MODULE asmlogchlbal_medusa !!====================================================================== !! *** MODULE asmlogchlbal_medusa *** !! Calculate increments to MEDUSA based on surface logchl increments !! !! IMPORTANT NOTE: This calls the bioanalysis routine of Hemmings et al. !! For licensing reasons this is kept in its own internal Met Office !! branch (dev/frdf/vn3.6_nitrogen_balancing) rather than in the Paris !! repository, and must be merged in when building. !! !!====================================================================== !! History : 3.6 ! 2017-08 (D. Ford) Adapted from asmlogchlbal_hadocc !!---------------------------------------------------------------------- #if defined key_asminc && defined key_medusa && defined key_foam_medusa !!---------------------------------------------------------------------- !! 'key_asminc' : assimilation increment interface !! 'key_medusa' : MEDUSA model !! 'key_foam_medusa' : MEDUSA extras for FOAM OBS and ASM !!---------------------------------------------------------------------- !! asm_logchl_bal_medusa : routine to calculate increments to MEDUSA !!---------------------------------------------------------------------- USE par_kind, ONLY: wp ! kind parameters USE par_oce, ONLY: jpi, jpj, jpk ! domain array sizes USE dom_oce, ONLY: gdepw_n ! domain information USE zdfmxl ! mixed layer depth USE zdftmx, ONLY: ln_tmx_itf, & ! Indonesian Throughflow & mask_itf ! tidal mixing mask USE iom ! i/o USE sms_medusa ! MEDUSA parameters USE par_medusa ! MEDUSA parameters USE par_trc, ONLY: jptra ! Tracer parameters USE bioanalysis ! Nitrogen balancing IMPLICIT NONE PRIVATE PUBLIC asm_logchl_bal_medusa ! Default values for biological assimilation parameters ! Should match Hemmings et al. (2008) REAL(wp), PARAMETER :: balnutext = 0.6 !: Default nutrient balancing factor REAL(wp), PARAMETER :: balnutmin = 0.1 !: Fraction of phytoplankton loss to nutrient REAL(wp), PARAMETER :: r = 1 !: Reliability of model specific growth rate REAL(wp), PARAMETER :: beta_g = 0.05 !: Low rate bias correction for growth rate estimator REAL(wp), PARAMETER :: beta_l = 0.05 !: Low rate bias correction for primary loss rate estimator REAL(wp), PARAMETER :: beta_m = 0.05 !: Low rate bias correction for secondary loss rate estimator REAL(wp), PARAMETER :: a_g = 0.2 !: Error s.d. for log10 of growth rate estimator REAL(wp), PARAMETER :: a_l = 0.4 !: Error s.d. for log10 of primary loss rate estimator REAL(wp), PARAMETER :: a_m = 0.7 !: Error s.d. for log10 of secondary loss rate estimator REAL(wp), PARAMETER :: zfracb0 = 0.7 !: Base zooplankton fraction of loss to Z & D REAL(wp), PARAMETER :: zfracb1 = 0 !: Phytoplankton sensitivity of zooplankton fraction REAL(wp), PARAMETER :: qrfmax = 1.1 !: Maximum nutrient limitation reduction factor REAL(wp), PARAMETER :: qafmax = 1.1 !: Maximum nutrient limitation amplification factor REAL(wp), PARAMETER :: zrfmax = 2 !: Maximum zooplankton reduction factor REAL(wp), PARAMETER :: zafmax = 2 !: Maximum zooplankton amplification factor REAL(wp), PARAMETER :: prfmax = 10 !: Maximum phytoplankton reduction factor (secondary) REAL(wp), PARAMETER :: incphymin = 0.0001 !: Minimum size of non-zero phytoplankton increment REAL(wp), PARAMETER :: integnstep = 20 !: Number of steps for p.d.f. integral evaluation REAL(wp), PARAMETER :: pthreshold = 0.01 !: Fractional threshold level for setting p.d.f. ! LOGICAL, PARAMETER :: diag_active = .TRUE. !: Depth-independent diagnostics LOGICAL, PARAMETER :: diag_fulldepth_active = .TRUE. !: Full-depth diagnostics LOGICAL, PARAMETER :: gl_active = .TRUE. !: Growth/loss-based balancing LOGICAL, PARAMETER :: nbal_active = .TRUE. !: Nitrogen balancing LOGICAL, PARAMETER :: subsurf_active = .TRUE. !: Increments below MLD LOGICAL, PARAMETER :: deepneg_active = .FALSE. !: Negative primary increments below MLD LOGICAL, PARAMETER :: deeppos_active = .FALSE. !: Positive primary increments below MLD LOGICAL, PARAMETER :: nutprof_active = .TRUE. !: Secondary increments CONTAINS SUBROUTINE asm_logchl_bal_medusa( logchl_bkginc, aincper, mld_choice_bgc, & & k_maxchlinc, ld_logchlbal, & & pgrow_avg_bkg, ploss_avg_bkg, & & phyt_avg_bkg, mld_max_bkg, & & tracer_bkg, logchl_balinc ) !!--------------------------------------------------------------------------- !! *** ROUTINE asm_logchl_bal_medusa *** !! !! ** Purpose : calculate increments to MEDUSA from logchl increments !! !! ** Method : convert logchl increments to chl increments !! average up MEDUSA to look like HadOCC !! call nitrogen balancing scheme !! separate back out to MEDUSA !! !! ** Action : populate logchl_balinc !! !! References : Hemmings et al., 2008, J. Mar. Res. !! Ford et al., 2012, Ocean Sci. !!--------------------------------------------------------------------------- !! REAL(wp), INTENT(in ), DIMENSION(jpi,jpj) :: logchl_bkginc ! logchl increments REAL(wp), INTENT(in ) :: aincper ! Assimilation period INTEGER, INTENT(in ) :: mld_choice_bgc ! MLD criterion REAL(wp), INTENT(in ) :: k_maxchlinc ! Max chl increment LOGICAL, INTENT(in ) :: ld_logchlbal ! Balancing y/n REAL(wp), INTENT(in ), DIMENSION(jpi,jpj) :: pgrow_avg_bkg ! Avg phyto growth REAL(wp), INTENT(in ), DIMENSION(jpi,jpj) :: ploss_avg_bkg ! Avg phyto loss REAL(wp), INTENT(in ), DIMENSION(jpi,jpj) :: phyt_avg_bkg ! Avg phyto REAL(wp), INTENT(in ), DIMENSION(jpi,jpj) :: mld_max_bkg ! Max MLD REAL(wp), INTENT(in ), DIMENSION(jpi,jpj,jpk,jptra) :: tracer_bkg ! State variables REAL(wp), INTENT( out), DIMENSION(jpi,jpj,jpk,jptra) :: logchl_balinc ! Balancing increments !! INTEGER :: ji, jj, jk, jn ! Loop counters INTEGER :: jkmax ! Loop index INTEGER, DIMENSION(6) :: i_tracer ! Tracer indices REAL(wp) :: n2be_p ! N:biomass for total phy REAL(wp) :: n2be_z ! N:biomass for total zoo REAL(wp) :: n2be_d ! N:biomass for detritus REAL(wp) :: zfrac_chn ! Fraction of jpchn REAL(wp) :: zfrac_chd ! Fraction of jpchd REAL(wp) :: zfrac_phn ! Fraction of jpphn REAL(wp) :: zfrac_phd ! Fraction of jpphd REAL(wp) :: zfrac_zmi ! Fraction of jpzmi REAL(wp) :: zfrac_zme ! Fraction of jpzme REAL(wp) :: zrat_pds_phd ! Ratio of jppds:jpphd REAL(wp) :: zrat_chd_phd ! Ratio of jpchd:jpphd REAL(wp) :: zrat_chn_phn ! Ratio of jpchn:jpphn REAL(wp) :: zrat_dtc_det ! Ratio of jpdtc:jpdet REAL(wp), DIMENSION(jpi,jpj) :: chl_inc ! Chlorophyll increments REAL(wp), DIMENSION(jpi,jpj) :: medusa_chl ! MEDUSA total chlorophyll REAL(wp), DIMENSION(jpi,jpj) :: cchl_p ! C:Chl for total phy REAL(wp), DIMENSION(jpi,jpj) :: zmld ! Mixed layer depth REAL(wp), DIMENSION(16) :: modparm ! Model parameters REAL(wp), DIMENSION(20) :: assimparm ! Assimilation parameters REAL(wp), DIMENSION(jpi,jpj,jpk,6) :: bstate ! Background state REAL(wp), DIMENSION(jpi,jpj,jpk,6) :: outincs ! Balancing increments REAL(wp), DIMENSION(jpi,jpj,22) :: diag ! Depth-indep diagnostics REAL(wp), DIMENSION(jpi,jpj,jpk,22) :: diag_fulldepth ! Full-depth diagnostics !!--------------------------------------------------------------------------- ! Convert log10(chlorophyll) increment back to a chlorophyll increment ! In order to transform logchl incs to chl incs, need to account for model ! background, cannot simply do 10^logchl_bkginc. Need to: ! 1) Add logchl inc to log10(background) to get log10(analysis) ! 2) Take 10^log10(analysis) to get analysis ! 3) Subtract background from analysis to get chl incs ! If k_maxchlinc > 0 then cap total absolute chlorophyll increment at that value medusa_chl(:,:) = tracer_bkg(:,:,1,jpchn) + tracer_bkg(:,:,1,jpchd) DO jj = 1, jpj DO ji = 1, jpi IF ( medusa_chl(ji,jj) > 0.0 ) THEN chl_inc(ji,jj) = 10**( LOG10( medusa_chl(ji,jj) ) + logchl_bkginc(ji,jj) ) - medusa_chl(ji,jj) IF ( k_maxchlinc > 0.0 ) THEN chl_inc(ji,jj) = MAX( -1.0 * k_maxchlinc, MIN( chl_inc(ji,jj), k_maxchlinc ) ) ENDIF ELSE chl_inc(ji,jj) = 0.0 ENDIF END DO END DO ! Select mixed layer SELECT CASE( mld_choice_bgc ) CASE ( 1 ) ! Turbocline/mixing depth [W points] zmld(:,:) = hmld(:,:) CASE ( 2 ) ! Density criterion (0.01 kg/m^3 change from 10m) [W points] zmld(:,:) = hmlp(:,:) CASE ( 3 ) ! Kara MLD [Interpolated] #if defined key_karaml IF ( ln_kara ) THEN zmld(:,:) = hmld_kara(:,:) ELSE CALL ctl_stop( ' Kara mixed layer requested for LogChl assimilation,', & & ' but ln_kara=.false.' ) ENDIF #else CALL ctl_stop( ' Kara mixed layer requested for LogChl assimilation,', & & ' but is not defined' ) #endif CASE ( 4 ) ! Temperature criterion (0.2 K change from surface) [T points] !zmld(:,:) = hmld_tref(:,:) CALL ctl_stop( ' hmld_tref mixed layer requested for LogChl assimilation,', & & ' but is not available in this version' ) CASE ( 5 ) ! Density criterion (0.01 kg/m^3 change from 10m) [T points] zmld(:,:) = hmlpt(:,:) END SELECT IF ( ld_logchlbal ) THEN ! Nitrogen balancing ! Set up model parameters to be passed into Hemmings balancing routine. ! For now these are hardwired to the standard HadOCC parameter values ! (except C:N ratios) as this is what the scheme was developed for. ! Obviously, HadOCC and MEDUSA are rather different models, so this ! isn't ideal, but there's not always direct analogues between the two ! parameter sets, so it's the easiest way to get something running. ! In the longer term, some serious MarMOT-based development is required. modparm(1) = 0.1 ! grow_sat modparm(2) = 2.0 ! psmax modparm(3) = 0.845 ! par modparm(4) = 0.02 ! alpha modparm(5) = 0.05 ! resp_rate modparm(6) = 0.05 ! pmort_rate modparm(7) = 0.01 ! phyto_min modparm(8) = 0.05 ! z_mort_1 modparm(9) = 1.0 ! z_mort_2 modparm(10) = ( xthetapn + xthetapd ) / 2.0 ! c2n_p modparm(11) = ( xthetazmi + xthetazme ) / 2.0 ! c2n_z modparm(12) = xthetad ! c2n_d modparm(13) = 0.01 ! graze_threshold modparm(14) = 2.0 ! holling_coef modparm(15) = 0.5 ! graze_sat modparm(16) = 2.0 ! graze_max ! Set up assimilation parameters to be passed into balancing routine ! Not sure what assimparm(1) is meant to be, but it doesn't get used assimparm(2) = balnutext assimparm(3) = balnutmin assimparm(4) = r assimparm(5) = beta_g assimparm(6) = beta_l assimparm(7) = beta_m assimparm(8) = a_g assimparm(9) = a_l assimparm(10) = a_m assimparm(11) = zfracb0 assimparm(12) = zfracb1 assimparm(13) = qrfmax assimparm(14) = qafmax assimparm(15) = zrfmax assimparm(16) = zafmax assimparm(17) = prfmax assimparm(18) = incphymin assimparm(19) = integnstep assimparm(20) = pthreshold ! Set up external tracer indices array bstate i_tracer(1) = 1 ! nutrient i_tracer(2) = 2 ! phytoplankton i_tracer(3) = 3 ! zooplankton i_tracer(4) = 4 ! detritus i_tracer(5) = 5 ! DIC i_tracer(6) = 6 ! Alkalinity ! Set background state bstate(:,:,:,i_tracer(1)) = tracer_bkg(:,:,:,jpdin) bstate(:,:,:,i_tracer(2)) = tracer_bkg(:,:,:,jpphn) + tracer_bkg(:,:,:,jpphd) bstate(:,:,:,i_tracer(3)) = tracer_bkg(:,:,:,jpzmi) + tracer_bkg(:,:,:,jpzme) bstate(:,:,:,i_tracer(4)) = tracer_bkg(:,:,:,jpdet) bstate(:,:,:,i_tracer(5)) = tracer_bkg(:,:,:,jpdic) bstate(:,:,:,i_tracer(6)) = tracer_bkg(:,:,:,jpalk) ! Calculate carbon to chlorophyll ratio for combined phytoplankton ! and nitrogen to biomass equivalent for PZD ! Hardwire nitrogen mass to 14.01 for now as it doesn't seem to be set in MEDUSA cchl_p(:,:) = 0.0 DO jj = 1, jpj DO ji = 1, jpi IF ( ( tracer_bkg(ji,jj,1,jpchn) + tracer_bkg(ji,jj,1,jpchd ) ) .GT. 0.0 ) THEN cchl_p(ji,jj) = ( ( tracer_bkg(ji,jj,1,jpphn) * xthetapn ) + ( tracer_bkg(ji,jj,1,jpphd) * xthetapd ) ) / & & ( tracer_bkg(ji,jj,1,jpchn) + tracer_bkg(ji,jj,1,jpchd ) ) ENDIF END DO END DO n2be_p = 14.01 + ( xmassc * ( ( xthetapn + xthetapd ) / 2.0 ) ) n2be_z = 14.01 + ( xmassc * ( ( xthetazmi + xthetazme ) / 2.0 ) ) n2be_d = 14.01 + ( xmassc * xthetad ) ! Call nitrogen balancing routine CALL bio_analysis( jpi, jpj, jpk, gdepw_n(:,:,2:jpk), i_tracer, modparm, & & n2be_p, n2be_z, n2be_d, assimparm, & & INT(aincper), 1, INT(SUM(tmask,3)), tmask(:,:,:), & & zmld(:,:), mld_max_bkg(:,:), chl_inc(:,:), cchl_p(:,:), & & nbal_active, phyt_avg_bkg(:,:), & & gl_active, pgrow_avg_bkg(:,:), ploss_avg_bkg(:,:), & & subsurf_active, deepneg_active, & & deeppos_active, nutprof_active, & & bstate, outincs, & & diag_active, diag, & & diag_fulldepth_active, diag_fulldepth ) ! Loop over each grid point partioning the increments logchl_balinc(:,:,:,:) = 0.0 DO jk = 1, jpk DO jj = 1, jpj DO ji = 1, jpi IF ( ( tracer_bkg(ji,jj,jk,jpphn) > 0.0 ) .AND. ( tracer_bkg(ji,jj,jk,jpphd) > 0.0 ) ) THEN ! Phytoplankton nitrogen and silicate split up based on existing ratios zfrac_phn = tracer_bkg(ji,jj,jk,jpphn) / (tracer_bkg(ji,jj,jk,jpphn) + tracer_bkg(ji,jj,jk,jpphd)) zfrac_phd = 1.0 - zfrac_phn zrat_pds_phd = tracer_bkg(ji,jj,jk,jppds) / tracer_bkg(ji,jj,jk,jpphd) logchl_balinc(ji,jj,jk,jpphn) = outincs(ji,jj,jk,i_tracer(2)) * zfrac_phn logchl_balinc(ji,jj,jk,jpphd) = outincs(ji,jj,jk,i_tracer(2)) * zfrac_phd logchl_balinc(ji,jj,jk,jppds) = logchl_balinc(ji,jj,jk,jpphd) * zrat_pds_phd ! Chlorophyll split up based on existing ratios to phytoplankton nitrogen ! Not using chl_inc directly as it's only 2D ! This method should give same results at surface as splitting chl_inc would zrat_chn_phn = tracer_bkg(ji,jj,jk,jpchn) / tracer_bkg(ji,jj,jk,jpphn) zrat_chd_phd = tracer_bkg(ji,jj,jk,jpchd) / tracer_bkg(ji,jj,jk,jpphd) logchl_balinc(ji,jj,jk,jpchn) = logchl_balinc(ji,jj,jk,jpphn) * zrat_chn_phn logchl_balinc(ji,jj,jk,jpchd) = logchl_balinc(ji,jj,jk,jpphd) * zrat_chd_phd ENDIF IF ( ( tracer_bkg(ji,jj,jk,jpzmi) > 0.0 ) .AND. ( tracer_bkg(ji,jj,jk,jpzme) > 0.0 ) ) THEN ! Zooplankton nitrogen split up based on existing ratios zfrac_zmi = tracer_bkg(ji,jj,jk,jpzmi) / (tracer_bkg(ji,jj,jk,jpzmi) + tracer_bkg(ji,jj,jk,jpzme)) zfrac_zme = 1.0 - zfrac_zmi logchl_balinc(ji,jj,jk,jpzmi) = outincs(ji,jj,jk,i_tracer(3)) * zfrac_zmi logchl_balinc(ji,jj,jk,jpzme) = outincs(ji,jj,jk,i_tracer(3)) * zfrac_zme ENDIF ! Nitrogen nutrient straight from balancing scheme logchl_balinc(ji,jj,jk,jpdin) = outincs(ji,jj,jk,i_tracer(1)) ! Nitrogen detritus straight from balancing scheme logchl_balinc(ji,jj,jk,jpdet) = outincs(ji,jj,jk,i_tracer(4)) ! DIC straight from balancing scheme logchl_balinc(ji,jj,jk,jpdic) = outincs(ji,jj,jk,i_tracer(5)) ! Alkalinity straight from balancing scheme logchl_balinc(ji,jj,jk,jpalk) = outincs(ji,jj,jk,i_tracer(6)) ! Remove diatom silicate increment from nutrient silicate to conserve mass IF ( ( tracer_bkg(ji,jj,jk,jpsil) - logchl_balinc(ji,jj,jk,jppds) ) > 0.0 ) THEN logchl_balinc(ji,jj,jk,jpsil) = logchl_balinc(ji,jj,jk,jppds) * (-1.0) ENDIF IF ( ( tracer_bkg(ji,jj,jk,jpdet) > 0.0 ) .AND. ( tracer_bkg(ji,jj,jk,jpdtc) > 0.0 ) ) THEN ! Carbon detritus based on existing ratios zrat_dtc_det = tracer_bkg(ji,jj,jk,jpdtc) / tracer_bkg(ji,jj,jk,jpdet) logchl_balinc(ji,jj,jk,jpdtc) = logchl_balinc(ji,jj,jk,jpdet) * zrat_dtc_det ENDIF ! Do nothing with iron or oxygen for the time being logchl_balinc(ji,jj,jk,jpfer) = 0.0 logchl_balinc(ji,jj,jk,jpoxy) = 0.0 END DO END DO END DO ELSE ! No nitrogen balancing ! Initialise individual chlorophyll increments to zero logchl_balinc(:,:,:,jpchn) = 0.0 logchl_balinc(:,:,:,jpchd) = 0.0 ! Split up total surface chlorophyll increments DO jj = 1, jpj DO ji = 1, jpi IF ( medusa_chl(ji,jj) > 0.0 ) THEN zfrac_chn = tracer_bkg(ji,jj,1,jpchn) / medusa_chl(ji,jj) zfrac_chd = 1.0 - zfrac_chn logchl_balinc(ji,jj,1,jpchn) = chl_inc(ji,jj) * zfrac_chn logchl_balinc(ji,jj,1,jpchd) = chl_inc(ji,jj) * zfrac_chd ENDIF END DO END DO ! Propagate through mixed layer DO jj = 1, jpj DO ji = 1, jpi ! jkmax = jpk-1 DO jk = jpk-1, 1, -1 IF ( ( zmld(ji,jj) > gdepw_n(ji,jj,jk) ) .AND. & & ( zmld(ji,jj) <= gdepw_n(ji,jj,jk+1) ) ) THEN zmld(ji,jj) = gdepw_n(ji,jj,jk+1) jkmax = jk ENDIF END DO ! DO jk = 2, jkmax logchl_balinc(ji,jj,jk,jpchn) = logchl_balinc(ji,jj,1,jpchn) logchl_balinc(ji,jj,jk,jpchd) = logchl_balinc(ji,jj,1,jpchd) END DO ! END DO END DO ! Set other balancing increments to zero logchl_balinc(:,:,:,jpphn) = 0.0 logchl_balinc(:,:,:,jpphd) = 0.0 logchl_balinc(:,:,:,jppds) = 0.0 logchl_balinc(:,:,:,jpzmi) = 0.0 logchl_balinc(:,:,:,jpzme) = 0.0 logchl_balinc(:,:,:,jpdin) = 0.0 logchl_balinc(:,:,:,jpsil) = 0.0 logchl_balinc(:,:,:,jpfer) = 0.0 logchl_balinc(:,:,:,jpdet) = 0.0 logchl_balinc(:,:,:,jpdtc) = 0.0 logchl_balinc(:,:,:,jpdic) = 0.0 logchl_balinc(:,:,:,jpalk) = 0.0 logchl_balinc(:,:,:,jpoxy) = 0.0 ENDIF ! If performing extra tidal mixing in the Indonesian Throughflow, ! increments have been found to make the carbon cycle unstable ! Therefore, mask these out IF ( ln_tmx_itf ) THEN DO jn = 1, jptra DO jk = 1, jpk logchl_balinc(:,:,jk,jn) = logchl_balinc(:,:,jk,jn) * ( 1.0 - mask_itf(:,:) ) END DO END DO ENDIF END SUBROUTINE asm_logchl_bal_medusa #else !!---------------------------------------------------------------------- !! Default option : Empty routine !!---------------------------------------------------------------------- CONTAINS SUBROUTINE asm_logchl_bal_medusa( logchl_bkginc, aincper, mld_choice_bgc, & & k_maxchlinc, ld_logchlbal, & & pgrow_avg_bkg, ploss_avg_bkg, & & phyt_avg_bkg, mld_max_bkg, & & tracer_bkg, logchl_balinc ) REAL :: logchl_bkginc(:,:) REAL :: aincper INTEGER :: mld_choice_bgc REAL :: k_maxchlinc LOGICAL :: ld_logchlbal REAL :: pgrow_avg_bkg(:,:) REAL :: ploss_avg_bkg(:,:) REAL :: phyt_avg_bkg(:,:) REAL :: mld_max_bkg(:,:) REAL :: tracer_bkg(:,:,:,:) REAL :: logchl_balinc(:,:,:,:) WRITE(*,*) 'asm_logchl_bal_medusa: You should not have seen this print! error?' END SUBROUTINE asm_logchl_bal_medusa #endif !!====================================================================== END MODULE asmlogchlbal_medusa