fennel_mod.h

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      MODULE mod_biology
!
!git $Id$
!================================================== Hernan G. Arango ===
!  Copyright (c) 2002-2025 The ROMS Group                              !
!    Licensed under a MIT/X style license                              !
!    See License_ROMS.md                                               !
!=======================================================================
!                                                                      !
!  Parameters for Fennel et al. (2006) model:                          !
!                                                                      !
!   AttSW    Light attenuation due to sea water [1/m].                 !
!   AttChl   Light attenuation by Chlorophyll [1/(mg_Chl m2)].         !
!   BioIter  Maximum number of iterations to achieve convergence       !
!              of the nonlinear solution.                              !
!   Chl2C_m  Maximum chlorophyll to carbon ratio [mg_Chl/mg_C].        !
!   ChlMin   Chlorophill minimum threshold value [mg_Chl/m3].          !
!   CoagR    Coagulation rate: agregation rate of SDeN + Phyt ==> LDeN !
!              [1/day].                                                !
!   D_p5NH4  Half-saturation radiation for nitrification inhibition    !
!              [Watts/m2].                                             !
!   I_thNH4  Radiation threshold for nitrification inhibition          !
!              [Watts/m2].                                             !
!   K_NH4    Inverse half-saturation for Phytoplankton NH4 uptake      !
!              [m3/(mmol_N)].                                          !
!   K_NO3    Inverse half-saturation for Phytoplankton NO3 uptake      !
!              [m3/(mmol_N)].                                          !
!   K_PO4    Inverse half-saturation for Phytoplankton PO4 uptake      !
!              [m3/(mmol_P)].                                          !
!   K_Phy    Zooplankton half-saturation, squared constant for         !
!              ingestion [mmol_N/m3]^2.                                !
!   LDeRR    Large Detrital re-mineralization rate [1/day].            !
!   NitriR   Nitrification rate: oxidation of NH4 to NO3 [1/day].      !
!   PARfrac  Fraction of shortwave radiation that is available for     !
!              photosyntesis [nondimensional].                         !
!   PhyCN    Phytoplankton Carbon:Nitrogen ratio [mol_C/mol_N].        !
!   R_P2N    Phytoplankton Phosphorus:Nitrogen ratio [mol_P/mol_N].    !
!   PhyIP    Phytoplankton NH4 inhibition parameter [1/(mmol_N)].      !
!   PhyIS    Phytoplankton, initial slope of the P-I curve             !
!              [1/(W m-2 day)].                                        !
!   ZooMin   Phytoplankton minimum threshold value [mmol_N/m3].        !
!   PhyMR    Phytoplankton mortality rate [1/day] to small detritus.   !
!   SDeAR    Small detritus aggregation rate into Large detritus       !
!              [1/day].                                                !
!   SDeBR    Small Detrital breakdown to NH4 rate [1/day].             !
!   SDeRR    Large Detrital re-mineralization rate [1/day].            !
!   RDeRR    River Detrital re-mineralization rate [1/day].            !
!   Vp0      Eppley temperature-limited and light-limited growth       !
!              tuning parameter [nondimensional].                      !
!   wLDet    Vertical sinking velocities for Large Detritus            !
!              fraction [m/day].                                       !
!   wPhy     Vertical sinking velocity for Phytoplankton               !
!              fraction [m/day].                                       !
!   wSDet    Vertical sinking velocities for Small Detritus            !
!              fraction [m/day].                                       !
!   ZooAE_N  Zooplankton nitrogen assimilation efficiency fraction     !
!              [nondimensional].                                       !
!   ZooBM    Zooplankton basal metabolism [1/day].                     !
!   ZooCN    Zooplankton Carbon:Nitrogen ratio [mol_C/mol_N].          !
!   ZooER    Zooplankton specific excretion rate [1/day].              !
!   ZooGR    Zooplankton maximum growth rate [1/day].                  !
!   ZooMin   Zooplankton minimum threshold value [mmol_N/m3].          !
!   ZooMR    Zooplankton mortality to Detritus [1/day].                !
!   pCO2air  CO2 partial pressure in the air [ppmv].                   !
!                                                                      !
!=======================================================================
!
      USE mod_param
!
      implicit none
!
!  Set biological tracer identification indices.
!
      integer, allocatable :: idbio(:)  ! Biological tracers
      integer :: iNO3_                  ! Nitrate concentration
      integer :: iNH4_                  ! Ammonium concentration
#ifdef PO4
      integer :: iPO4_                  ! Phosphate concentration
#endif
      integer :: ichlo                  ! Chlorophyll concentration
      integer :: iphyt                  ! Phytoplankton concentration
      integer :: izoop                  ! Zooplankton concentration
      integer :: ilden                  ! Large detritus N-concentration
      integer :: isden                  ! Small detritus N-concentration
#ifdef RIVER_DON
      integer :: irden                  ! River detritus N-concentration
#endif
#ifdef CARBON
      integer :: ildec                  ! Large detritus C-concentration
      integer :: isdec                  ! Small detritus C-concentration
      integer :: itic_                  ! Total inorganic carbon
      integer :: italk                  ! Total alkalinity
# ifdef RIVER_DON
      integer :: irdec                  ! River detritus C-concentration
# endif
#endif
#ifdef OXYGEN
      integer :: ioxyg                  ! Dissolved oxygen concentration
#endif
 
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!  Biological 2D diagnostic variable IDs.
!
      integer, allocatable :: idbio2(:)       ! 2D biological terms
 
      integer  :: icofx                       ! air-sea CO2 flux
      integer  :: idnit                       ! denitrification flux
      integer  :: ipco2                       ! partial pressure of CO2
      integer  :: io2fx                       ! air-sea O2 flux
!
!  Biological 3D diagnostic variable IDs.
!
      integer, allocatable :: idbio3(:)       ! 3D biological terms
 
      integer  :: ippro = 1                   ! primary productivity
      integer  :: ino3u = 2                   ! NO3 uptake
      integer  :: inifx = 3                   ! Nitrification flux
#endif
!
!  Biological parameters.
!
      integer, allocatable :: bioiter(:)
 
      real(r8), allocatable :: attsw(:)              ! 1/m
      real(r8), allocatable :: attchl(:)             ! 1/(mg_Chl m2)
      real(r8), allocatable :: chl2c_m(:)            ! mg_Chl/mg_C
      real(r8), allocatable :: chlmin(:)             ! mg_Chl/m3
      real(r8), allocatable :: coagr(:)              ! 1/day
      real(r8), allocatable :: d_p5nh4(:)            ! Watts/m2
      real(r8), allocatable :: i_thnh4(:)            ! Watts/m2
      real(r8), allocatable :: k_nh4(:)              ! m3/mmol_N
      real(r8), allocatable :: k_no3(:)              ! m3/mmol_N
      real(r8), allocatable :: k_po4(:)              ! m3/mmol_P
      real(r8), allocatable :: k_phy(:)              ! (mmol_N/m3)^2
      real(r8), allocatable :: lderrn(:)             ! 1/day
      real(r8), allocatable :: lderrc(:)             ! 1/day
      real(r8), allocatable :: nitrir(:)             ! 1/day
      real(r8), allocatable :: parfrac(:)            ! nondimensional
      real(r8), allocatable :: phycn(:)              ! mol_C/mol_N
      real(r8), allocatable :: r_p2n(:)              ! mol_P/mol_N
      real(r8), allocatable :: phyip(:)              ! 1/mmol_N
      real(r8), allocatable :: phyis(:)              ! 1/(Watts m-2 day)
      real(r8), allocatable :: phymin(:)             ! mmol_N/m3
      real(r8), allocatable :: phymr(:)              ! 1/day
      real(r8), allocatable :: sdear(:)              ! 1/day
      real(r8), allocatable :: sdebr(:)              ! 1/day
      real(r8), allocatable :: sderrn(:)             ! 1/day
      real(r8), allocatable :: sderrc(:)             ! 1/day
      real(r8), allocatable :: rderrn(:)             ! 1/day
      real(r8), allocatable :: rderrc(:)             ! 1/day
      real(r8), allocatable :: vp0(:)                ! nondimensional
      real(r8), allocatable :: wldet(:)              ! m/day
      real(r8), allocatable :: wphy(:)               ! m/day
      real(r8), allocatable :: wsdet(:)              ! m/day
      real(r8), allocatable :: zooae_n(:)            ! nondimensional
      real(r8), allocatable :: zoobm(:)              ! 1/day
      real(r8), allocatable :: zoocn(:)              ! mol_C/mol_N
      real(r8), allocatable :: zooer(:)              ! 1/day
      real(r8), allocatable :: zoogr(:)              ! 1/day
      real(r8), allocatable :: zoomin(:)             ! mmol_N/m3
      real(r8), allocatable :: zoomr(:)              ! 1/day
      real(r8), allocatable :: pco2air(:)            ! ppmv
!
      CONTAINS
!
      SUBROUTINE initialize_biology
!
!=======================================================================
!                                                                      !
!  This routine sets several variables needed by the biology model.    !
!  It allocates and assigns biological tracers indices.                !
!                                                                      !
!=======================================================================
!
!  Local variable declarations
!
      integer :: i, ic
!
!-----------------------------------------------------------------------
!  Determine number of biological tracers.
!-----------------------------------------------------------------------
!
#ifdef CARBON
# ifdef OXYGEN
#  if defined PO4 && defined RIVER_DON
      nbt=15
#  elif defined RIVER_DON && !defined PO4
      nbt=14
#  elif defined PO4 && !defined RIVER_DON
      nbt=13
#  else
      nbt=12
#  endif
# else
#  if defined PO4 && defined RIVER_DON
      nbt=14
#  elif defined RIVER_DON && !defined PO4
      nbt=13
#  elif defined PO4 && !defined RIVER_DON
      nbt=12
#  else
      nbt=11
#  endif
# endif
#else
# ifdef OXYGEN
#  if defined PO4 && defined RIVER_DON
      nbt=10
#  elif defined PO4 || defined RIVER_DON
      nbt=9
#  else
      nbt=8
#  endif
# else
#  if defined PO4 && defined RIVER_DON
      nbt=9
#  elif defined PO4 || defined RIVER_DON
      nbt=8
#  else
      nbt=7
#  endif
# endif
#endif
 
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!-----------------------------------------------------------------------
!  Set sources and sinks biology diagnostic parameters.
!-----------------------------------------------------------------------
!
!  Set number of diagnostics terms.
!
      ndbio3d=3
      ndbio2d=0
# ifdef DENITRIFICATION
      ndbio2d=ndbio2d+1
# endif
# ifdef CARBON
      ndbio2d=ndbio2d+2
# endif
# ifdef OXYGEN
      ndbio2d=ndbio2d+1
# endif
!
!  Initialize biology diagnostic indices.
!
      ic=0
# ifdef DENITRIFICATION
      idnit=ic+1
      ic=ic+1
# endif
# ifdef CARBON
      icofx=ic+1
      ipco2=ic+2
      ic=ic+2
# endif
# ifdef OXYGEN
      io2fx=ic+1
# endif
#endif
!
!-----------------------------------------------------------------------
!  Allocate various module variables.
!-----------------------------------------------------------------------
!
      IF (.not.allocated(bioiter)) THEN
        allocate ( bioiter(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(attsw)) THEN
        allocate ( attsw(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(attchl)) THEN
        allocate ( attchl(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(chl2c_m)) THEN
        allocate ( chl2c_m(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(chlmin)) THEN
        allocate ( chlmin(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(coagr)) THEN
        allocate ( coagr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(d_p5nh4)) THEN
        allocate ( d_p5nh4(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(i_thnh4)) THEN
        allocate ( i_thnh4(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(k_nh4)) THEN
        allocate ( k_nh4(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(k_no3)) THEN
        allocate ( k_no3(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(k_po4)) THEN
        allocate ( k_po4(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(k_phy)) THEN
        allocate ( k_phy(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(lderrn)) THEN
        allocate ( lderrn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(lderrc)) THEN
        allocate ( lderrc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(nitrir)) THEN
        allocate ( nitrir(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(parfrac)) THEN
        allocate ( parfrac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phycn)) THEN
        allocate ( phycn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(r_p2n)) THEN
        allocate ( r_p2n(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phyip)) THEN
        allocate ( phyip(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phyis)) THEN
        allocate ( phyis(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phymin)) THEN
        allocate ( phymin(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phymr)) THEN
        allocate ( phymr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(sdear)) THEN
        allocate ( sdear(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(sdebr)) THEN
        allocate ( sdebr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(sderrn)) THEN
        allocate ( sderrn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(sderrc)) THEN
        allocate ( sderrc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(rderrn)) THEN
        allocate ( rderrn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(rderrc)) THEN
        allocate ( rderrc(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(vp0)) THEN
        allocate ( vp0(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(wldet)) THEN
        allocate ( wldet(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(wphy)) THEN
        allocate ( wphy(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(wsdet)) THEN
        allocate ( wsdet(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zooae_n)) THEN
        allocate ( zooae_n(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoobm)) THEN
        allocate ( zoobm(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoocn)) THEN
        allocate ( zoocn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zooer)) THEN
        allocate ( zooer(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoogr)) THEN
        allocate ( zoogr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoomin)) THEN
        allocate ( zoomin(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoomr)) THEN
        allocate ( zoomr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(pco2air)) THEN
        allocate ( pco2air(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
!
!  Allocate biological tracer vector.
!
      IF (.not.allocated(idbio)) THEN
        allocate ( idbio(nbt) )
        dmem(1)=dmem(1)+real(nbt,r8)
      END IF
 
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!  Allocate biological diagnostics vectors
!
      IF (.not.allocated(idbio2)) THEN
        allocate ( idbio2(ndbio2d) )
        dmem(1)=dmem(1)+real(ndbio2d,r8)
      END IF
 
      IF (.not.allocated(idbio3)) THEN
        allocate ( idbio3(ndbio3d) )
        dmem(1)=dmem(1)+real(ndbio3d,r8)
      END IF
#endif
!
!-----------------------------------------------------------------------
!  Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
      ic=nat+npt+ncs+nns
      DO i=1,nbt
        idbio(i)=ic+i
      END DO
      ino3_=ic+1
      inh4_=ic+2
      ichlo=ic+3
      iphyt=ic+4
      izoop=ic+5
      ilden=ic+6
      isden=ic+7
      ic=ic+7
# ifdef RIVER_DON
      irden=ic+1
      ic=ic+1
# endif
# ifdef PO4
      ipo4_=ic+1
      ic=ic+1
# endif
# ifdef CARBON
      ildec=ic+1
      isdec=ic+2
      itic_=ic+3
      italk=ic+4
      ic=ic+4
#  ifdef RIVER_DON
      irdec=ic+1
      ic=ic+1
#  endif
# endif
# ifdef OXYGEN
      ioxyg=ic+1
      ic=ic+1
# endif
!
      RETURN
      END SUBROUTINE initialize_biology
 
      END MODULE mod_biology