red_tide_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:                                                         !
!                                                                      !
!  AttS         Mean light diffuse attenuation coefficient in the      !
!                 sediment (1/m)                                       !
!  AttW         Mean light diffuse attenuation coefficient in the      !
!                 water column (1/m)                                   !
!  DIN_Cdepth   Constant Dissolved Inorganic Nutrient concentration    !
!                 below of growth crical depth (millimole/m3)          !
!  Dg           Mean depth (m) of sediment over which cysts are able   !
!                 to germinate and contribute to the bloom             !
!  E_dark       Light level for germination under dark conditions      !
!                 (watt/m2)                                            !
!  E_light      Light level for germination under "light" conditions   !
!                 (Watt/m2)                                            !
!  Gmax         Maximum growth rate at optimal temperature and salinty !
!                 (1/day)                                              !
!  G_eff        Growth efficiency (m2/Watts/day)                       !
!  G_r          Maintanenance respiration rate (1/day)                 !
!  Kn           Half-saturation constant for nutrient limited growth   !
!                 (millimoles/m3)                                      !
!  Mor_a        Mortality rate equation, Q10 amplitude term (1/day)    !
!  Mor_b        Mortality rate equation, Q10 intercept term (1/day)    !
!  Mor_Q10      Mortality rate equation, Q10 reaction rate base        !
!  Mor_T0       Mortality rate equation, Q10 background temperature (C)!
!  Tmin_growth  Coldest temperature limit used to compute temperature- !
!                 dependent growth factor from cubic polynomial fit    !
!                 based on available data (Celsius)                    !
!  srad_Cdepth  Averaged solar shortwave radiation used to compute     !
!                 critical depth in the growth function (Watts/m2)     !
!  wDino        Dinoflagellate (Alexandrium Fundyense) vertical        !
!                 swimming rate (positive; m/day)                      !
!                                                                      !
!=======================================================================
!
      USE mod_param
!
      implicit none
!
!  Set biological tracer identification indices.
!
      integer, allocatable :: idbio(:)  ! Biological tracers
      integer :: idasrf                 ! Averaged shortwave radiation
      integer :: idcyst                 ! Bottom cyst concentration
      integer :: idodin                 ! Dissolved Inorganic Nutrient
      integer :: idino                  ! Dinoflagellate concentration
!
!  Biological parameters.
!
      integer, allocatable :: bioiter(:)
 
 
      real(r8), allocatable :: atts(:)         ! 1/m
      real(r8), allocatable :: attw(:)         ! 1/m
      real(r8), allocatable :: din_cdepth(:)   ! millimoles/m3
      real(r8), allocatable :: dg(:)           ! m
      real(r8), allocatable :: e_dark(:)       ! Watts/m2
      real(r8), allocatable :: e_light(:)      ! Watts/m2
      real(r8), allocatable :: gmax(:)         ! 1/day
      real(r8), allocatable :: g_eff(:)        ! m2/Watts/day
      real(r8), allocatable :: g_r(:)          ! 1/day
      real(r8), allocatable :: kn(:)           ! millimoles/m3
      real(r8), allocatable :: mor_a(:)        ! 1/day
      real(r8), allocatable :: mor_b(:)        ! 1/day
      real(r8), allocatable :: mor_q10(:)      ! nondimensional
      real(r8), allocatable :: mor_t0(:)       ! Celsius
      real(r8), allocatable :: tmin_growth(:)  ! Celsius
      real(r8), allocatable :: srad_cdepth(:)  ! Watts/m2
      real(r8), allocatable :: wdino(:)        ! m/day
!
!  Mid-day of each month (YearDay = 0 for Jan 1, 00:00:00).
!
      real(dp), dimension(12) :: month_midday =                         &
     &          (/ 15.5_dp,  45.0_dp,  74.5_dp, 105.0_dp,               &
     &            135.5_dp, 166.0_dp, 196.5_dp, 227.5_dp,               &
     &            258.0_dp, 288.5_dp, 319.0_dp, 349.5_dp /)
!
! Monthly median germination potential.
!
      real(r8), dimension(12) :: gp =                                   &
     &          (/ 21.90_r8, 11.25_r8, 78.0_r8, 85.0_r8,                &
     &             96.8_r8,  93.0_r8,  60.0_r8, 50.0_r8,                &
     &             10.0_r8,  11.5_r8,  17.0_r8, 34.5_r8 /)
!
! Normalized montly mean germination potential.
!
      real(r8), dimension(12) :: gpn
!
      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
 
      real(r8) :: gpmax
!
!-----------------------------------------------------------------------
!  Set number of biological tracers.
!-----------------------------------------------------------------------
!
      nbt=1
!
!-----------------------------------------------------------------------
!  Allocate various module variables.
!-----------------------------------------------------------------------
!
      IF (.not.allocated(bioiter)) THEN
        allocate ( bioiter(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(atts)) THEN
        allocate ( atts(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(attw)) THEN
        allocate ( attw(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(din_cdepth)) THEN
        allocate ( din_cdepth(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(dg)) THEN
        allocate ( dg(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(e_dark)) THEN
        allocate ( e_dark(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(e_light)) THEN
        allocate ( e_light(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(gmax)) THEN
        allocate ( gmax(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(g_eff)) THEN
        allocate ( g_eff(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(g_r)) THEN
        allocate ( g_r(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(kn)) THEN
        allocate ( kn(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(tmin_growth)) THEN
        allocate ( tmin_growth(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(srad_cdepth)) THEN
        allocate ( srad_cdepth(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(wdino)) THEN
        allocate ( wdino(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(mor_a)) THEN
        allocate ( mor_a(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(mor_b)) THEN
        allocate ( mor_b(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(mor_q10)) THEN
        allocate ( mor_q10(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
      IF (.not.allocated(mor_t0)) THEN
        allocate ( mor_t0(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
 
#ifdef TANGENT
      IF (.not.allocated(tl_wdino)) THEN
        allocate ( tl_wdino(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
 
#ifdef ADJOINT
      IF (.not.allocated(ad_wdino)) THEN
        allocate ( ad_wdino(ngrids) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
#endif
!
!  Allocate biological tracer vector.
!
      IF (.not.allocated(idbio)) THEN
        allocate ( idbio(nbt) )
        dmem(1)=dmem(1)+real(ngrids,r8)
      END IF
!
!-----------------------------------------------------------------------
!  Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
      ic=nat+npt+ncs+nns
      DO i=1,nbt
        idbio(i)=ic+i
      END DO
      idino=ic+1
!
!  Compute normalized montly germination poterntial.
!
      gpmax=maxval(gp)
      DO i=1,12
        gpn(i)=gp(i)/gpmax
      END DO
!
      RETURN
      END SUBROUTINE initialize_biology
 
      END MODULE mod_biology