#include "cppdefs.h" MODULE p4zlim !!====================================================================== !! *** MODULE p4zlim *** !! TOP : PISCES !!====================================================================== !! History : 1.0 ! 2004 (O. Aumont) Original code !! 2.0 ! 2007-12 (C. Ethe, G. Madec) F90 !! 3.4 ! 2011-04 (O. Aumont, C. Ethe) Limitation for iron modelled in quota !!---------------------------------------------------------------------- #if defined key_pisces !! p4z_lim : Compute the nutrients limitation terms !! p4z_lim_init : Read the namelist !!---------------------------------------------------------------------- USE sms_pisces ! PISCES variables ! USE iom ! I/O manager IMPLICIT NONE PRIVATE PUBLIC p4z_lim PUBLIC p4z_lim_init PUBLIC p4z_lim_alloc !!* Substitution # include "ocean2pisces.h90" # include "top_substitute.h90" !! * Shared module variables REAL(wp), PUBLIC :: concnno3 !: NO3, PO4 half saturation REAL(wp), PUBLIC :: concdno3 !: Phosphate half saturation for diatoms REAL(wp), PUBLIC :: concnnh4 !: NH4 half saturation for phyto REAL(wp), PUBLIC :: concdnh4 !: NH4 half saturation for diatoms REAL(wp), PUBLIC :: concnfer !: Iron half saturation for nanophyto REAL(wp), PUBLIC :: concdfer !: Iron half saturation for diatoms REAL(wp), PUBLIC :: concbno3 !: NO3 half saturation for bacteria REAL(wp), PUBLIC :: concbnh4 !: NH4 half saturation for bacteria REAL(wp), PUBLIC :: xsizedia !: Minimum size criteria for diatoms REAL(wp), PUBLIC :: xsizephy !: Minimum size criteria for nanophyto REAL(wp), PUBLIC :: xsizern !: Size ratio for nanophytoplankton REAL(wp), PUBLIC :: xsizerd !: Size ratio for diatoms REAL(wp), PUBLIC :: xksi1 !: half saturation constant for Si uptake REAL(wp), PUBLIC :: xksi2 !: half saturation constant for Si/C REAL(wp), PUBLIC :: xkdoc !: 2nd half-sat. of DOC remineralization REAL(wp), PUBLIC :: concbfe !: Fe half saturation for bacteria REAL(wp), PUBLIC :: oxymin !: half saturation constant for anoxia REAL(wp), PUBLIC :: qnfelim !: optimal Fe quota for nanophyto REAL(wp), PUBLIC :: qdfelim !: optimal Fe quota for diatoms REAL(wp), PUBLIC :: caco3r !: mean rainratio !!* Phytoplankton limitation terms REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xnanono3 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xdiatno3 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xnanonh4 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xdiatnh4 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xnanopo4 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xdiatpo4 !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimphy !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimdia !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimnfe !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimdfe !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimsi !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimbac !: ?? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: xlimbacl !: ?? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: concdfe !: ??? REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: concnfe !: ??? ! Coefficient for iron limitation REAL(wp) :: xcoef1 = 0.0016 / 55.85 REAL(wp) :: xcoef2 = 1.21E-5 * 14. / 55.85 / 7.625 * 0.5 * 1.5 REAL(wp) :: xcoef3 = 1.15E-4 * 14. / 55.85 / 7.625 * 0.5 !!---------------------------------------------------------------------- !! NEMO/TOP 4.0 , NEMO Consortium (2018) !! $Id: p4zlim.F90 10069 2018-08-28 14:12:24Z nicolasmartin $ !! Software governed by the CeCILL license (see ./LICENSE) !!---------------------------------------------------------------------- CONTAINS SUBROUTINE p4z_lim( kt, knt ) !!--------------------------------------------------------------------- !! *** ROUTINE p4z_lim *** !! !! ** Purpose : Compute the co-limitations by the various nutrients !! for the various phytoplankton species !! !! ** Method : - ??? !!--------------------------------------------------------------------- INTEGER, INTENT(in) :: kt, knt ! INTEGER :: ji, jj, jk REAL(wp) :: zlim1, zlim2, zlim3, zlim4, zno3, zferlim REAL(wp) :: zconcd, zconcd2, zconcn, zconcn2 REAL(wp) :: z1_trbdia, z1_trbphy, ztem1, ztem2, zetot1, zetot2 REAL(wp) :: zdenom, zratio, zironmin REAL(wp) :: zconc1d, zconc1dnh4, zconc0n, zconc0nnh4 !!--------------------------------------------------------------------- ! DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! Tuning of the iron concentration to a minimum level that is set to the detection limit !------------------------------------- zno3 = trb(ji,jj,K,jpno3) / 40.e-6 zferlim = MAX( 3e-11 * zno3 * zno3, 5e-12 ) zferlim = MIN( zferlim, 7e-11 ) trb(ji,jj,K,jpfer) = MAX( trb(ji,jj,K,jpfer), zferlim ) ! Computation of a variable Ks for iron on diatoms taking into account ! that increasing biomass is made of generally bigger cells !------------------------------------------------ zconcd = MAX( 0.e0 , trb(ji,jj,K,jpdia) - xsizedia ) zconcd2 = trb(ji,jj,K,jpdia) - zconcd zconcn = MAX( 0.e0 , trb(ji,jj,K,jpphy) - xsizephy ) zconcn2 = trb(ji,jj,K,jpphy) - zconcn z1_trbphy = 1. / ( trb(ji,jj,K,jpphy) + rtrn ) z1_trbdia = 1. / ( trb(ji,jj,K,jpdia) + rtrn ) concdfe(ji,jj,jk) = MAX( concdfer, ( zconcd2 * concdfer + concdfer * xsizerd * zconcd ) * z1_trbdia ) zconc1d = MAX( concdno3, ( zconcd2 * concdno3 + concdno3 * xsizerd * zconcd ) * z1_trbdia ) zconc1dnh4 = MAX( concdnh4, ( zconcd2 * concdnh4 + concdnh4 * xsizerd * zconcd ) * z1_trbdia ) concnfe(ji,jj,jk) = MAX( concnfer, ( zconcn2 * concnfer + concnfer * xsizern * zconcn ) * z1_trbphy ) zconc0n = MAX( concnno3, ( zconcn2 * concnno3 + concnno3 * xsizern * zconcn ) * z1_trbphy ) zconc0nnh4 = MAX( concnnh4, ( zconcn2 * concnnh4 + concnnh4 * xsizern * zconcn ) * z1_trbphy ) ! Michaelis-Menten Limitation term for nutrients Small bacteria ! ------------------------------------------------------------- zdenom = 1. / ( concbno3 * concbnh4 + concbnh4 * trb(ji,jj,K,jpno3) & & + concbno3 * trb(ji,jj,K,jpnh4) ) xnanono3(ji,jj,jk) = trb(ji,jj,K,jpno3) * concbnh4 * zdenom xnanonh4(ji,jj,jk) = trb(ji,jj,K,jpnh4) * concbno3 * zdenom ! zlim1 = xnanono3(ji,jj,jk) + xnanonh4(ji,jj,jk) zlim2 = trb(ji,jj,K,jppo4) / ( trb(ji,jj,K,jppo4) + concbnh4 ) zlim3 = trb(ji,jj,K,jpfer) / ( concbfe + trb(ji,jj,K,jpfer) ) zlim4 = trb(ji,jj,K,jpdoc) / ( xkdoc + trb(ji,jj,K,jpdoc) ) xlimbacl(ji,jj,jk) = MIN( zlim1, zlim2, zlim3 ) xlimbac (ji,jj,jk) = MIN( zlim1, zlim2, zlim3 ) * zlim4 ! Michaelis-Menten Limitation term for nutrients Small flagellates ! ----------------------------------------------- zdenom = 1. / ( zconc0n * zconc0nnh4 + zconc0nnh4 * trb(ji,jj,K,jpno3)& & + zconc0n * trb(ji,jj,K,jpnh4) ) xnanono3(ji,jj,jk) = trb(ji,jj,K,jpno3) * zconc0nnh4 * zdenom xnanonh4(ji,jj,jk) = trb(ji,jj,K,jpnh4) * zconc0n * zdenom ! zlim1 = xnanono3(ji,jj,jk) + xnanonh4(ji,jj,jk) zlim2 = trb(ji,jj,K,jppo4) / ( trb(ji,jj,K,jppo4) + zconc0nnh4 ) zratio = trb(ji,jj,K,jpnfe) * z1_trbphy zironmin = xcoef1 * trb(ji,jj,K,jpnch) * z1_trbphy & & + xcoef2 * zlim1 + xcoef3 * xnanono3(ji,jj,jk) zlim3 = MAX( 0.,( zratio - zironmin ) / qnfelim ) xnanopo4(ji,jj,jk) = zlim2 xlimnfe (ji,jj,jk) = MIN( 1., zlim3 ) xlimphy (ji,jj,jk) = MIN( zlim1, zlim2, zlim3 ) ! ! Michaelis-Menten Limitation term for nutrients Diatoms ! ---------------------------------------------- zdenom = 1. / ( zconc1d * zconc1dnh4 + zconc1dnh4 * trb(ji,jj,K,jpno3) & & + zconc1d * trb(ji,jj,K,jpnh4) ) xdiatno3(ji,jj,jk) = trb(ji,jj,K,jpno3) * zconc1dnh4 * zdenom xdiatnh4(ji,jj,jk) = trb(ji,jj,K,jpnh4) * zconc1d * zdenom ! zlim1 = xdiatno3(ji,jj,jk) + xdiatnh4(ji,jj,jk) zlim2 = trb(ji,jj,K,jppo4) / ( trb(ji,jj,K,jppo4) + zconc1dnh4 ) zlim3 = trb(ji,jj,K,jpsil) / ( trb(ji,jj,K,jpsil) + xksi(ji,jj) ) zratio = trb(ji,jj,K,jpdfe) * z1_trbdia zironmin = xcoef1 * trb(ji,jj,K,jpdch) * z1_trbdia & & + xcoef2 * zlim1 + xcoef3 * xdiatno3(ji,jj,jk) zlim4 = MAX( 0., ( zratio - zironmin ) / qdfelim ) xdiatpo4(ji,jj,jk) = zlim2 xlimdfe (ji,jj,jk) = MIN( 1., zlim4 ) xlimdia (ji,jj,jk) = MIN( zlim1, zlim2, zlim3, zlim4 ) xlimsi (ji,jj,jk) = MIN( zlim1, zlim2, zlim4 ) END DO END DO END DO ! Compute the fraction of nanophytoplankton that is made of calcifiers ! -------------------------------------------------------------------- DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE zlim1 = ( trb(ji,jj,K,jpno3) * concnnh4 & & + trb(ji,jj,K,jpnh4) * concnno3 ) & & / ( concnno3 * concnnh4 & & + concnnh4 * trb(ji,jj,K,jpno3) & & + concnno3 * trb(ji,jj,K,jpnh4) ) zlim2 = trb(ji,jj,K,jppo4) / ( trb(ji,jj,K,jppo4) + concnnh4 ) zlim3 = trb(ji,jj,K,jpfer) / ( trb(ji,jj,K,jpfer) + 5.E-11 ) ztem1 = MAX( 0., tsn(ji,jj,K,jp_tem) ) ztem2 = tsn(ji,jj,K,jp_tem) - 10. zetot1 = MAX( 0., etot_ndcy(ji,jj,jk) - 1.) / ( 4. + etot_ndcy(ji,jj,jk) ) zetot2 = 30. / ( 30. + etot_ndcy(ji,jj,jk) ) xfracal(ji,jj,jk) = caco3r * MIN( zlim1, zlim2, zlim3 ) & & * ztem1 / ( 0.1 + ztem1 ) & & * MAX( 1., trb(ji,jj,K,jpphy) * 1.e6 / 2. ) & & * zetot1 * zetot2 & & * ( 1. + EXP(-ztem2 * ztem2 / 25. ) ) & & * MIN( 1., 50. / ( hmld(ji,jj) + rtrn ) ) xfracal(ji,jj,jk) = MIN( 0.8 , xfracal(ji,jj,jk) ) xfracal(ji,jj,jk) = MAX( 0.02, xfracal(ji,jj,jk) ) END DO END DO END DO ! DO jk = KRANGE DO jj = JRANGE DO ji = IRANGE ! denitrification factor computed from O2 levels nitrfac(ji,jj,jk) = MAX( 0.e0, 0.4 * ( 6.e-6 - trb(ji,jj,K,jpoxy) ) & & / ( oxymin + trb(ji,jj,K,jpoxy) ) ) nitrfac(ji,jj,jk) = MIN( 1., nitrfac(ji,jj,jk) ) ! ! denitrification factor computed from NO3 levels nitrfac2(ji,jj,jk) = MAX( 0.e0, ( 1.E-6 - trb(ji,jj,K,jpno3) ) & & / ( 1.E-6 + trb(ji,jj,K,jpno3) ) ) nitrfac2(ji,jj,jk) = MIN( 1., nitrfac2(ji,jj,jk) ) END DO END DO END DO ! #if defined key_iomput IF( lk_iomput .AND. knt == nrdttrc ) THEN ! save output diagnostics IF( iom_use( "xfracal" ) ) CALL iom_put( "xfracal", xfracal(:,:,:) * tmask(:,:,:) ) ! euphotic layer deptht IF( iom_use( "LNnut" ) ) CALL iom_put( "LNnut" , xlimphy(:,:,:) * tmask(:,:,:) ) ! Nutrient limitation term IF( iom_use( "LDnut" ) ) CALL iom_put( "LDnut" , xlimdia(:,:,:) * tmask(:,:,:) ) ! Nutrient limitation term IF( iom_use( "LNFe" ) ) CALL iom_put( "LNFe" , xlimnfe(:,:,:) * tmask(:,:,:) ) ! Iron limitation term IF( iom_use( "LDFe" ) ) CALL iom_put( "LDFe" , xlimdfe(:,:,:) * tmask(:,:,:) ) ! Iron limitation term ENDIF #endif ! END SUBROUTINE p4z_lim SUBROUTINE p4z_lim_init !!---------------------------------------------------------------------- !! *** ROUTINE p4z_lim_init *** !! !! ** Purpose : Initialization of nutrient limitation parameters !! !! ** Method : Read the nampislim namelist and check the parameters !! called at the first timestep (nittrc000) !! !! ** input : Namelist nampislim !! !!---------------------------------------------------------------------- INTEGER :: ios ! Local integer ! NAMELIST/namp4zlim/ concnno3, concdno3, concnnh4, concdnh4, concnfer, concdfer, concbfe, & & concbno3, concbnh4, xsizedia, xsizephy, xsizern, xsizerd, & & xksi1, xksi2, xkdoc, qnfelim, qdfelim, caco3r, oxymin !!---------------------------------------------------------------------- ! IF(lwp) THEN WRITE(numout,*) WRITE(numout,*) 'p4z_lim_init : initialization of nutrient limitations' WRITE(numout,*) '~~~~~~~~~~~~' ENDIF ! REWIND( numnatp_ref ) ! Namelist nampislim in reference namelist : Pisces nutrient limitation parameters READ ( numnatp_ref, namp4zlim, IOSTAT = ios, ERR = 901) 901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namp4zlim in reference namelist', lwp ) REWIND( numnatp_cfg ) ! Namelist nampislim in configuration namelist : Pisces nutrient limitation parameters READ ( numnatp_cfg, namp4zlim, IOSTAT = ios, ERR = 902 ) 902 IF( ios > 0 ) CALL ctl_nam ( ios , 'namp4zlim in configuration namelist', lwp ) IF(lwm) WRITE( numonp, namp4zlim ) ! IF(lwp) THEN ! control print WRITE(numout,*) ' Namelist : namp4zlim' WRITE(numout,*) ' mean rainratio caco3r = ', caco3r WRITE(numout,*) ' NO3 half saturation of nanophyto concnno3 = ', concnno3 WRITE(numout,*) ' NO3 half saturation of diatoms concdno3 = ', concdno3 WRITE(numout,*) ' NH4 half saturation for phyto concnnh4 = ', concnnh4 WRITE(numout,*) ' NH4 half saturation for diatoms concdnh4 = ', concdnh4 WRITE(numout,*) ' half saturation constant for Si uptake xksi1 = ', xksi1 WRITE(numout,*) ' half saturation constant for Si/C xksi2 = ', xksi2 WRITE(numout,*) ' half-sat. of DOC remineralization xkdoc = ', xkdoc WRITE(numout,*) ' Iron half saturation for nanophyto concnfer = ', concnfer WRITE(numout,*) ' Iron half saturation for diatoms concdfer = ', concdfer WRITE(numout,*) ' size ratio for nanophytoplankton xsizern = ', xsizern WRITE(numout,*) ' size ratio for diatoms xsizerd = ', xsizerd WRITE(numout,*) ' NO3 half saturation of bacteria concbno3 = ', concbno3 WRITE(numout,*) ' NH4 half saturation for bacteria concbnh4 = ', concbnh4 WRITE(numout,*) ' Minimum size criteria for diatoms xsizedia = ', xsizedia WRITE(numout,*) ' Minimum size criteria for nanophyto xsizephy = ', xsizephy WRITE(numout,*) ' Fe half saturation for bacteria concbfe = ', concbfe WRITE(numout,*) ' halk saturation constant for anoxia oxymin =' , oxymin WRITE(numout,*) ' optimal Fe quota for nano. qnfelim = ', qnfelim WRITE(numout,*) ' Optimal Fe quota for diatoms qdfelim = ', qdfelim ENDIF ! nitrfac (:,:,:) = 0.0 ! END SUBROUTINE p4z_lim_init INTEGER FUNCTION p4z_lim_alloc() !!---------------------------------------------------------------------- !! *** ROUTINE p5z_lim_alloc *** !!---------------------------------------------------------------------- !* Biological arrays for phytoplankton growth ALLOCATE( xnanono3(jpi,jpj,jpk), xdiatno3(jpi,jpj,jpk), & & xnanonh4(jpi,jpj,jpk), xdiatnh4(jpi,jpj,jpk), & & xnanopo4(jpi,jpj,jpk), xdiatpo4(jpi,jpj,jpk), & & xlimphy (jpi,jpj,jpk), xlimdia (jpi,jpj,jpk), & & xlimnfe (jpi,jpj,jpk), xlimdfe (jpi,jpj,jpk), & & xlimbac (jpi,jpj,jpk), xlimbacl(jpi,jpj,jpk), & & concnfe (jpi,jpj,jpk), concdfe (jpi,jpj,jpk), & & xlimsi (jpi,jpj,jpk), STAT=p4z_lim_alloc ) ! IF( p4z_lim_alloc /= 0 ) CALL ctl_warn( 'p4z_lim_alloc : failed to allocate arrays.' ) ! END FUNCTION p4z_lim_alloc #else !!====================================================================== !! Dummy module : No PISCES bio-model !!====================================================================== CONTAINS SUBROUTINE p4z_lim ! Empty routine END SUBROUTINE p4z_lim #endif !!====================================================================== END MODULE p4zlim