+    @pytest.mark.skip()
     def test_netcdf_func_calls(self):
         """
         Check the number of func calls for NETCDF modules stays the same

github-actions/pyfabm-ersem/pyfabm-ersem-build.sh

@@ -10,7 +10,9 @@ git clone https://github.com/fabm-model/fabm.git
 echo "Checking out branch: $BRANCH"
 cd ersem && git checkout $BRANCH && cd ..
 
+echo "Moving ERSEM config files for pyFABM"
+cp github-actions/pyfabm-ersem/setup.cfg fabm
+
 echo "Building PyFABM-ERSEM"
-mkdir build && cd build
-cmake ../fabm/src/drivers/python -DFABM_ERSEM_BASE=../ersem
-make install
+cd fabm
+python -m pip install .

github-actions/pyfabm-ersem/setup.cfg

@@ -0,0 +1,4 @@
+[build_ext]
+cmake_opts=-DFABM_ERSEM_BASE=../ersem
+force=1
+debug=1

src/benthic_column_particulate_matter.F90

@@ -318,7 +318,8 @@ module ersem_benthic_column_particulate_matter
    type,extends(type_ersem_benthic_base),public :: type_ersem_benthic_column_particulate_matter
       type (type_bottom_state_variable_id) :: id_penetration_c,id_penetration_n,id_penetration_p,id_penetration_s
       type (type_bottom_state_variable_id) :: id_buried_c,id_buried_n,id_buried_p,id_buried_s
-      type (type_bottom_state_variable_id) :: id_resuspendable_c,id_resuspendable_p,id_resuspendable_n,id_resuspendable_s
+      type (type_horizontal_diagnostic_variable_id) :: id_burial_flux_c, id_burial_flux_n, id_burial_flux_p, id_burial_flux_s
+      type (type_bottom_state_variable_id) :: id_resuspendable_c,id_resuspendable_p,id_resuspendable_n,id_resuspendable_s         
       type (type_horizontal_dependency_id) :: id_D, id_z_tur, id_d_tot, id_er
 
       logical :: burial
@@ -426,18 +427,22 @@ subroutine initialize(self,configunit)
          if (_VARIABLE_REGISTERED_(self%id_c)) then
             call self%register_state_dependency(self%id_buried_c,'buried_c','mg C/m^2','buried carbon')
             call self%request_coupling_to_model(self%id_buried_c,'burial_target','c')
+            call self%register_diagnostic_variable(self%id_burial_flux_c,'burial_flux_c','mg C/m^2/d','burial of carbon',source=source_do_bottom)
          end if
          if (_VARIABLE_REGISTERED_(self%id_p)) then
             call self%register_state_dependency(self%id_buried_p,'buried_p','mmol P/m^2','buried phosphorus')
             call self%request_coupling_to_model(self%id_buried_p,'burial_target','p')
+            call self%register_diagnostic_variable(self%id_burial_flux_p,'burial_flux_p','mmol P/m^2/d','burial of phosphorus',source=source_do_bottom)
          end if
          if (_VARIABLE_REGISTERED_(self%id_n)) then
             call self%register_state_dependency(self%id_buried_n,'buried_n','mmol N/m^2','buried nitrogen')
             call self%request_coupling_to_model(self%id_buried_n,'burial_target','n')
+            call self%register_diagnostic_variable(self%id_burial_flux_n,'burial_flux_n','mmol N/m^2/d','burial of nitrogen',source=source_do_bottom)
          end if
          if (_VARIABLE_REGISTERED_(self%id_s)) then
             call self%register_state_dependency(self%id_buried_s,'buried_s','mmol Si/m^2','buried silicate')
             call self%request_coupling_to_model(self%id_buried_s,'burial_target','s')
+            call self%register_diagnostic_variable(self%id_burial_flux_s,'burial_flux_s','mmol Si/m^2/d','burial of silicate',source=source_do_bottom)
          end if
       end if
 
@@ -508,6 +513,7 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
                burial_flux = C_int/(1.0_rk - exp(-z_bot/z_mean))*exp(-z_bot/z_mean)*z_bot/z_mean*z_mean_sms/z_mean
                _SET_BOTTOM_ODE_(self%id_c,-burial_flux)
                _SET_BOTTOM_ODE_(self%id_buried_c,burial_flux)
+               _SET_HORIZONTAL_DIAGNOSTIC_(self%id_burial_flux_c,burial_flux)
             end if
             if (self%resuspension) then
                _GET_HORIZONTAL_(self%id_c,C_int)
@@ -526,6 +532,7 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
                burial_flux = C_int/(1.0_rk - exp(-z_bot/z_mean))*exp(-z_bot/z_mean)*z_bot/z_mean*z_mean_sms/z_mean
                _SET_BOTTOM_ODE_(self%id_p,-burial_flux)
                _SET_BOTTOM_ODE_(self%id_buried_p,burial_flux)
+               _SET_HORIZONTAL_DIAGNOSTIC_(self%id_burial_flux_p,burial_flux)
             end if
             if (self%resuspension) then
                _GET_HORIZONTAL_(self%id_p,C_int)
@@ -544,6 +551,7 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
                burial_flux = C_int/(1.0_rk - exp(-z_bot/z_mean))*exp(-z_bot/z_mean)*z_bot/z_mean*z_mean_sms/z_mean
                _SET_BOTTOM_ODE_(self%id_n,-burial_flux)
                _SET_BOTTOM_ODE_(self%id_buried_n,burial_flux)
+               _SET_HORIZONTAL_DIAGNOSTIC_(self%id_burial_flux_n,burial_flux)
             end if
             if (self%resuspension) then
                _GET_HORIZONTAL_(self%id_n,C_int)
@@ -562,6 +570,7 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
                burial_flux = C_int/(1.0_rk - exp(-z_bot/z_mean))*exp(-z_bot/z_mean)*z_bot/z_mean*z_mean_sms/z_mean
                _SET_BOTTOM_ODE_(self%id_s,-burial_flux)
                _SET_BOTTOM_ODE_(self%id_buried_s,burial_flux)
+               _SET_HORIZONTAL_DIAGNOSTIC_(self%id_burial_flux_s,burial_flux)
             end if
             if (self%resuspension) then
                _GET_HORIZONTAL_(self%id_s,C_int)

src/benthic_fauna.F90

@@ -420,9 +420,10 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
 
       _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYKIn,excess_n)
       _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYK1p,excess_p)
-      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPc,mortflux*cP+excess_c)
-      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPn,mortflux*cP*self%qnc)
-      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPp,mortflux*cP*self%qpc)
+      ! fluxes from fauna to POC 
+      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPc,mortflux*cP+excess_c+fBTYc-nfBTYc) 
+      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPn,mortflux*cP*self%qnc+sum(grossfluxn)-sum(netfluxn)) 
+      _SET_HORIZONTAL_DIAGNOSTIC_(self%id_fYQPp,mortflux*cP*self%qpc+sum(grossfluxp) - sum(netfluxp)) 
 
       if (.not.legacy_ersem_compatibility) then
          ! Alkalinity contributions: +1 for NH4, -1 for PO4

testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-denit.yaml

@@ -67,6 +67,7 @@ instances:
       iswbioalk: 1                                         # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                            # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base
@@ -803,6 +804,7 @@ instances:
       minD: 0.0001                                         # minimum depth of zero-concentration isocline (m)
     initialization:
       o: 0.0225                                            # oxygen (mmol/m^2)
+      o_deep: 0                                            # oxygen below zero isocline (mmol/m^2)
     coupling:
       o_pel: O2/o                                          # pelagic oxygen (mmol/m^3)
   G3:
@@ -863,6 +865,8 @@ instances:
       K4n2: K4/per_layer/n2                                # benthic ammonium in 2nd layer (mmol N/m^2)
       G2o2: G2/per_layer/o2                                # oxygen in 2nd layer (mmol O_2/m^2)
       layer2_thickness: ben_col/layer2_thickness           # thickness of 2nd layer (m)
+    initialization:
+      G4n: 0                                               # dinitrogen gas (mmol N/m^2)
   H1:
     long_name: benthic aerobic bacteria
     model: ersem/benthic_bacteria

testcases/fabm-ersem-15.06-L4-ben-docdyn-iop-n2o.yaml

@@ -65,6 +65,7 @@ instances:
       iswbioalk: 1                                         # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                            # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base
@@ -796,6 +797,7 @@ instances:
       minD: 0.0001                                         # minimum depth of zero-concentration isocline (m)
     initialization:
       o: 0.0225                                            # oxygen (mmol/m^2)
+      o_deep: 0                                            # oxygen below zero isocline (mmol/m^2)
     coupling:
       o_pel: O2/o                                          # pelagic oxygen (mmol/m^3)
   G5:
@@ -868,6 +870,8 @@ instances:
       K4n2: K4/per_layer/n2                                # benthic ammonium in 2nd layer (mmol N/m^2)
       G2o2: G2/per_layer/o2                                # oxygen in 2nd layer (mmol O_2/m^2)
       layer2_thickness: ben_col/layer2_thickness           # thickness of 2nd layer (m)
+    initialization:
+      G4n: 0                                               # dinitrogen gas (mmol N/m^2)
   H1:
     long_name: benthic aerobic bacteria
     model: ersem/benthic_bacteria

testcases/fabm-ersem-15.06-L4-ben-docdyn-iop.yaml

@@ -59,6 +59,7 @@ instances:
       iswbioalk: 1                                         # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                            # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base
@@ -787,6 +788,7 @@ instances:
       minD: 0.0001                                         # minimum depth of zero-concentration isocline (m)
     initialization:
       o: 0.0225                                            # oxygen (mmol/m^2)
+      o_deep: 0                                            # oxygen below zero isocline (mmol/m^2)
     coupling:
       o_pel: O2/o                                          # pelagic oxygen (mmol/m^3)
   G3:
@@ -847,6 +849,8 @@ instances:
       K4n2: K4/per_layer/n2                                # benthic ammonium in 2nd layer (mmol N/m^2)
       G2o2: G2/per_layer/o2                                # oxygen in 2nd layer (mmol O_2/m^2)
       layer2_thickness: ben_col/layer2_thickness           # thickness of 2nd layer (m)
+    initialization:
+      G4n: 0                                               # dinitrogen gas (mmol N/m^2)
   H1:
     long_name: benthic aerobic bacteria
     model: ersem/benthic_bacteria

testcases/fabm-ersem-15.06-L4-noben-docdyn-iop.yaml

@@ -59,6 +59,7 @@ instances:
       iswbioalk: 1                                        # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                           # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base

testcases/fabm-ersem-Blackford2004-L4-ben-stdbac-stdlight.yaml

@@ -57,6 +57,7 @@ instances:
       iswbioalk: 1                                         # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                            # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base
@@ -768,6 +769,7 @@ instances:
       minD: 0.0001                                         # minimum depth of zero-concentration isocline (m)
     initialization:
       o: 0.0225                                            # oxygen (mmol/m^2)
+      o_deep: 0                                            # oxygen below zero isocline (mmol/m^2)
     coupling:
       o_pel: O2/o                                          # pelagic oxygen (mmol/m^3)
   G3:
@@ -828,6 +830,8 @@ instances:
       K4n2: K4/per_layer/n2                                # benthic ammonium in 2nd layer (mmol N/m^2)
       G2o2: G2/per_layer/o2                                # oxygen in 2nd layer (mmol O_2/m^2)
       layer2_thickness: ben_col/layer2_thickness           # thickness of 2nd layer (m)
+    initialization:
+      G4n: 0                                               # dinitrogen gas (mmol N/m^2)
   H1:
     long_name: benthic aerobic bacteria
     model: ersem/benthic_bacteria

testcases/fabm-ersem-Blackford2004-L4-noben-stdbac-stdlight.yaml

@@ -57,6 +57,7 @@ instances:
       iswbioalk: 1                                    # use bioalkalinity (0: off, 1: on), default = 1
     initialization:
       c: 2130.0                                       # total dissolved inorganic carbon (mmol C/m^3)
+      bioalk: 0                                            # bioalkalinity (mmol/m^3)
   R1:
     long_name: labile dissolved organic matter
     model: ersem/pelagic_base