Merge pull request #30 from MichaelBarryBMT/MetabolismAndDO

Metabolism and do

src/aed_organic_matter.F90

@@ -648,7 +648,6 @@ SUBROUTINE aed_define_organic_matter(data, namlst)
        aed_define_diag_variable('photolysis','mmol C/m3/d',  'photolysis rate of breakdown of DOC')
 
      data%id_pom_vvel  = aed_define_diag_variable('pom_vvel','m/d','POM vertical velocity')
-
      IF (simRpools) data%id_cpom_vvel = aed_define_diag_variable('cpom_vvel','m/d','CPOM vertical velocity')
 
    ENDIF

src/aed_phosphorus.F90

@@ -375,9 +375,6 @@ SUBROUTINE aed_calculate_surface_phosphorus(data,column,layer_idx)
    ELSE
         _DIAG_VAR_S_(data%id_atm_dep) = _FLUX_VAR_T_(data%id_frp) * secs_per_day
    END IF
-
-
-  ENDIF
 
 END SUBROUTINE aed_calculate_surface_phosphorus
 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

src/aed_phytoplankton.F90

@@ -909,8 +909,8 @@ SUBROUTINE aed_calculate_phytoplankton(data,column,layer_idx)
          _DIAG_VAR_(data%id_fPho(phy_i)) =  fPho
          _DIAG_VAR_(data%id_fSil(phy_i)) =  fSil
          _DIAG_VAR_(data%id_fSal(phy_i)) =  fSal
-         _DIAG_VAR_(data%id_PhyCUP(phy_i)) =  cuptake(phy_i) * secs_per_day !BMT
-         _DIAG_VAR_(data%id_PhyNCP(phy_i)) =  (cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy) * secs_per_day !BMT
+         _DIAG_VAR_(data%id_PhyCUP(phy_i)) =  cuptake(phy_i) * secs_per_day
+         _DIAG_VAR_(data%id_PhyNCP(phy_i)) =  (-cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy) * secs_per_day
       ENDIF
    END DO
 
@@ -1047,12 +1047,12 @@ SUBROUTINE aed_calculate_phytoplankton(data,column,layer_idx)
       ENDIF
       IF (data%do_Cuptake) THEN
          _FLUX_VAR_(data%id_Cupttarget) = _FLUX_VAR_(data%id_Cupttarget) +           &
-                       (  cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy )
+                       (  cuptake(phy_i) + respiration(phy_i)*data%phytos(phy_i)%k_fres*phy )
       ENDIF
-      net_cuptake = net_cuptake + (cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy)
+      net_cuptake = net_cuptake + (-cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy)
       IF (data%do_DOuptake) THEN
          _FLUX_VAR_(data%id_DOupttarget) = _FLUX_VAR_(data%id_DOupttarget) +         &
-                   ( -cuptake(phy_i) + respiration(phy_i)*data%phytos(phy_i)%k_fres*phy )
+                   ( -cuptake(phy_i) - respiration(phy_i)*data%phytos(phy_i)%k_fres*phy )
       ENDIF
       IF (data%do_Siuptake) THEN
          _FLUX_VAR_(data%id_Siupttarget) = _FLUX_VAR_(data%id_Siupttarget) + ( siuptake(phy_i))
@@ -1108,14 +1108,14 @@ SUBROUTINE aed_calculate_phytoplankton(data,column,layer_idx)
 
    !---------------------------------------------------------------------------+
    ! Set diagnostic arrays for combined assemblage properties
-   _DIAG_VAR_(data%id_GPP) =  sum(cuptake)*secs_per_day
+   _DIAG_VAR_(data%id_GPP) =  sum(-cuptake)*secs_per_day
    _DIAG_VAR_(data%id_NCP) =  net_cuptake*secs_per_day
    IF ( diag_level >= 10 ) _DIAG_VAR_(data%id_PPR) =  -999. !sum(cuptake) / ( sum(cuptake) - net_cuptake)
    IF ( diag_level >= 10 ) _DIAG_VAR_(data%id_NPR) =  -999. !net_cuptake / ( sum(cuptake) - net_cuptake)
-   _DIAG_VAR_(data%id_NUP) =  sum(nuptake(:,1))*secs_per_day
-   _DIAG_VAR_(data%id_NUP2)=  sum(nuptake(:,2))*secs_per_day
-   _DIAG_VAR_(data%id_PUP) =  sum(puptake)*secs_per_day
-   _DIAG_VAR_(data%id_CUP) =  sum(cuptake)*secs_per_day
+   _DIAG_VAR_(data%id_NUP) =  sum(-nuptake(:,1))*secs_per_day
+   _DIAG_VAR_(data%id_NUP2)=  sum(-nuptake(:,2))*secs_per_day
+   _DIAG_VAR_(data%id_PUP) =  sum(-puptake)*secs_per_day
+   _DIAG_VAR_(data%id_CUP) =  sum(-cuptake)*secs_per_day
 
    IF ( diag_level >= 10 ) _DIAG_VAR_(data%id_dPAR) =  par
    _DIAG_VAR_(data%id_TCHLA)=  tchla

src/aed_sedflux.F90

@@ -512,6 +512,7 @@ SUBROUTINE aed_define_sedflux(data, namlst)
       CALL aed_set_const_var(data%id_Fsed_pop)
       CALL aed_set_const_var(data%id_Fsed_dop)
       CALL aed_set_const_var(data%id_Fsed_poc)
+      CALL aed_set_const_var(data%id_Fsed_doc)
       CALL aed_set_const_var(data%id_Fsed_dic)
       CALL aed_set_const_var(data%id_Fsed_ch4)
       CALL aed_set_const_var(data%id_Fsed_ch4_ebb)