!
!svn $Id: estuarybgc_mod.h 2232 2012-01-03 18:55:20Z arango $
!================================================== Hernan G. Arango ===
! Copyright (c) 2002-2012 The ROMS/TOMS Group !
! Licensed under a MIT/X style license !
! See License_ROMS.txt !
!=======================================================================
! !
! Parameters for Fennel et al. (2006) model: !
! !
! AttSW Light attenuation due to sea water [1/m]. !
! AttChl Light attenuation by Chlorophyll [1/(mg_Chl m2)]. !
! BioIter Maximum number of iterations to achieve convergence !
! of the nonlinear solution. !
! Chl2C_m Maximum chlorophyll to carbon ratio [mg_Chl/mg_C]. !
! ChlMin Chlorophill minimum threshold value [mg_Chl/m3]. !
! CoagR Coagulation rate: agregation rate of SDeN + Phyt ==> LDeN !
! [1/day]. !
! D_p5NH4 Half-saturation radiation for nitrification inhibition !
! [Watts/m2]. !
! I_thNH4 Radiation threshold for nitrification inhibition !
! [Watts/m2]. !
! K_NH4 Inverse half-saturation for Phytoplankton NH4 uptake !
! [m3/(mmol_N)]. !
! K_NO3 Inverse half-saturation for Phytoplankton NO3 uptake !
! [m3/(mmol_N)]. !
! K_Phy Zooplankton half-saturation, squared constant for !
! ingestion [mmol_N/m3]^2. !
! LDeRR Large Detrital re-mineralization rate [1/day]. !
! NitriR Nitrification rate: oxidation of NH4 to NO3 [1/day]. !
! PARfrac Fraction of shortwave radiation that is available for !
! photosyntesis [nondimensional]. !
! PhyCN Phytoplankton Carbon:Nitrogen ratio [mol_C/mol_N]. !
! PhyIP Phytoplankton NH4 inhibition parameter [1/(mmol_N)]. !
! PhyIS Phytoplankton, initial slope of the P-I curve !
! [mg_C/(mg_Chl W m-2 day)]. !
! ZooMin Phytoplankton minimum threshold value [mmol_N/m3]. !
! PhyMR Phytoplankton mortality rate [1/day] to small detritus. !
! SDeAR Small detritus aggregation rate into Large detritus !
! [1/day]. !
! SDeBR Small Detrital breakdown to NH4 rate [1/day]. !
! SDeRR Large Detrital re-mineralization rate [1/day]. !
! Vp0 Eppley temperature-limited and light-limited growth !
! tuning parameter [nondimensional]. !
! wLDet Vertical sinking velocities for Large Detritus !
! fraction [m/day]. !
! wPhy Vertical sinking velocity for Phytoplankton !
! fraction [m/day]. !
! wSDet Vertical sinking velocities for Small Detritus !
! fraction [m/day]. !
! ZooAE_N Zooplankton nitrogen assimilation efficiency fraction !
! [nondimensional]. !
! ZooBM Zooplankton basal metabolism [1/day]. !
! ZooCN Zooplankton Carbon:Nitrogen ratio [mol_C/mol_N]. !
! ZooER Zooplankton specific excretion rate [1/day]. !
! ZooGR Zooplankton maximum growth rate [1/day]. !
! ZooMin Zooplankton minimum threshold value [mmol_N/m3]. !
! ZooMR Zooplankton mortality to Detritus [1/day]. !
! pCO2air CO2 partial pressure in the air [ppmv]. !
#ifdef SPECTRAL_LIGHT
! SIGATRB NAP absorb. cross section at 440 nm [meter2 gram-1]. !
! STRB Spectral slope of NAP absorption !
! BLTRB Baseline NAP absorption [meter2 gram-1]. !
! SIGBTRB Scattering cross section of turbidity [meter2 gram-1]. !
! ETASPEC Scattering spectral exponent. !
! BB2B Particulate backscattering ratio. !
! Ndom Number of dissolved matter constituents. !
#endif
! !
!=======================================================================
!
USE mod_param
USE mod_scalars
!
implicit none
!
! Set biological tracer identification indices.
!
integer, allocatable :: idbio(:) ! Biological tracers
integer :: iNO3_ ! Nitrate concentration
integer :: iNH4_ ! Ammonium concentration
integer :: iChlo ! Chlorophyll concentration
integer :: iPhyt ! Phytoplankton concentration
integer :: iZoop ! Zooplankton concentration
integer :: iLDeN ! Large detritus N-concentration
integer :: iSDeN ! Small detritus N-concentration
#ifdef CARBON
integer :: iLDeC ! Large detritus C-concentration
integer :: iSDeC ! Small detritus C-concentration
integer :: iTIC_ ! Total inorganic carbon
integer :: iTAlk ! Total alkalinity
#endif
#ifdef OXYGEN
integer :: iOxyg ! Dissolved oxygen concentration
#endif
#ifdef SPECTRAL_LIGHT
integer :: idPARo ! PAR Photosynthetically Available Radiation (PAR)
integer :: idPARs ! PARs Spectral PAR
integer :: idSpKd ! SpKd Spectral Attenuation
#endif
#ifdef SAV_BIOMASS
integer :: iddinw ! DINwcr Dissolved Inorganic Nitrogen (water column)
integer :: iddins ! DINsed Dissolved Inorganic Nitrogen (sediment column)
integer :: iddowc ! DOwcr Dissolved Oxygen (water column)
integer :: idwsvl ! DINwcr_sav Dissolved Inorganic N in water column due to SAV
integer :: idsagb ! AGB Above ground biomass
integer :: idsbgb ! BGB Below ground biomass
integer :: idsvpp ! PP
integer :: idsvam ! AGM
integer :: idsgar ! AGAR
integer :: idsvbr ! AGBR
integer :: idsvrs ! SEARS
integer :: idsvbg ! AGBG
integer :: idsvag ! BGAG
integer :: idsbgr ! BGR
integer :: idsbgm ! BGM
#endif
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
! Biological 2D diagnostic variable IDs.
!
integer, allocatable :: iDbio2(:) ! 2D biological terms
integer :: iCOfx ! air-sea CO2 flux
integer :: iDNIT ! denitrification flux
integer :: ipCO2 ! partial pressure of CO2
integer :: iO2fx ! air-sea O2 flux
!
! Biological 3D diagnostic variable IDs.
!
integer, allocatable :: iDbio3(:) ! 3D biological terms
integer :: iPPro = 1 ! primary productivity
integer :: iNO3u = 2 ! NO3 uptake
#endif
!
! Biological parameters.
!
integer, allocatable :: BioIter(:)
real(r8), allocatable :: AttSW(:) ! 1/m
real(r8), allocatable :: AttChl(:) ! 1/(mg_Chl m2)
real(r8), allocatable :: Chl2C_m(:) ! mg_Chl/mg_C
real(r8), allocatable :: ChlMin(:) ! mg_Chl/m3
real(r8), allocatable :: CoagR(:) ! 1/day
real(r8), allocatable :: D_p5NH4(:) ! Watts/m2
real(r8), allocatable :: I_thNH4(:) ! Watts/m2
real(r8), allocatable :: K_NH4(:) ! m3/mmol_N
real(r8), allocatable :: K_NO3(:) ! m3/mmol_N
real(r8), allocatable :: K_Phy(:) ! (mmol_N/m3)^2
real(r8), allocatable :: LDeRRN(:) ! 1/day
real(r8), allocatable :: LDeRRC(:) ! 1/day
real(r8), allocatable :: NitriR(:) ! 1/day
real(r8), allocatable :: PARfrac(:) ! nondimensional
real(r8), allocatable :: PhyCN(:) ! mol_C/mol_N
real(r8), allocatable :: PhyIP(:) ! 1/mmol_N
real(r8), allocatable :: PhyIS(:) ! 1/(Watts m-2 day)
real(r8), allocatable :: PhyMin(:) ! mmol_N/m3
real(r8), allocatable :: PhyMR(:) ! 1/day
real(r8), allocatable :: SDeAR(:) ! 1/day
real(r8), allocatable :: SDeBR(:) ! 1/day
real(r8), allocatable :: SDeRRN(:) ! 1/day
real(r8), allocatable :: SDeRRC(:) ! 1/day
real(r8), allocatable :: Vp0(:) ! nondimensional
real(r8), allocatable :: wLDet(:) ! m/day
real(r8), allocatable :: wPhy(:) ! m/day
real(r8), allocatable :: wSDet(:) ! m/day
real(r8), allocatable :: ZooAE_N(:) ! nondimensional
real(r8), allocatable :: ZooBM(:) ! 1/day
real(r8), allocatable :: ZooCN(:) ! mol_C/mol_N
real(r8), allocatable :: ZooER(:) ! 1/day
real(r8), allocatable :: ZooGR(:) ! 1/day
real(r8), allocatable :: ZooMin(:) ! mmol_N/m3
real(r8), allocatable :: ZooMR(:) ! 1/day
real(r8), allocatable :: pCO2air(:) ! ppmv
#ifdef SPECTRAL_LIGHT
integer, parameter :: NBands = 60 ! spectral bands
! Spectral band width used in light calculations.
real(r8), parameter :: DLAM = 5.0_r8
integer, parameter :: Nphy = 1 ! Phytoplankton groups
integer, parameter :: Npig = 1 ! Pigments
real(r8), dimension(NBands) :: wavedp ! a and b factor
# ifdef CDOM_VARIABLE
integer, parameter :: Ndom = 2 ! DOM constituents
integer, allocatable :: iCDMC(:) ! Color degradational matter
integer, parameter :: ilab=1 ! labile index for DOC.
integer, parameter :: irct=2 ! relict index for DOC.
character (len=11), dimension(Ndom) :: DomName
# endif
real(r8), allocatable :: SIGATRB(:)
real(r8), allocatable :: STRB(:)
real(r8), allocatable :: BLTRB(:)
real(r8), allocatable :: SIGBTRB(:)
real(r8), allocatable :: ETASPEC(:)
real(r8), allocatable :: BB2B(:)
#endif
#ifdef SAV_BIOMASS
integer, allocatable :: GMODopt(:)
real(r8), allocatable :: KNSED(:)
real(r8), allocatable :: KNWC(:)
real(r8), allocatable :: TOPT(:)
real(r8), allocatable :: THTA(:)
real(r8), allocatable :: THTA2(:)
real(r8), allocatable :: SCL(:)
real(r8), allocatable :: SCL2(:)
real(r8), allocatable :: KI(:)
real(r8), allocatable :: SR(:)
real(r8), allocatable :: LMBAMX(:)
real(r8), allocatable :: KMAG(:)
real(r8), allocatable :: ARSC(:)
real(r8), allocatable :: ARC(:)
real(r8), allocatable :: BSRC(:)
real(r8), allocatable :: RC(:)
real(r8), allocatable :: RTStTL(:)
real(r8), allocatable :: DOWNt(:)
real(r8), allocatable :: TRNS(:)
real(r8), allocatable :: TCRIT(:)
real(r8), allocatable :: KM(:)
#endif
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
#ifdef SPECTRAL_LIGHT
integer :: iband
#endif
!
!-----------------------------------------------------------------------
! Determine number of biological tracers.
!-----------------------------------------------------------------------
!
#ifdef CARBON
# ifdef OXYGEN
NBT=12
# else
NBT=11
# endif
#else
# ifdef OXYGEN
NBT=8
# else
NBT=7
# endif
#endif
# ifdef CDOM_VARIABLE
NBT=NBT+Ndom
# endif
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
!-----------------------------------------------------------------------
! Set sources and sinks biology diagnostic parameters.
!-----------------------------------------------------------------------
!
! Set number of diagnostics terms.
!
NDbio3d=2
NDbio2d=0
# ifdef DENITRIFICATION
NDbio2d=NDbio2d+1
# endif
# ifdef CARBON
NDbio2d=NDbio2d+2
# endif
# ifdef OXYGEN
NDbio2d=NDbio2d+1
# endif
!
! Initialize biology diagnostic indices.
!
ic=0
# ifdef DENITRIFICATION
iDNIT=ic+1
ic=ic+1
# endif
# ifdef CARBON
iCOfx=ic+1
ipCO2=ic+2
ic=ic+2
# endif
# ifdef OXYGEN
iO2fx=ic+1
# endif
#endif
!
!-----------------------------------------------------------------------
! Allocate various module variables.
!-----------------------------------------------------------------------
!
IF (.not.allocated(BioIter)) THEN
allocate ( BioIter(Ngrids) )
END IF
IF (.not.allocated(AttSW)) THEN
allocate ( AttSW(Ngrids) )
END IF
IF (.not.allocated(AttChl)) THEN
allocate ( AttChl(Ngrids) )
END IF
IF (.not.allocated(Chl2C_m)) THEN
allocate ( Chl2C_m(Ngrids) )
END IF
IF (.not.allocated(ChlMin)) THEN
allocate ( ChlMin(Ngrids) )
END IF
IF (.not.allocated(CoagR)) THEN
allocate ( CoagR(Ngrids) )
END IF
IF (.not.allocated(D_p5NH4)) THEN
allocate ( D_p5NH4(Ngrids) )
END IF
IF (.not.allocated(I_thNH4)) THEN
allocate ( I_thNH4(Ngrids) )
END IF
IF (.not.allocated(K_NH4)) THEN
allocate ( K_NH4(Ngrids) )
END IF
IF (.not.allocated(K_NO3)) THEN
allocate ( K_NO3(Ngrids) )
END IF
IF (.not.allocated(K_Phy)) THEN
allocate ( K_Phy(Ngrids) )
END IF
IF (.not.allocated(LDeRRN)) THEN
allocate ( LDeRRN(Ngrids) )
END IF
IF (.not.allocated(LDeRRC)) THEN
allocate ( LDeRRC(Ngrids) )
END IF
IF (.not.allocated(NitriR)) THEN
allocate ( NitriR(Ngrids) )
END IF
IF (.not.allocated(PARfrac)) THEN
allocate ( PARfrac(Ngrids) )
END IF
IF (.not.allocated(PhyCN)) THEN
allocate ( PhyCN(Ngrids) )
END IF
IF (.not.allocated(PhyIP)) THEN
allocate ( PhyIP(Ngrids) )
END IF
IF (.not.allocated(PhyIS)) THEN
allocate ( PhyIS(Ngrids) )
END IF
IF (.not.allocated(PhyMin)) THEN
allocate ( PhyMin(Ngrids) )
END IF
IF (.not.allocated(PhyMR)) THEN
allocate ( PhyMR(Ngrids) )
END IF
IF (.not.allocated(SDeAR)) THEN
allocate ( SDeAR(Ngrids) )
END IF
IF (.not.allocated(SDeBR)) THEN
allocate ( SDeBR(Ngrids) )
END IF
IF (.not.allocated(SDeRRN)) THEN
allocate ( SDeRRN(Ngrids) )
END IF
IF (.not.allocated(SDeRRC)) THEN
allocate ( SDeRRC(Ngrids) )
END IF
IF (.not.allocated(Vp0)) THEN
allocate ( Vp0(Ngrids) )
END IF
IF (.not.allocated(wLDet)) THEN
allocate ( wLDet(Ngrids) )
END IF
IF (.not.allocated(wPhy)) THEN
allocate ( wPhy(Ngrids) )
END IF
IF (.not.allocated(wSDet)) THEN
allocate ( wSDet(Ngrids) )
END IF
IF (.not.allocated(ZooAE_N)) THEN
allocate ( ZooAE_N(Ngrids) )
END IF
IF (.not.allocated(ZooBM)) THEN
allocate ( ZooBM(Ngrids) )
END IF
IF (.not.allocated(ZooCN)) THEN
allocate ( ZooCN(Ngrids) )
END IF
IF (.not.allocated(ZooER)) THEN
allocate ( ZooER(Ngrids) )
END IF
IF (.not.allocated(ZooGR)) THEN
allocate ( ZooGR(Ngrids) )
END IF
IF (.not.allocated(ZooMin)) THEN
allocate ( ZooMin(Ngrids) )
END IF
IF (.not.allocated(ZooMR)) THEN
allocate ( ZooMR(Ngrids) )
END IF
IF (.not.allocated(pCO2air)) THEN
allocate ( pCO2air(Ngrids) )
END IF
#ifdef SPECTRAL_LIGHT
IF (.not.allocated(SIGATRB)) THEN
allocate ( SIGATRB(Ngrids) )
END IF
IF (.not.allocated(STRB)) THEN
allocate ( STRB(Ngrids) )
END IF
IF (.not.allocated(BLTRB)) THEN
allocate ( BLTRB(Ngrids) )
END IF
IF (.not.allocated(SIGBTRB)) THEN
allocate ( SIGBTRB(Ngrids) )
END IF
IF (.not.allocated(ETASPEC)) THEN
allocate ( ETASPEC(Ngrids) )
END IF
IF (.not.allocated(BB2B)) THEN
allocate ( BB2B(Ngrids) )
END IF
#endif
#ifdef SAV_BIOMASS
IF (.not.allocated(GMODopt)) THEN
allocate ( GMODopt(Ngrids) )
END IF
IF (.not.allocated(KNSED)) THEN
allocate ( KNSED(Ngrids) )
END IF
IF (.not.allocated(KNWC)) THEN
allocate ( KNWC(Ngrids) )
END IF
IF (.not.allocated(TOPT)) THEN
allocate ( TOPT(Ngrids) )
END IF
IF (.not.allocated(THTA)) THEN
allocate ( THTA(Ngrids) )
END IF
IF (.not.allocated(THTA2)) THEN
allocate ( THTA2(Ngrids) )
END IF
IF (.not.allocated(SCL)) THEN
allocate ( SCL(Ngrids) )
END IF
IF (.not.allocated(SCL2)) THEN
allocate ( SCL2(Ngrids) )
END IF
IF (.not.allocated(KI)) THEN
allocate ( KI(Ngrids) )
END IF
IF (.not.allocated(SR)) THEN
allocate ( SR(Ngrids) )
END IF
IF (.not.allocated(LMBAMX)) THEN
allocate ( LMBAMX(Ngrids) )
END IF
IF (.not.allocated(KMAG)) THEN
allocate ( KMAG(Ngrids) )
END IF
IF (.not.allocated(ARSC)) THEN
allocate ( ARSC(Ngrids) )
END IF
IF (.not.allocated(ARC)) THEN
allocate ( ARC(Ngrids) )
END IF
IF (.not.allocated(BSRC)) THEN
allocate ( BSRC(Ngrids) )
END IF
IF (.not.allocated(RC)) THEN
allocate ( RC(Ngrids) )
END IF
IF (.not.allocated(RtStTL)) THEN
allocate (RtStTL(Ngrids) )
END IF
IF (.not.allocated(DOWNt)) THEN
allocate ( DOWNt(Ngrids) )
END IF
IF (.not.allocated(TRNS)) THEN
allocate ( TRNS(Ngrids) )
END IF
IF (.not.allocated(TCRIT)) THEN
allocate ( TCRIT(Ngrids) )
END IF
IF (.not.allocated(KM)) THEN
allocate ( KM(Ngrids) )
END IF
#endif
!
! Allocate biological tracer vector.
!
IF (.not.allocated(idbio)) THEN
allocate ( idbio(NBT) )
END IF
# ifdef CDOM_VARIABLE
IF (.not.allocated(iCDMC)) THEN
allocate ( iCDMC(Ndom) )
END IF
# endif
#if defined DIAGNOSTICS && defined DIAGNOSTICS_BIO
!
! Allocate biological diagnostics vectors
!
IF (.not.allocated(iDbio2)) THEN
allocate ( iDbio2(NDbio2d) )
END IF
IF (.not.allocated(iDbio3)) THEN
allocate ( iDbio3(NDbio3d) )
END IF
#endif
#ifdef SPECTRAL_LIGHT
!
! Spectral dependency for scattering and backscattering.
!
DO iband=1,NBands
wavedp(iband)=(550.0_r8/(397.0_r8+REAL(iband,r8)*DLAM))
END DO
#endif
!
!-----------------------------------------------------------------------
! Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
ic=NAT+NPT+NCS+NNS
DO i=1,NBT
idbio(i)=ic+i
END DO
iNO3_=ic+1
iNH4_=ic+2
iChlo=ic+3
iPhyt=ic+4
iZoop=ic+5
iLDeN=ic+6
iSDeN=ic+7
ic=ic+7
# ifdef CDOM_VARIABLE
DO i=1,Ndom
iCDMC(i)=ic+1
ic=ic+1
END DO
# endif
# ifdef CARBON
iLDeC=ic+1
iSDeC=ic+2
iTIC_=ic+3
iTAlk=ic+4
ic=ic+4
# endif
# ifdef OXYGEN
iOxyg=ic+1
ic=ic+1
# endif
RETURN
END SUBROUTINE initialize_biology
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