MODULE mod_biology
!
!git $Id$
!svn $Id: red_tide_mod.h 1151 2023-02-09 03:08:53Z arango $
!================================================== Hernan G. Arango ===
! Copyright (c) 2002-2023 The ROMS/TOMS 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