npzd_Franks_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 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
 
      END MODULE mod_biology