npzd_iron_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 Powell et al. (2006) ecosystem model with iron       !
!  limitation:                                                         !
!                                                                      !
!  AttPhy     Light attenuation due to phytoplankton (self-shading     !
!               coefficient), [m2/millimole_N].                        !
!  AttSW      Light attenuation due to sea water, [1/m].               !
!  A_Fe       Empirical Fe:C power, [nondimensional].                  !
!  B_Fe       Empirical Fe:C coefficient, [1/M-C].                     !
!  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].                  !
!  FeRR       Fe remineralization rate, [1/day].                       !
!  FeHmin     Minimum bathymetry value (meter; positive) considered to !
!               nudge dissolved iron over the shelf (h <= FeHmin).     !
!  FeMax      Dissolved iron value to nudge over the shelf to simulate !
!               Fe coastal source.                                     !
!  FeNudgTime Dissolved iron nudging time scale (days) over the shelf. !
!               Inverse scale will be computed internally.             !
!  K_FeC      Fe:C at F=0.5, [muM-Fe/M-C].                             !
!  K_NO3      Inverse half-saturation for phytoplankton nitrate uptake !
!               [1/(millimole_N m-3)].                                 !
!  Ivlev      Ivlev constant for zooplankton grazin parameterization,  !
!               [nondimensional].                                      !
!  PARfrac    Fraction of shortwave radiation that is available for    !
!               photosyntesis [non-dimensional].                       !
!  PhyIS      Phytoplankton, initial slope of the P-I curve [m2/W].    !
!  PhyMRD     Phytoplankton mortality rate to the Detritus pool,       !
!               [1/day].                                               !
!  PhyMRN     Phytoplankton mortality rate to the Nitrogen pool,       !
!              [1/day].                                                !
!  T_Fe       Iron uptake timescale, [day].                            !
!  Vm_NO3     Nitrate uptake rate, [1/day].                            !
!  wDet       Detrital sinking rate, [m/day].                          !
!  wPhy       Phytoplankton sinking rate, [m/day].                     !
!  ZooEED     Zooplankton excretion efficiency to Detritus pool,       !
!               [nondimensional].                                      !
!  ZooEEN     Zooplankton excretion efficiency to Nitrogen pool,       !
!               [nondimensional].                                      !
!  ZooGR      Zooplankton grazing rate, [1/day].                       !
!  ZooMRD     Zooplankton mortality rate to Detritus pool, [1/day].    !
!  ZooMRN     Zooplankton mortality rate to Nitrogen pool, [1/day].    !
!                                                                      !
!=======================================================================
!
      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
#ifdef IRON_LIMIT
      integer :: ifphy                  ! Phytoplankton-associated iron
      integer :: ifdis                  ! Available disolved iron
#endif
!
!  Biological parameters.
!
      integer, allocatable :: bioiter(:)
 
      real(r8), allocatable :: bioini(:,:)
      real(r8), allocatable :: attphy(:)       ! m2/mmole
      real(r8), allocatable :: attsw(:)        ! 1/m
      real(r8), allocatable :: detrr(:)        ! 1/day
      real(r8), allocatable :: k_no3(:)        ! 1/(mmol/m3)
      real(r8), allocatable :: ivlev(:)        ! nondimensional
      real(r8), allocatable :: parfrac(:)      ! nondimensional
#ifdef IRON_LIMIT
      real(r8), allocatable :: a_fe(:)         ! nondimensional
      real(r8), allocatable :: b_fe(:)         ! 1/M-C
      real(r8), allocatable :: ferr(:)         ! 1/day
# ifdef IRON_RELAX
      real(r8), allocatable :: fehmin(:)       ! m
      real(r8), allocatable :: femax(:)        ! mmole/m3
      real(r8), allocatable :: fenudgtime(:)   ! day
# endif
      real(r8), allocatable :: k_fec(:)        ! muM-Fe/M-C
      real(r8), allocatable :: t_fe(:)         ! day
#endif
#ifdef TANGENT
      real(r8), allocatable :: tl_parfrac(:)   ! nondimensional
#endif
#ifdef ADJOINT
      real(r8), allocatable :: ad_parfrac(:)   ! nondimensional
#endif
      real(r8), allocatable :: phyis(:)        ! m2/W
      real(r8), allocatable :: phymrd(:)       ! 1/day
      real(r8), allocatable :: phymrn(:)       ! 1/day
      real(r8), allocatable :: vm_no3(:)       ! 1/day
      real(r8), allocatable :: wdet(:)         ! m/day
#ifdef TANGENT
      real(r8), allocatable :: tl_wdet(:)      ! m/day
#endif
#ifdef ADJOINT
      real(r8), allocatable :: ad_wdet(:)      ! m/day
#endif
      real(r8), allocatable :: wphy(:)         ! m/day
#ifdef TANGENT
      real(r8), allocatable :: tl_wphy(:)      ! m/day
#endif
#ifdef ADJOINT
      real(r8), allocatable :: ad_wphy(:)      ! m/day
#endif
      real(r8), allocatable :: zooeed(:)       ! nondimensional
      real(r8), allocatable :: zooeen(:)       ! nondimensional
      real(r8), allocatable :: zoogr(:)        ! 1/day
      real(r8), allocatable :: zoomrd(:)       ! 1/day
      real(r8), allocatable :: zoomrn(:)       ! 1/day
 
      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.
!-----------------------------------------------------------------------
!
#ifdef IRON_LIMIT
      nbt=6
#else
      nbt=4
#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(attphy)) THEN
        allocate ( attphy(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(detrr)) THEN
        allocate ( detrr(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(ivlev)) THEN
        allocate ( ivlev(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
 
#ifdef IRON_LIMIT
      IF (.not.allocated(a_fe)) THEN
        allocate ( a_fe(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(b_fe)) THEN
        allocate ( b_fe(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(ferr)) THEN
        allocate ( ferr(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
# ifdef IRON_RELAX
      IF (.not.allocated(fehmin)) THEN
        allocate ( fehmin(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(femax)) THEN
        allocate ( femax(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(fenudgtime)) THEN
        allocate ( fenudgtime(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
# endif
 
      IF (.not.allocated(k_fec)) THEN
        allocate ( k_fec(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(t_fe)) THEN
        allocate ( t_fe(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
#ifdef TANGENT
      IF (.not.allocated(tl_parfrac)) THEN
        allocate ( tl_parfrac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
#ifdef ADJOINT
      IF (.not.allocated(ad_parfrac)) THEN
        allocate ( ad_parfrac(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
      IF (.not.allocated(phyis)) THEN
        allocate ( phyis(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phymrd)) THEN
        allocate ( phymrd(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(phymrn)) THEN
        allocate ( phymrn(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(wphy)) THEN
        allocate ( wphy(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
#ifdef TANGENT
      IF (.not.allocated(tl_wphy)) THEN
        allocate ( tl_wphy(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
#ifdef ADJOINT
      IF (.not.allocated(ad_wphy)) THEN
        allocate ( ad_wphy(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
      IF (.not.allocated(zooeed)) THEN
        allocate ( zooeed(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zooeen)) THEN
        allocate ( zooeen(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(zoomrd)) THEN
        allocate ( zoomrd(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(zoomrn)) THEN
        allocate ( zoomrn(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
#ifdef IRON_LIMIT
      ifphy=ic+5
      ifdis=ic+6
#endif
 
      RETURN
      END SUBROUTINE initialize_biology
 
      END MODULE mod_biology