!=======================================================================
! Parameters for BEST NPZ Biological Model
! Georgina Gibson
!=======================================================================
USE mod_param
implicit none
!
! Set biological tracer identification indices.
!
integer, allocatable :: idbio(:)! Biological tracers
integer :: iNO3 ! Nitrate
integer :: iNH4 ! Ammonium
integer :: iPhS ! Small Phytoplankton
integer :: iPhL ! Large Phytoplankton
integer :: iMZS ! Small Microzooplankton
integer :: iMZL ! Large Microzooplankton
integer :: iCop ! Small Coastal Copepods
integer :: iNCaS ! Neocalanus
integer :: iEupS ! Euphausiids
integer :: iNCaO ! Neocalanus
integer :: iEupO ! Euphausiids
#ifdef JELLY
integer :: iJel ! Jellfish
#endif
integer :: iDet ! Detritus
integer :: iDetF ! Fast Sinking Detritus
#ifdef BIOFLUX
integer :: iBF
#endif
# ifdef CLIM_ICE_1D
integer :: i1CI
# endif
# ifdef AKT_3D
integer ::iAKt3
# endif
#ifdef IRON_LIMIT
integer :: iFe ! Iron
#endif
#ifdef BENTHIC
integer, pointer :: idben(:) ! Benthic tracers
integer :: iBen
integer :: iBenDet
#endif
#ifdef ICE_BIO
integer, pointer :: idice(:) ! Ice tracers
# ifdef CLIM_ICE_1D
integer, pointer :: idiceLog(:) ! Ice tracers
# endif
integer :: iIcePhL
integer :: iIceNO3
integer :: iIceNH4
integer :: iIceZ
integer :: iIceLog
#endif
#ifdef STATIONARY
integer, pointer :: idbio3(:)
integer :: i3Stat1
integer :: i3Stat2
integer :: i3Stat3
integer :: i3Stat4
integer :: i3Stat5
integer :: i3Stat6
integer :: i3Stat7
integer :: i3Stat8
integer :: i3Stat9
integer :: i3Stat10
integer :: i3Stat11
integer :: i3Stat12
integer :: i3Stat13
integer :: i3Stat14
integer :: i3Stat15
integer :: i3Stat16
#endif
#ifdef STATIONARY2
integer, pointer :: idbio2(:)
integer :: i2Stat1
integer :: i2Stat2
integer :: i2Stat3
integer :: i2Stat4
integer :: i2Stat5
integer :: i2Stat6
integer :: i2Stat7
integer :: i2Stat8
#endif
#ifdef PROD2
integer, pointer :: idbioP2(:)
integer :: iIAPrd
integer :: iBenPrd
integer :: iXPrd
#endif
#ifdef PROD3
integer, pointer :: idbioP3(:)
integer :: iPhSprd ! Small Phytoplankton Production
integer :: iPhLprd ! Large Phytoplankton Production
integer :: iMZSprd ! Small Microzooplankton Production
integer :: iMZLprd ! Large Microzooplankton Production
integer :: iCopPrd ! Copepod production
integer :: iNCaPrd ! Neocalanus production
integer :: iEupPrd ! Euphausiid production
# ifdef JELLY
integer :: iJelPrd ! Jellyfish production
# endif
#endif
#if defined BENTHIC
integer,parameter :: NBEN=2
integer :: MBT
integer, allocatable :: NBeT(:)
#endif
#if defined ICE_BIO
integer, parameter :: NIB=4
integer, allocatable :: NIceT(:)
integer, allocatable :: NIceLog(:)
#endif
#ifdef STATIONARY
!------------------------------------
!3D stationary tracers
!------------------------------------
integer, allocatable :: NTS(:)
integer, parameter :: NBTS = 16
#endif
#ifdef STATIONARY2
!------------------------------------
!2D stationary tracers
!------------------------------------
integer, allocatable :: NTS2(:)
integer, parameter :: NBTS2 = 8
#endif
#ifdef PROD2
!------------------------------------
!2D producrion tracers (stationary)
!------------------------------------
integer, allocatable :: NPT2(:)
integer, parameter :: NBPT2 = 3
#endif
#ifdef PROD3
!------------------------------------
!3D producrion tracers (stationary)
!------------------------------------
integer, allocatable :: NPT3(:)
# if defined JELLY
integer, parameter :: NBPT3 = 8
# else
integer, parameter :: NBPT3 = 7
# endif
#endif
integer, allocatable :: BioIter(:)
real(r8) :: VertMixIncr
real(r8), allocatable :: PARfrac(:) ! nondimensional
! Bio- conversions
real(r8) :: xi, ccr, ccrPhL
! extinction coefficients
real(r8) :: k_ext, k_chl
! PhS growth params
real(r8) :: DiS, DpS, aPS
real(r8) :: alphaPhS
real(r8) :: psiPhS
real(r8) :: k1PhS, k2PhS
! PhL growth params
real(r8) :: DiL, aPL
real(r8) :: DpL
real(r8) :: alphaPhL
real(r8) :: psiPhL
real(r8) :: k1PhL
real(r8) :: k2PhL
! MZS preference params
real(r8) :: fpPhSMZS, fpPhLMZS
! MZS growth and feeding params
real(r8) :: eMZS
real(r8) :: Q10MZS
real(r8) :: Q10MZST
real(r8) :: fMZS
real(r8) :: kMZS
real(r8) :: gammaMZS
! MZL preferences params
real(r8) :: fpPhSMZL, fpPhLMZL, fpMZSMZL
! MZL growth and feeding params
real(r8) :: eMZL
real(r8) :: Q10MZL
real(r8) :: Q10MZLT
real(r8) :: fMZL
real(r8) :: kMZL
real(r8) :: gammaMZL
! Cop preference params
real(r8) :: fpPhSCop, fpPhLCop, fpMZSCop, fpMZLCop
! Cop growth and feeding params
real(r8) :: eCop
real(r8) :: Q10Cop
real(r8) :: Q10CopT
real(r8) :: fCop
real(r8) :: gammaCop
real(r8) :: kCop
! NCa preference params
real(r8) :: fpPhSNCa, fpPhLNCa, fpMZSNCa, fpMZLNCa
! NCa growth and feeding params
real(r8) :: eNCa
real(r8) :: Q10NCa
real(r8) :: Q10NCaT
real(r8) :: fNCa
real(r8) :: gammaNCa
real(r8) :: kNCa
! Eup preference params
real(r8) :: fpPhSEup, fpPhLEup, fpMZSEup, fpMZLEup, fpCopEup
! Eup growth and feeding params
real(r8) :: eEup
real(r8) :: Q10Eup
real(r8) :: Q10EupT
real(r8) :: fEup
real(r8) :: gammaEup
real(r8) :: kEup
#ifdef JELLY
! Jellyfish Parameters
real(r8) :: eJel, gammaJel, fJel
real(r8) :: respJel,mpredJel
real(r8) :: fpCopJel, fpNCaJel, fpEupJel
real(r8) :: Q10Jelr, Q10JelTr,Q10Jele, Q10JelTe
real(r8) :: bmJ,ktbmJ,TrefJ
#endif
! Phytoplankton senescence
real(r8) :: mPhS, maxmPhS, NcritPhS,minmPhS
real(r8) :: mPhL, maxmPhL, NcritPhL, minmPhL
! Zoopkankton mortality
real(r8) :: mMZS, mMZL, mCop, mNCa, mEup
! predation closure
real(r8) :: mpredCop, mpredNCa, mpredEup
real(r8) :: mpredMZS, mpredMZL
! sinking
real(r8) :: wPhS, wPhL, wDet, wDetF
! Terms to define the Iron climatology field
real(r8) :: Feinlo, Feinhi, Feinh, Feofflo, Feoffhi, Feoffh
! Terms to define respiration
real(r8) :: respPhS, respPhL, respMZS, respMZL
real(r8) :: respCop, respNCa, respEup
real(r8) :: TmaxPhS,TminPhS, Topt_PhS, KtBm_PhS
real(r8) :: TmaxPhL, TminPhL, Topt_PhL, KtBm_PhL
real(r8) :: TmaxMZS, KtBm_MZS, TmaxMZL, KtBm_MZL
real(r8) :: ktbmC,TrefC
real(r8) :: ktbmN,TrefN
real(r8) :: ktbmE,TrefE
! Detrital Remineralization and Nitrification
real(r8) :: regen, dgrad
real(r8) :: Pv0, PvT
real(r8) :: KnT, Nitr0,ToptNtr,ktntr,KNH4Nit
real(r8) :: tI0,KI
! Iron limitation terms
real(r8) :: kfePhS, kfePhL, FeC
! Diapause
real(r8) :: NCmaxz
real(r8) :: wNCrise,wNCsink
real(r8) :: RiseStart, RiseEnd, SinkStart, SinkEnd
#ifdef BENTHIC
real(r8) :: bmB,ktbmB,TrefB
real(r8) :: iremin
real(r8) :: q10,q10r
real(r8) :: Rup,KupP,LupD, LupP,KupD
real(r8) :: Qres,Rres,rmort,eex,eexD,BenPred
real(r8) :: prefD,prefPS,prefPL,T0ben,T0benr
#endif
#ifdef ICE_BIO
real(r8) :: alphaIb, betaI, inhib
real(r8) :: ksnut1,ksnut2,mu0, R0i
real(r8) :: rg0,rg,annit
real(r8) :: aidz
#endif
!#if defined BIOFLUX
! real(r8), dimension(NAT+NBT,NAT+NBT) :: bflx
!#endif
#ifdef BIOFLUX
integer, allocatable :: idTBFvar(:) ! 3D Stationary variables
integer, allocatable :: avgTBFid(:,:) ! averages stationary tracer IDs
#endif
#ifdef STATIONARY
integer, allocatable :: idTSvar(:) ! 3D Stationary variables
integer, allocatable :: hisTSid(:,:) ! history St tracer IDs
integer, allocatable :: avgTSid(:,:) ! averages stationary tracer IDs
#endif
#ifdef STATIONARY2
integer, allocatable :: idTS2var(:) ! 2D Stationary variables
integer, allocatable :: hisTS2id(:,:) ! history St tracer IDs
integer, allocatable :: avgTS2id(:,:) ! averages stationary tracer IDs
#endif
#ifdef PROD3
integer, allocatable :: idPT3var(:) ! 3D production variables
integer, allocatable :: hisPT3id(:,:) ! history St tracer IDs
integer, allocatable :: avgPT3id(:,:) ! averages stationary tracer IDs
#endif
#ifdef PROD2
integer, allocatable :: idPT2var(:) ! 2D production variables
integer, allocatable :: hisPT2id(:,:) ! history St tracer IDs
integer, allocatable :: avgPT2id(:,:) ! averages stationary tracer IDs
#endif
#if defined BENTHIC
integer, allocatable :: idBeTvar(:)
integer, allocatable :: hisBid(:,:)
integer, allocatable :: avgBid(:,:)
integer, allocatable :: rstBid(:,:)
#endif
#if defined ICE_BIO
# if defined CLIM_ICE_1D
integer, allocatable :: idIceBvar(:)
integer, allocatable :: hisIceBid(:,:)
integer, allocatable :: rstIceBid(:,:)
integer, allocatable :: avgIceBid(:,:)
integer, allocatable :: idIceLogvar(:)
# elif defined BERING_10K
integer :: idIcePhL
integer :: idIceNO3
integer :: idIceNH4
integer :: idIceLog
integer :: idIcePhLbc(4) ! ice algae boundary conditions
integer :: idIceNO3bc(4) ! ice nitrate boundary conditions
integer :: idIceNH4bc(4) ! ice ammonium boundary conditions
integer :: idIceLogbc(4) ! ice switch boundary conditions
# endif
#endif
CONTAINS
SUBROUTINE initialize_biology
!
!=======================================================================
! !
! This routine sets several variables needed by the biology model. !
! It allocates and assigns biological tracers indices. !
! !
!=======================================================================
USE mod_param
!
! Local variable declarations
!
integer :: i, ic, ng
!
!-----------------------------------------------------------------------
! Determine number of biological tracers.
!-----------------------------------------------------------------------
!
#if defined JELLY
# if defined IRON_LIMIT
NBT = 15
# else
NBT = 14
# endif
#else
# if defined IRON_LIMIT
NBT = 14
# else
NBT = 13
# endif
#endif
!-----------------------------------------------------------------------
! Allocate various module variables.
!-----------------------------------------------------------------------
IF (.not.allocated(BioIter)) THEN
allocate ( BioIter(Ngrids) )
END IF
IF (.not.allocated(Parfrac)) THEN
allocate ( Parfrac(Ngrids) )
END IF
#ifdef BENTHIC
IF (.not.allocated(NBeT)) THEN
allocate ( NBeT(Ngrids) )
END IF
#endif
#ifdef ICE_BIO
IF (.not.allocated(NIceT)) THEN
allocate ( NIceT(Ngrids) )
END IF
IF (.not.allocated(NIceLog)) THEN
allocate ( NIceLog(Ngrids) )
END IF
#endif
#ifdef STATIONARY
IF (.not.allocated(NTS)) THEN
allocate ( NTS(Ngrids) )
END IF
#endif
#ifdef STATIONARY2
IF (.not.allocated(NTS2)) THEN
allocate ( NTS2(Ngrids) )
END IF
#endif
#ifdef PROD2
IF (.not.allocated(NPT2)) THEN
allocate ( NPT2(Ngrids) )
END IF
#endif
#ifdef PROD3
IF (.not.allocated(NPT3)) THEN
allocate ( NPT3(Ngrids) )
END IF
#endif
!
!-----------------------------------------------------------------------
! Set sources and sinks biology diagnostic parameters.
!-----------------------------------------------------------------------
!
! Set number of diagnostics terms.
!
#ifdef STATIONARY
allocate ( idTSvar(NBTS) )
allocate ( hisTSid(NBTS,Ngrids) )
allocate ( avgTSid(NBTS,Ngrids) )
#endif
#ifdef STATIONARY2
allocate ( idTS2var(NBTS2) )
allocate ( hisTS2id(NBTS2,Ngrids) )
allocate ( avgTS2id(NBTS2,Ngrids) )
#endif
#ifdef PROD2
allocate ( idPT2var(NBPT2) )
allocate ( hisPT2id(NBPT2,Ngrids) )
allocate ( avgPT2id(NBPT2,Ngrids) )
#endif
#ifdef PROD3
allocate ( idPT3var(NBPT3) )
allocate ( hisPT3id(NBPT3,Ngrids) )
allocate ( avgPT3id(NBPT3,Ngrids) )
#endif
#if defined BENTHIC
allocate ( idBeTvar(NBEN) )
allocate ( hisBid(NBEN,Ngrids) )
allocate ( avgBid(NBEN,Ngrids) )
allocate ( rstBid(NBEN,Ngrids) )
#endif
#if defined ICE_BIO
# ifdef CLIM_ICE_1D
allocate ( idIceBvar(NIB) )
allocate ( idIceLogvar(1) )
allocate ( hisIceBid(NIB,Ngrids) )
allocate ( rstIceBid(NIB,Ngrids) )
allocate ( avgIceBid(NIB,Ngrids) )
# endif
#endif
#if defined BIOFLUX
allocate ( idTBFvar(1) )
allocate ( avgTBFid(1,Ngrids) )
#endif
!
!-----------------------------------------------------------------------
! Initialize tracer identification indices.
!-----------------------------------------------------------------------
!
! Allocate biological tracer vector.
!
IF (.not.allocated(idbio)) THEN
allocate ( idbio(NBT) )
END IF
#ifdef STATIONARY
allocate ( idbio3(NBTS) )
#endif
#ifdef STATIONARY2
allocate ( idbio2(NBTS2) )
#endif
#ifdef PROD2
allocate ( idbioP2(NBPT2) )
#endif
#ifdef PROD3
allocate ( idbioP3(NBPT3) )
#endif
#ifdef BENTHIC
allocate ( idben(NBEN) )
#endif
#ifdef ICE_BIO
allocate ( idice(NIB) )
# ifdef CLIM_ICE_1D
allocate ( idiceLog(1) )
# endif
#endif
!
! Set identification indices.
!
ic=NAT+NPT+NCS+NNS
DO i=1,NBT
idbio(i)=ic+i
END DO
iNO3=ic+1
iNH4=ic+2
iPhS=ic+3
iPhL=ic+4
iMZS=ic+5
iMZL=ic+6
iCop=ic+7
iNCaS=ic+8
iEupS=ic+9
iNCaO=ic+10
iEupO=ic+11
iDet=ic+12
iDetF=ic+13
#ifdef JELLY
iJel=ic+14
ic=ic+14
#else
ic=ic+13
#endif
#ifdef IRON_LIMIT
iFe=ic+1
ic=ic+1
#endif
# ifdef CLIM_ICE_1D
i1CI=ic+1
ic=ic+1
# endif
# ifdef AKT_3D
iAKt3=ic+1
ic=ic+1
# endif
#ifdef BIOFLUX
iBF=1
#endif
#ifdef STATIONARY
DO i=1,NBTS
idbio3(i)=i
END DO
i3Stat1 = 1
i3Stat2 = 2
i3Stat3 = 3
i3Stat4 = 4
i3Stat5 = 5
i3Stat6 = 6
i3Stat7 = 7
i3Stat8 = 8
i3Stat9 = 9
i3Stat10 = 10
i3Stat11 = 11
i3Stat12 = 12
i3Stat13 = 13
i3Stat14 = 14
i3Stat15 = 15
i3Stat16 = 16
#endif
#ifdef STATIONARY2
DO i=1,NBTS2
idbio2(i)=i
END DO
i2Stat1 = 1
i2Stat2 = 2
i2Stat3 = 3
i2Stat4 = 4
i2Stat5 = 5
i2Stat6 = 6
i2Stat7 = 7
i2Stat8 = 8
#endif
#ifdef PROD3
DO i=1,NBPT3
idbioP3(i)=ic+i
END DO
iPhSprd = 1
iPhLprd = 2
iMZSprd = 3
iMZLprd = 4
iCopPrd = 5
iNCaPrd = 6
iEupPrd = 7
# ifdef JELLY
iJelPrd = 8
# endif
#endif
#ifdef PROD2
DO i=1,NBPT2
idbioP2(i)=ic+i
END DO
iBenPrd = 1
iIAPrd = 2
iXPrd = 3
#endif
#ifdef BENTHIC
DO i=1,NBEN
idben(i)=i
END DO
iBen=1
iBenDet=2
#endif
#ifdef ICE_BIO
DO i=1,NIB
idice(i)=i
END DO
# ifdef CLIM_ICE_1D
iIceLog=1
iIcePhL=1
iIceNO3=2
iIceNH4=3
iIceZ=4
# elif defined BERING_10K
iIcePhL=1
iIceNO3=2
iIceNH4=3
# endif
#endif
!---------------------------------------------
!Adding stationary and production tracers to model
!---------------------------------------------
#ifdef STATIONARY
DO ng=1,Ngrids
NTS(ng) = NBTS
END DO
#endif
#ifdef STATIONARY2
DO ng=1,Ngrids
NTS2(ng) = NBTS2
END DO
#endif
#ifdef PROD2
DO ng=1,Ngrids
NPT2(ng) = NBPT2
END DO
#endif
#ifdef PROD3
DO ng=1,Ngrids
NPT3(ng) = NBPT3
END DO
#endif
#ifdef BENTHIC
DO ng=1,Ngrids
NBeT(ng) =NBEN
END DO
#endif
#ifdef ICE_BIO
DO ng=1,Ngrids
NIceT(ng) =NIB
NIceLog(ng) =1
END DO
# endif
RETURN
END SUBROUTINE initialize_biology
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