Merge pull request #23 from MichaelBarryBMT/diag_var_requests

Changes to diagnostic variables in order and number

src/aed_organic_matter.F90

@@ -648,7 +648,8 @@ 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')
- data%id_cpom_vvel = aed_define_diag_variable('cpom_vvel','m/d','CPOM vertical velocity')
+
+ IF (simRpools) data%id_cpom_vvel = aed_define_diag_variable('cpom_vvel','m/d','CPOM vertical velocity')
 
  ENDIF
 

src/aed_phytoplankton.F90

@@ -72,7 +72,8 @@ MODULE aed_phytoplankton
  INTEGER,ALLOCATABLE :: id_NtoP(:)
  INTEGER,ALLOCATABLE :: id_vvel(:)
  INTEGER,ALLOCATABLE :: id_fT(:), id_fI(:), id_fNit(:), &
- id_fPho(:), id_fSil(:), id_fSal(:)
+ id_fPho(:), id_fSil(:), id_fSal(:), &
+ id_PhyCUP(:), id_PhyNCP(:), id_PhySed(:)
  INTEGER :: id_Pexctarget,id_Pmorttarget,id_Pupttarget(1:2)
  INTEGER :: id_Nexctarget,id_Nmorttarget,id_Nupttarget(1:4)
  INTEGER :: id_Cexctarget,id_Cmorttarget,id_Cupttarget
@@ -269,6 +270,9 @@ SUBROUTINE aed_phytoplankton_load_params(data, dbase, count, list, settling, res
  ALLOCATE(data%id_fSil(count)) ; data%id_fSil(:) = 0
  ALLOCATE(data%id_fSal(count)) ; data%id_fSal(:) = 0
  ALLOCATE(data%id_vvel(count)) ; data%id_vvel(:) = 0
+ ALLOCATE(data%id_PhyCUP(count)) ; data%id_PhyCUP(:) = 0
+ ALLOCATE(data%id_PhyNCP(count)) ; data%id_PhyNCP(:) = 0
+ ALLOCATE(data%id_PhySed(count)) ; data%id_PhySed(:) = 0
  ENDIF
 
  DO i=1,count
@@ -400,6 +404,9 @@ SUBROUTINE aed_phytoplankton_load_params(data, dbase, count, list, settling, res
  data%id_fSil(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_fSil', '-', 'fSil (0-1)')
  data%id_fT(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_fT', '-', 'fT (>0)')
  data%id_fSal(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_fSal', '-', 'fSal (>1)')
+ data%id_PhyCUP(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_GPP', 'mmol/m**3/d', 'group primary production')
+ data%id_PhyNCP(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_NCP', 'mmol/m**3/d', 'group net production')
+ data%id_PhySed(i) = aed_define_diag_variable( TRIM(data%phytos(i)%p_name)//'_SED', 'mmol/m**2/d', 'group sedimentation')
  ! Register vertical velocity diagnostic, where relevant
  IF (data%phytos(i)%settling == _MOB_STOKES_ .OR. &
  data%phytos(i)%settling == _MOB_MOTILE_) THEN
@@ -902,6 +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
  ENDIF
  END DO
 
@@ -1300,6 +1309,7 @@ SUBROUTINE aed_mobility_phytoplankton(data,column,layer_idx,mobility)
  ! set sedimentation flux (mmmol/m2) for later use/reporting
  _DIAG_VAR_(data%id_Psed_phy) = &
  _DIAG_VAR_(data%id_Psed_phy) + vvel*_STATE_VAR_(data%id_p(phy_i))
+ _DIAG_VAR_(data%id_PhySed(phy_i)) = vvel*_STATE_VAR_(data%id_p(phy_i))
  ENDDO
 END SUBROUTINE aed_mobility_phytoplankton
 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

src/aed_sedflux.F90

@@ -454,6 +454,15 @@ SUBROUTINE aed_define_sedflux(data, namlst)
  IF ( Fsed_oxy .GT. MISVAL ) &
  data%id_Fsed_oxy = aed_define_sheet_diag_variable('Fsed_oxy','mmol/m**2', &
  'flux rate of oxygen across the swi')
+ IF ( Fsed_dic .GT. MISVAL ) &
+ data%id_Fsed_dic = aed_define_sheet_diag_variable('Fsed_dic','mmol/m**2', &
+ 'flux rate of dic across the swi')
+ IF ( Fsed_ch4 .GT. MISVAL ) &
+ data%id_Fsed_ch4 = aed_define_sheet_diag_variable('Fsed_ch4','mmol/m**2', &
+ 'flux rate of ch4 across the swi')
+ IF ( Fsed_ch4_ebb .GT. MISVAL ) &
+ data%id_Fsed_ch4_ebb = aed_define_sheet_diag_variable('Fsed_ch4_ebb','mmol/m**2', &
+ 'flux rate of ch4 bubbles across the swi')
  IF ( Fsed_rsi .GT. MISVAL ) &
  data%id_Fsed_rsi = aed_define_sheet_diag_variable('Fsed_rsi','mmol/m**2', &
  'flux rate of rsi across the swi')
@@ -469,6 +478,12 @@ SUBROUTINE aed_define_sedflux(data, namlst)
  IF ( Fsed_frp .GT. MISVAL ) &
  data%id_Fsed_frp = aed_define_sheet_diag_variable('Fsed_frp','mmol/m**2', &
  'flux rate of frp across the swi')
+ IF ( Fsed_poc .GT. MISVAL ) &
+ data%id_Fsed_poc = aed_define_sheet_diag_variable('Fsed_poc','mmol/m**2', &
+ 'sedimentation rate of poc')
+ IF ( Fsed_doc .GT. MISVAL ) &
+ data%id_Fsed_doc = aed_define_sheet_diag_variable('Fsed_doc','mmol/m**2', &
+ 'flux rate of doc across the swi')
  IF ( Fsed_pon .GT. MISVAL ) &
  data%id_Fsed_pon = aed_define_sheet_diag_variable('Fsed_pon','mmol/m**2', &
  'sedimentation rate of pon')
@@ -481,21 +496,6 @@ SUBROUTINE aed_define_sedflux(data, namlst)
  IF ( Fsed_dop .GT. MISVAL ) &
  data%id_Fsed_dop = aed_define_sheet_diag_variable('Fsed_dop','mmol/m**2', &
  'flux rate of dop across the swi')
- IF ( Fsed_poc .GT. MISVAL ) &
- data%id_Fsed_poc = aed_define_sheet_diag_variable('Fsed_poc','mmol/m**2', &
- 'sedimentation rate of poc')
- IF ( Fsed_doc .GT. MISVAL ) &
- data%id_Fsed_doc = aed_define_sheet_diag_variable('Fsed_doc','mmol/m**2', &
- 'flux rate of doc across the swi')
- IF ( Fsed_dic .GT. MISVAL ) &
- data%id_Fsed_dic = aed_define_sheet_diag_variable('Fsed_dic','mmol/m**2', &
- 'flux rate of dic across the swi')
- IF ( Fsed_ch4 .GT. MISVAL ) &
- data%id_Fsed_ch4 = aed_define_sheet_diag_variable('Fsed_ch4','mmol/m**2', &
- 'flux rate of ch4 across the swi')
- IF ( Fsed_ch4_ebb .GT. MISVAL ) &
- data%id_Fsed_ch4_ebb = aed_define_sheet_diag_variable('Fsed_ch4_ebb','mmol/m**2', &
- 'flux rate of ch4 bubbles across the swi')
  IF ( Fsed_feii .GT. MISVAL ) &
  data%id_Fsed_feii = aed_define_sheet_diag_variable('Fsed_feii','mmol/m**2', &
  'flux rate of feii across the swi')