!
!svn $Id: npzd_Franks_mod.h 921 2018-09-06 18:27:34Z arango $
!================================================== Hernan G. Arango ===
!  Copyright (c) 2002-2019 The ROMS/TOMS Group                         !
!    Licensed under a MIT/X style license                              !
!    See License_ROMS.txt                                              !
!=======================================================================
!                                                                      !
!  Parameters for Franks et al. (1986) type model:                     !
!                                                                      !
!  BioIter   Maximum number of iterations to achieve convergence of    !
!              the nonlinear solution.                                 !
!  BioIni    Initial concentration for analytical initial (uniform)    !
!              conditions.                                             !
!  DetRR     Detritus remineraliztion rate, [1/day].                   !
!  K_ext     Light extinction coefficient, [1/m].                      !
!  K_NO3     Inverse half-saturation for phytoplankton nitrate uptake  !
!              [1/(millimole_N m-3)].                                  !
!  K_Phy     Phytoplankton saturation coefficient, [millimole_N m-3].  !
!  PhyMR     Phytoplankton senescence/mortality rate, [1/day].         !
!  Vm_NO3    Nitrate uptake rate, [1/day].                             !
!  wDet      Detrital sinking rate, [m/day].                           !
!  ZooGR     Zooplankton maximum growth rate, [1/day].                 !
!  ZooMR     Zooplankton mortality rate, [1/day].                      !
!  ZooMD     Zooplankton death bits rate, [1/day].                     !
!  ZooGA     Zooplankton grazing inefficiency, [nondimensional].       !
!  ZooEC     Zooplankton excreted fraction, [nondimensional].          !
!                                                                      !
!=======================================================================
!
      USE mod_param
!
      implicit none
!
!  Set biological tracer identification indices.
!
      integer, allocatable :: idbio(:)  ! Biological tracers
      integer :: iNO3_                  ! Nitrate concentration
      integer :: iPhyt                  ! Phytoplankton concentration
      integer :: iZoop                  ! Zooplankton concentration
      integer :: iSDet                  ! Small detritus concentration
!
!  Biological parameters.
!
      integer, allocatable :: BioIter(:)

#ifdef ANA_BIOLOGY
      real(r8), allocatable :: BioIni(:,:)
#endif
      real(r8), allocatable :: DetRR(:)        ! 1/day
      real(r8), allocatable :: K_ext(:)        ! 1/m
      real(r8), allocatable :: K_NO3(:)        ! 1/(mmol/m3)
      real(r8), allocatable :: K_Phy(:)        ! mmol/m3
      real(r8), allocatable :: PhyMR(:)        ! 1/day
      real(r8), allocatable :: Vm_NO3(:)       ! 1/day
      real(r8), allocatable :: wDet(:)         ! m/day
#ifdef TANGENT
      real(r8), allocatable :: tl_wDet(:)
#endif
#ifdef ADJOINT
      real(r8), allocatable :: ad_wDet(:)
#endif
      real(r8), allocatable :: ZooGR(:)        ! 1/day
      real(r8), allocatable :: ZooMR(:)        ! 1/day
      real(r8), allocatable :: ZooMD(:)        ! 1/day
      real(r8), allocatable :: ZooGA(:)        ! nondimensional
      real(r8), allocatable :: ZooEC(:)        ! nondimensional

      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
!
!-----------------------------------------------------------------------
!  Set number of biological tracers.
!-----------------------------------------------------------------------
!
      NBT=4
!
!-----------------------------------------------------------------------
!  Allocate various module variables.
!-----------------------------------------------------------------------
!
      IF (.not.allocated(BioIter)) THEN
        allocate ( BioIter(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(DetRR)) THEN
        allocate ( DetRR(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(K_ext)) THEN
        allocate ( K_ext(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_Phy)) THEN
        allocate ( K_Phy(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(Vm_NO3)) THEN
        allocate ( Vm_NO3(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(wDet)) THEN
        allocate ( wDet(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

#ifdef TANGENT
      IF (.not.allocated(tl_wDet)) THEN
        allocate ( tl_wDet(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF
#endif

#ifdef ADJOINT
      IF (.not.allocated(ad_wDet)) THEN
        allocate ( ad_wDet(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF
#endif

      IF (.not.allocated(ZooGR)) THEN
        allocate ( ZooGR(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(ZooMD)) THEN
        allocate ( ZooMD(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(ZooGA)) THEN
        allocate ( ZooGA(Ngrids) )
        Dmem(1)=Dmem(1)+REAL(Ngrids,r8)
      END IF

      IF (.not.allocated(ZooEC)) THEN
        allocate ( ZooEC(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
!
!-----------------------------------------------------------------------
!  Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
      ic=NAT+NPT+NCS+NNS
      DO i=1,NBT
        idbio(i)=ic+i
      END DO
      iNO3_=ic+1
      iPhyt=ic+2
      iZoop=ic+3
      iSDet=ic+4

      RETURN
      END SUBROUTINE initialize_biology