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C $Header: /u/gcmpack/MITgcm/pkg/bling/bling_remineralization.F,v 1.10 2017/03/29 15:51:19 mmazloff Exp $ |
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C $Name: $ |
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|
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#include "BLING_OPTIONS.h" |
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|
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CBOP |
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subroutine BLING_REMIN( |
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I PTR_NO3, PTR_FE, PTR_O2, irr_inst, |
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I N_spm, P_spm, Fe_spm, CaCO3_uptake, |
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O N_reminp, P_reminp, Fe_reminsum, |
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O N_den_benthic, CaCO3_diss, |
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I bi, bj, imin, imax, jmin, jmax, |
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I myIter, myTime, myThid ) |
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|
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C ================================================================= |
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C | subroutine bling_remin |
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C | o Organic matter export and remineralization. |
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C | - Sinking particulate flux and diel migration contribute to |
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C | export. |
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C | - Benthic denitrification |
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C | - Iron source from sediments |
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C | - Iron scavenging |
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C ================================================================= |
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|
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implicit none |
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|
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C === Global variables === |
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|
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#include "SIZE.h" |
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#include "DYNVARS.h" |
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#include "EEPARAMS.h" |
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#include "PARAMS.h" |
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#include "GRID.h" |
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#include "BLING_VARS.h" |
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#include "PTRACERS_SIZE.h" |
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#include "PTRACERS_PARAMS.h" |
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#ifdef ALLOW_AUTODIFF |
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# include "tamc.h" |
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#endif |
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|
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C === Routine arguments === |
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C bi,bj :: tile indices |
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C iMin,iMax :: computation domain: 1rst index range |
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C jMin,jMax :: computation domain: 2nd index range |
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C myTime :: current time |
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C myIter :: current timestep |
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C myThid :: thread Id. number |
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INTEGER bi, bj, imin, imax, jmin, jmax |
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_RL myTime |
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INTEGER myIter |
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INTEGER myThid |
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C === Input === |
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C PTR_NO3 :: nitrate concentration |
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C PTR_FE :: iron concentration |
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C PTR_O2 :: oxygen concentration |
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_RL PTR_NO3(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL PTR_FE(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL PTR_O2(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL irr_inst(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL N_spm(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL P_spm(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL Fe_spm(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL CaCO3_uptake(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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|
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C === Output === |
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C N_reminp :: remineralization of particulate organic nitrogen |
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C N_den_benthic :: Benthic denitrification |
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C P_reminp :: remineralization of particulate organic nitrogen |
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C Fe_reminsum :: iron remineralization and adsorption |
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C CaCO3_diss :: Calcium carbonate dissolution |
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_RL N_reminp(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL N_den_benthic(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL P_reminp(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL Fe_reminsum(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL CaCO3_diss(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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|
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#ifdef ALLOW_BLING |
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C === Local variables === |
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C i,j,k :: loop indices |
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|
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INTEGER i,j,k |
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INTEGER bttmlyr |
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_RL PONflux_u |
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_RL PONflux_l |
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_RL POPflux_u |
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_RL POPflux_l |
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_RL PFEflux_u |
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_RL PFEflux_l |
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_RL CaCO3flux_u |
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_RL CaCO3flux_l |
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_RL depth_l |
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_RL zremin |
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_RL zremin_caco3 |
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_RL wsink |
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_RL POC_sed |
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_RL Fe_sed(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL NO3_sed(1-OLx:sNx+OLx,1-OLy:sNy+OLy) |
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_RL PO4_sed(1-OLx:sNx+OLx,1-OLy:sNy+OLy) |
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_RL O2_sed(1-OLx:sNx+OLx,1-OLy:sNy+OLy) |
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_RL lig_stability |
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_RL FreeFe |
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_RL Fe_ads_inorg(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL Fe_ads_org(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL log_btm_flx |
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_RL Fe_reminp(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr) |
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_RL Fe_burial(1-OLx:sNx+OLx,1-OLy:sNy+OLy) |
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CEOP |
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|
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C --------------------------------------------------------------------- |
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C Initialize output and diagnostics |
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|
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DO k=1,Nr |
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DO j=jmin,jmax |
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DO i=imin,imax |
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Fe_ads_org(i,j,k) = 0. _d 0 |
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Fe_ads_inorg(i,j,k) = 0. _d 0 |
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N_reminp(i,j,k) = 0. _d 0 |
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P_reminp(i,j,k) = 0. _d 0 |
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Fe_reminp(i,j,k) = 0. _d 0 |
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Fe_reminsum(i,j,k) = 0. _d 0 |
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N_den_benthic(i,j,k)= 0. _d 0 |
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CaCO3_diss(i,j,k) = 0. _d 0 |
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ENDDO |
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ENDDO |
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ENDDO |
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DO j=jmin,jmax |
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DO i=imin,imax |
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Fe_burial(i,j) = 0. _d 0 |
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NO3_sed(i,j) = 0. _d 0 |
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PO4_sed(i,j) = 0. _d 0 |
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O2_sed(i,j) = 0. _d 0 |
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ENDDO |
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ENDDO |
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|
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C --------------------------------------------------------------------- |
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C Remineralization |
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|
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C$TAF LOOP = parallel |
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DO j=jmin,jmax |
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C$TAF LOOP = parallel |
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DO i=imin,imax |
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|
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C Initialize upper flux |
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PONflux_u = 0. _d 0 |
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POPflux_u = 0. _d 0 |
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PFEflux_u = 0. _d 0 |
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CaCO3flux_u = 0. _d 0 |
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|
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DO k=1,Nr |
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|
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C Initialization here helps taf |
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Fe_ads_org(i,j,k) = 0. _d 0 |
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|
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C ARE WE ON THE BOTTOM |
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bttmlyr = 1 |
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IF (k.LT.Nr) THEN |
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IF (hFacC(i,j,k+1,bi,bj).GT.0) bttmlyr = 0 |
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C we are not yet at the bottom |
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ENDIF |
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|
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IF ( hFacC(i,j,k,bi,bj).gt.0. _d 0 ) THEN |
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|
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C Sinking speed is evaluated at the bottom of the cell |
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depth_l=-rF(k+1) |
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IF (depth_l .LE. wsink0z) THEN |
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wsink = wsink0_2d(i,j,bi,bj) |
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ELSE |
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wsink = wsinkacc * (depth_l - wsink0z) + wsink0_2d(i,j,bi,bj) |
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ENDIF |
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|
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C Nutrient remineralization lengthscale |
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C Not an e-folding scale: this term increases with remineralization. |
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zremin = gamma_POM2d(i,j,bi,bj) * ( PTR_O2(i,j,k)**2 / |
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& (k_O2**2 + PTR_O2(i,j,k)**2) * (1-remin_min) |
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& + remin_min )/(wsink + epsln) |
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|
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C Calcium remineralization relaxed toward the inverse of the |
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C ca_remin_depth constant value as the calcite saturation approaches 0. |
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zremin_caco3 = 1. _d 0/ca_remin_depth*(1. _d 0 - min(1. _d 0, |
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& omegaC(i,j,k,bi,bj) + epsln )) |
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|
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C POM flux leaving the cell |
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PONflux_l = (PONflux_u+N_spm(i,j,k)*drF(k) |
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& *hFacC(i,j,k,bi,bj))/(1+zremin*drF(k) |
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& *hFacC(i,j,k,bi,bj)) |
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|
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POPflux_l = (POPflux_u+P_spm(i,j,k)*drF(k) |
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& *hFacC(i,j,k,bi,bj))/(1+zremin*drF(k) |
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& *hFacC(i,j,k,bi,bj)) |
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|
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C CaCO3 flux leaving the cell |
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CaCO3flux_l = (caco3flux_u+CaCO3_uptake(i,j,k)*drF(k) |
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& *hFacC(i,j,k,bi,bj))/(1+zremin_caco3*drF(k) |
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& *hFacC(i,j,k,bi,bj)) |
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|
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C Start with cells that are not the deepest cells |
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IF (bttmlyr.EQ.0) THEN |
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C Nutrient accumulation in a cell is given by the biological production |
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C (and instant remineralization) of particulate organic matter |
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C plus flux thought upper interface minus flux through lower interface. |
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C (Since not deepest cell: hFacC=1) |
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N_reminp(i,j,k) = (PONflux_u + N_spm(i,j,k)*drF(k) |
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& - PONflux_l)*recip_drF(k) |
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|
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P_reminp(i,j,k) = (POPflux_u + P_spm(i,j,k)*drF(k) |
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& - POPflux_l)*recip_drF(k) |
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|
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CaCO3_diss(i,j,k) = (CaCO3flux_u + CaCO3_uptake(i,j,k) |
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& *drF(k) - CaCO3flux_l)*recip_drF(k) |
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|
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Fe_sed(i,j,k) = 0. _d 0 |
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C NOW DO BOTTOM LAYER |
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ELSE |
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C If this layer is adjacent to bottom topography or it is the deepest |
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C cell of the domain, then remineralize/dissolve in this grid cell |
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C i.e. do not subtract off lower boundary fluxes when calculating remin |
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|
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N_reminp(i,j,k) = PONflux_u*recip_drF(k) |
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& *recip_hFacC(i,j,k,bi,bj) + N_spm(i,j,k) |
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|
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P_reminp(i,j,k) = POPflux_u*recip_drF(k) |
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& *recip_hFacC(i,j,k,bi,bj) + P_spm(i,j,k) |
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|
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CaCO3_diss(i,j,k) = CaCO3flux_u*recip_drF(k) |
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& *recip_hFacC(i,j,k,bi,bj) + CaCO3_uptake(i,j,k) |
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|
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C Efflux Fed out of sediments |
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C The phosphate flux hitting the bottom boundary |
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C is used to scale the return of iron to the water column. |
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C Maximum value added for numerical stability. |
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|
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POC_sed = PONflux_l * CtoN |
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|
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Fe_sed(i,j,k) = max(epsln, FetoC_sed * POC_sed * recip_drF(k) |
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& *recip_hFacC(i,j,k,bi,bj)) |
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|
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cav log_btm_flx = 0. _d 0 |
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log_btm_flx = 1. _d -20 |
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|
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CMM: this is causing instability in the adjoint. Needs debugging |
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#ifndef BLING_ADJOINT_SAFE |
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IF (POC_sed .gt. 0. _d 0) THEN |
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|
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C Convert from mol N m-2 s-1 to umol C cm-2 d-1 and take the log |
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|
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log_btm_flx = log10(min(43.0 _d 0, POC_sed * |
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& 86400. _d 0 * 100.0 _d 0)) |
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|
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C Metamodel gives units of umol C cm-2 d-1, convert to mol N m-2 s-1 and |
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C multiply by no3_2_n to give NO3 consumption rate |
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|
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N_den_benthic(i,j,k) = min (POC_sed * NO3toN / CtoN, |
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& (10 _d 0)**(-0.9543 _d 0 + 0.7662 _d 0 * |
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& log_btm_flx - 0.235 _d 0 * log_btm_flx * log_btm_flx) |
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& / (CtoN * 86400. _d 0 * 100.0 _d 0) * NO3toN * |
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& PTR_NO3(i,j,k) / (k_no3 + PTR_NO3(i,j,k)) ) * |
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& recip_drF(k) |
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|
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ENDIF |
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#endif |
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|
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C --------------------------------------------------------------------- |
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C Calculate external bottom fluxes for tracer_vertdiff. Positive fluxes |
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C are into the water column from the seafloor. For P, the bottom flux puts |
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C the sinking flux reaching the bottom cell into the water column through |
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C diffusion. For iron, the sinking flux disappears into the sediments if |
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C bottom waters are oxic (assumed adsorbed as oxides). If bottom waters are |
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C anoxic, the sinking flux of Fe is returned to the water column. |
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C |
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C For oxygen, the consumption of oxidant required to respire the settling flux |
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C of organic matter (in support of the no3 bottom flux) diffuses from the |
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C bottom water into the sediment. |
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|
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C Assume all NO3 for benthic denitrification is supplied from the bottom water, |
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C and that all organic N is also consumed under denitrification (Complete |
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C Denitrification, sensu Paulmier, Biogeosciences 2009). Therefore, no NO3 is |
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C regenerated from organic matter respired by benthic denitrification |
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C (necessitating the second term in b_no3). |
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|
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NO3_sed(i,j) = PONflux_l*drF(k)*hFacC(i,j,k,bi,bj) |
| 281 |
& - N_den_benthic(i,j,k) / NO3toN |
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|
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PO4_sed(i,j) = POPflux_l*drF(k)*hFacC(i,j,k,bi,bj) |
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|
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C Oxygen flux into sediments is that required to support non-denitrification |
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C respiration, assuming a 4/5 oxidant ratio of O2 to NO3. Oxygen consumption |
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C is allowed to continue at negative oxygen concentrations, representing |
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C sulphate reduction. |
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|
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O2_sed(i,j) = -(O2toN * PONflux_l*drF(k)*hFacC(i,j,k,bi,bj) |
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& - N_den_benthic(i,j,k)* 1.25) |
| 292 |
|
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ENDIF |
| 294 |
|
| 295 |
C Begin iron uptake calculations by determining ligand bound and free iron. |
| 296 |
C Both forms are available for biology, but only free iron is scavenged |
| 297 |
C onto particles and forms colloids. |
| 298 |
|
| 299 |
lig_stability = kFe_eq_lig_max-(KFe_eq_lig_max-kFe_eq_lig_min) |
| 300 |
& *(irr_inst(i,j,k)**2 |
| 301 |
& /(kFe_eq_lig_irr**2+irr_inst(i,j,k)**2)) |
| 302 |
& *max(epsln,min(1. _d 0,(PTR_FE(i,j,k) |
| 303 |
& -kFe_eq_lig_Femin)/ |
| 304 |
& (PTR_FE(i,j,k)+epsln)*1.2 _d 0)) |
| 305 |
|
| 306 |
C Use the quadratic equation to solve for binding between iron and ligands |
| 307 |
|
| 308 |
FreeFe = (-(1+lig_stability*(ligand-PTR_FE(i,j,k))) |
| 309 |
& +((1+lig_stability*(ligand-PTR_FE(i,j,k)))**2+4* |
| 310 |
& lig_stability*PTR_FE(i,j,k))**(0.5))/(2* |
| 311 |
& lig_stability) |
| 312 |
|
| 313 |
C Iron scavenging does not occur in anoxic water (Fe2+ is soluble), so set |
| 314 |
C FreeFe = 0 when anoxic. FreeFe should be interpreted the free iron that |
| 315 |
C participates in scavenging. |
| 316 |
|
| 317 |
IF (PTR_O2(i,j,k) .LT. oxic_min) THEN |
| 318 |
FreeFe = 0. _d 0 |
| 319 |
ENDIF |
| 320 |
|
| 321 |
C Two mechanisms for iron uptake, in addition to biological production: |
| 322 |
C colloidal scavenging and scavenging by organic matter. |
| 323 |
|
| 324 |
Fe_ads_inorg(i,j,k) = |
| 325 |
& kFe_inorg*(max(1. _d -8,FreeFe))**(1.5) |
| 326 |
|
| 327 |
C Scavenging of iron by organic matter: |
| 328 |
C The POM value used is the bottom boundary flux. This does not occur in |
| 329 |
C oxic waters, but FreeFe is set to 0 in such waters earlier. |
| 330 |
IF ( PONflux_l .GT. 0. _d 0 ) THEN |
| 331 |
Fe_ads_org(i,j,k) = |
| 332 |
& kFE_org*(PONflux_l/(epsln + wsink) |
| 333 |
& * MasstoN)**(0.58)*FreeFe |
| 334 |
ENDIF |
| 335 |
|
| 336 |
C If water is oxic then the iron is remineralized normally. Otherwise |
| 337 |
C it is completely remineralized (fe 2+ is soluble, but unstable |
| 338 |
C in oxidizing environments). |
| 339 |
|
| 340 |
PFEflux_l = (PFEflux_u+(Fe_spm(i,j,k)+Fe_ads_inorg(i,j,k) |
| 341 |
& +Fe_ads_org(i,j,k))*drF(k) |
| 342 |
& *hFacC(i,j,k,bi,bj))/(1+zremin*drF(k) |
| 343 |
& *hFacC(i,j,k,bi,bj)) |
| 344 |
|
| 345 |
C Added the burial flux of sinking particulate iron here as a |
| 346 |
C diagnostic, needed to calculate mass balance of iron. |
| 347 |
C this is calculated last for the deepest cell |
| 348 |
|
| 349 |
Fe_burial(i,j) = PFEflux_l |
| 350 |
|
| 351 |
IF ( PTR_O2(i,j,k) .LT. oxic_min ) THEN |
| 352 |
PFEflux_l = 0. _d 0 |
| 353 |
ENDIF |
| 354 |
|
| 355 |
Fe_reminp(i,j,k) = (PFEflux_u+(Fe_spm(i,j,k) |
| 356 |
& +Fe_ads_inorg(i,j,k) |
| 357 |
& +Fe_ads_org(i,j,k))*drF(k) |
| 358 |
& *hFacC(i,j,k,bi,bj)-PFEflux_l)*recip_drF(k) |
| 359 |
& *recip_hFacC(i,j,k,bi,bj) |
| 360 |
|
| 361 |
C Prepare the tracers for the next layer down |
| 362 |
PONflux_u = PONflux_l |
| 363 |
POPflux_u = POPflux_l |
| 364 |
PFEflux_u = PFEflux_l |
| 365 |
CaCO3flux_u = CaCO3flux_l |
| 366 |
|
| 367 |
Fe_reminsum(i,j,k) = Fe_reminp(i,j,k) + Fe_sed(i,j,k) |
| 368 |
& - Fe_ads_org(i,j,k) - Fe_ads_inorg(i,j,k) |
| 369 |
|
| 370 |
ENDIF |
| 371 |
|
| 372 |
ENDDO |
| 373 |
ENDDO |
| 374 |
ENDDO |
| 375 |
|
| 376 |
c --------------------------------------------------------------------- |
| 377 |
|
| 378 |
#ifdef ALLOW_DIAGNOSTICS |
| 379 |
IF ( useDiagnostics ) THEN |
| 380 |
|
| 381 |
c 3d local variables |
| 382 |
CALL DIAGNOSTICS_FILL(Fe_ads_org, 'BLGFEADO',0,Nr,2,bi,bj, |
| 383 |
& myThid) |
| 384 |
CALL DIAGNOSTICS_FILL(Fe_ads_inorg, 'BLGFEADI',0,Nr,2,bi,bj, |
| 385 |
& myThid) |
| 386 |
CALL DIAGNOSTICS_FILL(Fe_sed, 'BLGFESED',0,Nr,2,bi,bj,myThid) |
| 387 |
CALL DIAGNOSTICS_FILL(Fe_reminp,'BLGFEREM',0,Nr,2,bi,bj,myThid) |
| 388 |
CALL DIAGNOSTICS_FILL(N_reminp, 'BLGNREM ',0,Nr,2,bi,bj,myThid) |
| 389 |
CALL DIAGNOSTICS_FILL(P_reminp, 'BLGPREM ',0,Nr,2,bi,bj,myThid) |
| 390 |
c 2d local variables |
| 391 |
CALL DIAGNOSTICS_FILL(Fe_burial,'BLGFEBUR',0,1,2,bi,bj,myThid) |
| 392 |
CALL DIAGNOSTICS_FILL(NO3_sed, 'BLGNSED ',0,1,2,bi,bj,myThid) |
| 393 |
CALL DIAGNOSTICS_FILL(PO4_sed, 'BLGPSED ',0,1,2,bi,bj,myThid) |
| 394 |
CALL DIAGNOSTICS_FILL(O2_sed, 'BLGO2SED',0,1,2,bi,bj,myThid) |
| 395 |
|
| 396 |
ENDIF |
| 397 |
#endif /* ALLOW_DIAGNOSTICS */ |
| 398 |
|
| 399 |
#endif /* ALLOW_BLING */ |
| 400 |
|
| 401 |
RETURN |
| 402 |
END |
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