Changeset 9157 for branches/NERC
- Timestamp:
- 2017-12-21T16:51:24+01:00 (7 years ago)
- Location:
- branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM
- Files:
-
- 17 edited
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CONFIG/SHARED/field_def_bgc.xml (modified) (3 diffs)
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NEMO/OPA_SRC/DIA/diaptr.F90 (modified) (10 diffs)
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NEMO/OPA_SRC/TRA/trabbl.F90 (modified) (1 diff)
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NEMO/TOP_SRC/MEDUSA/air_sea.F90 (modified) (2 diffs)
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NEMO/TOP_SRC/MEDUSA/bio_medusa_diag_slice.F90 (modified) (3 diffs)
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NEMO/TOP_SRC/MEDUSA/bio_medusa_fin.F90 (modified) (9 diffs)
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NEMO/TOP_SRC/MEDUSA/bio_medusa_init.F90 (modified) (3 diffs)
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NEMO/TOP_SRC/MEDUSA/bio_medusa_mod.F90 (modified) (5 diffs)
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NEMO/TOP_SRC/MEDUSA/bio_medusa_update.F90 (modified) (5 diffs)
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NEMO/TOP_SRC/MEDUSA/detritus.F90 (modified) (3 diffs)
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NEMO/TOP_SRC/MEDUSA/phytoplankton.F90 (modified) (4 diffs)
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NEMO/TOP_SRC/MEDUSA/sms_medusa.F90 (modified) (1 diff)
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NEMO/TOP_SRC/MEDUSA/trcini_medusa.F90 (modified) (2 diffs)
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NEMO/TOP_SRC/MEDUSA/trcnam_medusa.F90 (modified) (6 diffs)
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NEMO/TOP_SRC/MEDUSA/trcsms_medusa.F90 (modified) (2 diffs)
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NEMO/TOP_SRC/trc.F90 (modified) (1 diff)
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NEMO/TOP_SRC/trcrst.F90 (modified) (4 diffs)
Legend:
- Unmodified
- Added
- Removed
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branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/CONFIG/SHARED/field_def_bgc.xml
r8308 r9157 448 448 <field id= "DMS_HALL" long_name="DMS Surface Concentration, Halloran" unit="nmol/L" /> 449 449 <field id= "DMS_ANDM" long_name="DMS Surface Concentration, Anderson modif" unit="nmol/L" /> 450 <field id= "CHL_MLD" long_name="MLD averaged Chlorophyll" unit="mg Chl/m3" /> 451 <field id= "CHL_CPL" long_name="Scaled Surf or MLD Chlorophyll to UM" unit="kg Chl/m3" /> 450 452 <field id= "ATM_XCO2" long_name="Atmospheric xCO2" unit="ppm" /> 451 453 <field id= "OCN_FCO2" long_name="Surface ocean fCO2" unit="uatm" /> … … 702 704 <field field_ref= "OCN_CO3" name="OCN_CO3" /> 703 705 <field field_ref= "CO2FLUX" name="CO2FLUX" /> 704 <field field_ref= "FGCO2" name="FGCO2" />705 706 <field field_ref= "OM_CAL" name="OM_CAL" /> 706 707 <field field_ref= "OM_ARG" name="OM_ARG" /> … … 784 785 <field field_ref= "CO2STARAIR" name="CO2STARAIR" /> 785 786 <field field_ref= "OCN_DPCO2" name="OCN_DPCO2" /> 787 <field field_ref= "CHL_MLD" name="CHL_MLD" /> 788 </field_group> 789 790 <field_group id="groupMEDUSA_cpl" > 791 <field field_ref= "CHL_CPL" name="CHL_CPL" /> 792 <field field_ref= "FGCO2" name="FGCO2_CPL" /> 793 <field field_ref= "DMS_SURF" name="DMS_CPL" /> 794 <field field_ref= "ATM_XCO2" name="AXCO2_CPL" /> 795 <field field_ref= "AEOLIAN" name="DUST_CPL" /> 786 796 </field_group> 787 797 -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/OPA_SRC/DIA/diaptr.F90
r7747 r9157 84 84 REAL(wp), DIMENSION(jpi,jpj) :: z2d ! 2D workspace 85 85 REAL(wp), DIMENSION(jpi,jpj,jpk) :: z3d ! 3D workspace 86 REAL(wp), DIMENSION(jpi,jpj,jpk) :: zvn ! 3D workspace 86 87 REAL(wp), DIMENSION(jpi,jpj,jpk) :: zmask ! 3D workspace 87 88 REAL(wp), DIMENSION(jpi,jpj,jpk,jpts) :: zts ! 3D workspace … … 93 94 REAL(wp), DIMENSION(jpj,jpk,nptr) :: sjk , r1_sjk ! i-mean i-k-surface and its inverse 94 95 REAL(wp), DIMENSION(jpj,jpk,nptr) :: v_msf, sn_jk , tn_jk ! i-mean T and S, j-Stream-Function 95 REAL(wp), DIMENSION(jpi,jpj,jpk) :: zvn ! 3D workspace96 96 97 97 … … 130 130 zmask(:,:,:) = 0._wp 131 131 zts(:,:,:,:) = 0._wp 132 zvn(:,:,:) = 0._wp133 132 DO jk = 1, jpkm1 134 133 DO jj = 1, jpjm1 … … 138 137 zts(ji,jj,jk,jp_tem) = (tsn(ji,jj,jk,jp_tem)+tsn(ji,jj+1,jk,jp_tem)) * 0.5 * zvfc !Tracers averaged onto V grid 139 138 zts(ji,jj,jk,jp_sal) = (tsn(ji,jj,jk,jp_sal)+tsn(ji,jj+1,jk,jp_sal)) * 0.5 * zvfc 140 zvn(ji,jj,jk) = vn(ji,jj,jk) * zvfc141 139 ENDDO 142 140 ENDDO … … 151 149 tn_jk(:,:,1) = ptr_sjk( zts(:,:,:,jp_tem) ) * r1_sjk(:,:,1) 152 150 sn_jk(:,:,1) = ptr_sjk( zts(:,:,:,jp_sal) ) * r1_sjk(:,:,1) 153 v_msf(:,:,1) = ptr_sjk( zvn(:,:,:) )151 v_msf(:,:,1) = ptr_sjk( pvtr(:,:,:) ) 154 152 155 153 htr_ove(:,1) = SUM( v_msf(:,:,1)*tn_jk(:,:,1) ,2 ) … … 177 175 tn_jk(:,:,jn) = ptr_sjk( zts(:,:,:,jp_tem), btmsk(:,:,jn) ) * r1_sjk(:,:,jn) 178 176 sn_jk(:,:,jn) = ptr_sjk( zts(:,:,:,jp_sal), btmsk(:,:,jn) ) * r1_sjk(:,:,jn) 179 v_msf(:,:,jn) = ptr_sjk( zvn(:,:,:), btmsk(:,:,jn) )177 v_msf(:,:,jn) = ptr_sjk( pvtr(:,:,:), btmsk(:,:,jn) ) 180 178 htr_ove(:,jn) = SUM( v_msf(:,:,jn)*tn_jk(:,:,jn) ,2 ) 181 179 str_ove(:,jn) = SUM( v_msf(:,:,jn)*sn_jk(:,:,jn) ,2 ) … … 202 200 WHERE( sjk(:,1,1) /= 0._wp ) r1_sjk(:,1,1) = 1._wp / sjk(:,1,1) 203 201 204 vsum = ptr_sj( zvn(:,:,:), btmsk(:,:,1))202 vsum = ptr_sj( pvtr(:,:,:), btmsk(:,:,1)) 205 203 tssum(:,jp_tem) = ptr_sj( zts(:,:,:,jp_tem), btmsk(:,:,1) ) 206 204 tssum(:,jp_sal) = ptr_sj( zts(:,:,:,jp_sal), btmsk(:,:,1) ) … … 224 222 r1_sjk(:,1,jn) = 0._wp 225 223 WHERE( sjk(:,1,jn) /= 0._wp ) r1_sjk(:,1,jn) = 1._wp / sjk(:,1,jn) 226 vsum = ptr_sj( zvn(:,:,:), btmsk(:,:,jn))224 vsum = ptr_sj( pvtr(:,:,:), btmsk(:,:,jn)) 227 225 tssum(:,jp_tem) = ptr_sj( zts(:,:,:,jp_tem), btmsk(:,:,jn) ) 228 226 tssum(:,jp_sal) = ptr_sj( zts(:,:,:,jp_sal), btmsk(:,:,jn) ) … … 408 406 ENDIF 409 407 IF( iom_use("zomsfeivglo") ) THEN 410 z3d(1,:,:) = ptr_sjk( v_eiv(:,:,:) ) ! zonal cumulative effective transport 408 DO jk=1,jpk 409 DO jj=1,jpj 410 DO ji=1,jpi 411 zvn(ji,jj,jk) = v_eiv(ji,jj,jk) * fse3v(ji,jj,jk) * e1v(ji,jj) 412 ENDDO 413 ENDDO 414 ENDDO 415 z3d(1,:,:) = ptr_sjk( zvn(:,:,:) ) ! zonal cumulative effective transport 411 416 DO jk = jpkm1,1,-1 412 417 z3d(1,:,jk) = z3d(1,:,jk+1) - z3d(1,:,jk) ! effective j-Stream-Function (MSF) … … 419 424 IF( ln_subbas ) THEN 420 425 DO jn = 2, nptr ! by sub-basins 421 z3d(1,:,:) = ptr_sjk( v_eiv(:,:,:), btmsk(:,:,jn) )426 z3d(1,:,:) = ptr_sjk( zvn(:,:,:), btmsk(:,:,jn) ) 422 427 DO jk = jpkm1,1,-1 423 428 z3d(1,:,jk) = z3d(1,:,jk+1) - z3d(1,:,jk) ! effective j-Stream-Function (MSF) -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/OPA_SRC/TRA/trabbl.F90
r7771 r9157 549 549 zmbk(:,:) = REAL( mbkv_d(:,:), wp ) ; CALL lbc_lnk(zmbk,'V',1.) ; mbkv_d(:,:) = MAX( INT( zmbk(:,:) ), 1 ) 550 550 551 !* sign of grad(H) at u- and v-points 552 mgrhu(jpi,:) = 0 ; mgrhu(:,jpj) = 0 ; mgrhv(jpi,:) = 0 ; mgrhv(:,jpj) = 0 551 !! AXY (16/08/17): remove the following per George and Andrew bug-hunt 552 !! !* sign of grad(H) at u- and v-points 553 !! mgrhu(jpi,:) = 0 ; mgrhu(:,jpj) = 0 ; mgrhv(jpi,:) = 0 ; mgrhv(:,jpj) = 0 554 !! DO jj = 1, jpjm1 555 !! DO ji = 1, jpim1 556 !! mgrhu(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji+1,jj,mbkt(ji+1,jj)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 557 !! mgrhv(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji,jj+1,mbkt(ji,jj+1)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 558 !! END DO 559 !! END DO 560 561 !! AXY (16/08/17): add the following replacement per George and Andrew bug-hunt 562 !* sign of grad(H) at u- and v-points; zero if grad(H) = 0 563 mgrhu(:,:) = 0 ; mgrhv(:,:) = 0 553 564 DO jj = 1, jpjm1 554 565 DO ji = 1, jpim1 555 mgrhu(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji+1,jj,mbkt(ji+1,jj)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 556 mgrhv(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji,jj+1,mbkt(ji,jj+1)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 566 #if defined key_bbl_old_nonconserve 567 ! This key allows old (non conservative version) to be used for continuity of results 568 mgrhu(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji+1,jj,mbkt(ji+1,jj)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 569 mgrhv(ji,jj) = INT( SIGN( 1.e0, gdept_0(ji,jj+1,mbkt(ji,jj+1)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 570 #else 571 IF( gdept_0(ji+1,jj,mbkt(ji+1,jj)) - gdept_0(ji,jj,mbkt(ji,jj)) /= 0._wp ) THEN 572 mgrhu(ji,jj) = INT( SIGN( 1.e0, & 573 gdept_0(ji+1,jj,mbkt(ji+1,jj)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 574 ENDIF 575 ! 576 IF( gdept_0(ji,jj+1,mbkt(ji,jj+1)) - gdept_0(ji,jj,mbkt(ji,jj)) /= 0._wp ) THEN 577 mgrhv(ji,jj) = INT( SIGN( 1.e0, & 578 gdept_0(ji,jj+1,mbkt(ji,jj+1)) - gdept_0(ji,jj,mbkt(ji,jj)) ) ) 579 ENDIF 580 #endif 557 581 END DO 558 582 END DO -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/air_sea.F90
r9073 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Add air-sea flux kill switch 8 9 !!---------------------------------------------------------------------- 9 10 #if defined key_medusa … … 372 373 ENDDO 373 374 ENDDO 375 # endif 376 377 # if defined key_axy_killco2flux 378 !! AXY (18/08/17): single kill switch on air-sea CO2 flux for budget checking 379 f_co2flux(:,:) = 0. 374 380 # endif 375 381 -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_diag_slice.F90
r9070 r9157 39 39 # endif 40 40 USE lbclnk, ONLY: lbc_lnk 41 USE trc, ONLY: trn 42 USE oce, ONLY: CO2Flux_out_cpl, DMS_out_cpl, chloro_out_cpl 41 USE oce, ONLY: CO2Flux_out_cpl, DMS_out_cpl 43 42 USE par_oce, ONLY: jpi, jpj 44 43 USE sbc_oce, ONLY: lk_oasis, qsr, wndm … … 48 47 jdms, ocal_ccd, xpar, xze, & 49 48 zb_co2_flx, zb_dms_srf, & 50 zn_co2_flx, zn_dms_srf , zn_chl_srf49 zn_co2_flx, zn_dms_srf 51 50 USE trc, ONLY: med_diag 52 51 … … 66 65 !! 67 66 IF (jk.eq.1) THEN 68 !! JPALM -- 02-06-2017 --69 !! add Chl surf coupling70 !! no need to output, just pass to cpl var71 IF (lk_oasis) THEN72 zn_chl_srf(:,:) = (trn(:,:,1,jpchd) + trn(:,:,1,jpchn)) * 1.0E-6 !! surf Chl in Kg-chl/m3 as needed for cpl73 chloro_out_cpl(:,:) = zn_chl_srf(:,:) !! Coupling Chl74 END IF75 67 IF( med_diag%MED_QSR%dgsave ) THEN 76 68 CALL iom_put( "MED_QSR" , qsr ) ! -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_fin.F90
r9070 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Amend bethic reservoir updating 8 9 !!---------------------------------------------------------------------- 9 10 #if defined key_medusa … … 38 39 # endif 39 40 USE lbclnk, ONLY: lbc_lnk 41 USE oce, ONLY: chloro_out_cpl 40 42 USE par_medusa, ONLY: jp_medusa_2d, jp_medusa_3d, & 41 jp_medusa_trd 43 jp_medusa_trd, jpchd, jpchn 42 44 USE par_oce, ONLY: jpi, jpim1, jpj, jpjm1, jpk 43 45 USE phycst, ONLY: rsmall 46 USE sbc_oce, ONLY: lk_oasis 44 47 USE sms_medusa, ONLY: jinorgben, jorgben, & 45 48 f3_co3, f3_h2co3, f3_hco3, & … … 50 53 zb_sed_n, zb_sed_si, & 51 54 zn_sed_c, zn_sed_ca, zn_sed_fe, & 52 zn_sed_n, zn_sed_si 53 USE trc, ONLY: med_diag, nittrc000 55 zn_sed_n, zn_sed_si, zn_chl_srf, & 56 scl_chl, chl_out 57 USE trc, ONLY: med_diag, nittrc000, trn 54 58 USE trcnam_trp, ONLY: ln_trcadv_cen2, ln_trcadv_tvd 55 59 … … 62 66 REAL(wp) :: fq0,fq1,fq2,fq3 63 67 68 # if defined key_roam 69 !!---------------------------------------------------------------------- 70 !! AXY (09/08/17): fix benthic submodel 64 71 !!---------------------------------------------------------------------- 65 72 !! Process benthic in/out fluxes 66 73 !! These can be handled outside of the 3D calculations since the 67 !! benthic pools (and fluxes) are 2D in nature; this code is68 !! (shamelessly) borrowed from corresponding code in the LOBSTER69 !! model74 !! benthic pools (and fluxes) are 2D in nature; this code was 75 !! developed with help from George Nurser (NOC); it cannot be run 76 !! in a configuration with variable time-stepping with depth 70 77 !!---------------------------------------------------------------------- 71 78 !! 72 !! IF(lwp) WRITE(numout,*) 'AXY: rdt = ', rdt79 !! time-step calculation 73 80 if (jorgben.eq.1) then 74 za_sed_n(:,:) = zn_sed_n(:,:) + & 75 ( f_sbenin_n(:,:) + f_fbenin_n(:,:) - & 76 f_benout_n(:,:) ) * (rdt / 86400.) 81 za_sed_n(:,:) = zb_sed_n(:,:) + ((2. * (rdt / 86400.)) * & 82 ( f_sbenin_n(:,:) + f_fbenin_n(:,:) - f_benout_n(:,:) )) 83 za_sed_fe(:,:) = zb_sed_fe(:,:) + ((2. * (rdt / 86400.)) * & 84 ( f_sbenin_fe(:,:) + f_fbenin_fe(:,:) - f_benout_fe(:,:) )) 85 za_sed_c(:,:) = zb_sed_c(:,:) + ((2. * (rdt / 86400.)) * & 86 ( f_sbenin_c(:,:) + f_fbenin_c(:,:) - f_benout_c(:,:) )) 87 endif 88 if (jinorgben.eq.1) then 89 za_sed_si(:,:) = zb_sed_si(:,:) + ((2. * (rdt / 86400.)) * & 90 ( f_fbenin_si(:,:) - f_benout_si(:,:) )) 91 za_sed_ca(:,:) = zb_sed_ca(:,:) + ((2. * (rdt / 86400.)) * & 92 ( f_fbenin_ca(:,:) - f_benout_ca(:,:) )) 93 endif 94 !! 95 !! time-level calculation 96 if (jorgben.eq.1) then 97 zb_sed_n(:,:) = zn_sed_n(:,:) + (atfp * & 98 ( za_sed_n(:,:) - (2. * zn_sed_n(:,:)) + zb_sed_n(:,:) )) 77 99 zn_sed_n(:,:) = za_sed_n(:,:) 78 !! 79 za_sed_fe(:,:) = zn_sed_fe(:,:) + & 80 ( f_sbenin_fe(:,:) + f_fbenin_fe(:,:) - & 81 f_benout_fe(:,:) ) * (rdt / 86400.) 100 zb_sed_fe(:,:) = zn_sed_fe(:,:) + (atfp * & 101 ( za_sed_fe(:,:) - (2. * zn_sed_fe(:,:)) + zb_sed_fe(:,:) )) 82 102 zn_sed_fe(:,:) = za_sed_fe(:,:) 83 !! 84 za_sed_c(:,:) = zn_sed_c(:,:) + & 85 ( f_sbenin_c(:,:) + f_fbenin_c(:,:) - & 86 f_benout_c(:,:) ) * (rdt / 86400.) 103 zb_sed_c(:,:) = zn_sed_c(:,:) + (atfp * & 104 ( za_sed_c(:,:) - (2. * zn_sed_c(:,:)) + zb_sed_c(:,:) )) 87 105 zn_sed_c(:,:) = za_sed_c(:,:) 88 106 endif 89 107 if (jinorgben.eq.1) then 90 za_sed_si(:,:) = zn_sed_si(:,:) + & 91 ( f_fbenin_si(:,:) - f_benout_si(:,:) ) * & 92 (rdt / 86400.) 108 zb_sed_si(:,:) = zn_sed_si(:,:) + (atfp * & 109 ( za_sed_si(:,:) - (2. * zn_sed_si(:,:)) + zb_sed_si(:,:) )) 93 110 zn_sed_si(:,:) = za_sed_si(:,:) 94 !! 95 za_sed_ca(:,:) = zn_sed_ca(:,:) + & 96 ( f_fbenin_ca(:,:) - f_benout_ca(:,:) ) * & 97 (rdt / 86400.) 111 zb_sed_ca(:,:) = zn_sed_ca(:,:) + (atfp * & 112 ( za_sed_ca(:,:) - (2. * zn_sed_ca(:,:)) + zb_sed_ca(:,:) )) 98 113 zn_sed_ca(:,:) = za_sed_ca(:,:) 99 114 endif 100 !! 101 if (ibenthic.eq.2) then 102 !! The code below (in this if ... then ... endif loop) is 103 !! effectively commented out because it does not work as 104 !! anticipated; it can be deleted at a later date 105 if (jorgben.eq.1) then 106 za_sed_n(:,:) = ( f_sbenin_n(:,:) + f_fbenin_n(:,:) - & 107 f_benout_n(:,:) ) * rdt 108 za_sed_fe(:,:) = ( f_sbenin_fe(:,:) + f_fbenin_fe(:,:) - & 109 f_benout_fe(:,:) ) * rdt 110 za_sed_c(:,:) = ( f_sbenin_c(:,:) + f_fbenin_c(:,:) - & 111 f_benout_c(:,:) ) * rdt 112 endif 113 if (jinorgben.eq.1) then 114 za_sed_si(:,:) = ( f_fbenin_si(:,:) - f_benout_si(:,:) ) * rdt 115 za_sed_ca(:,:) = ( f_fbenin_ca(:,:) - f_benout_ca(:,:) ) * rdt 116 endif 117 !! 118 !! Leap-frog scheme - only in explicit case, otherwise the 119 !! time stepping is already being done in trczdf 120 !! IF( l_trczdf_exp .AND. (ln_trcadv_cen2 .OR. ln_trcadv_tvd) ) THEN 121 !! zfact = 2. * rdttra(jk) * FLOAT( ndttrc ) 122 !! IF( neuler == 0 .AND. kt == nittrc000 ) zfact = rdttra(jk) * 123 !! FLOAT(ndttrc) 124 !! if (jorgben.eq.1) then 125 !! za_sed_n(:,:) = zb_sed_n(:,:) + ( zfact * za_sed_n(:,:) ) 126 !! za_sed_fe(:,:) = zb_sed_fe(:,:) + ( zfact * za_sed_fe(:,:) ) 127 !! za_sed_c(:,:) = zb_sed_c(:,:) + ( zfact * za_sed_c(:,:) ) 128 !! endif 129 !! if (jinorgben.eq.1) then 130 !! za_sed_si(:,:) = zb_sed_si(:,:) + ( zfact * za_sed_si(:,:) ) 131 !! za_sed_ca(:,:) = zb_sed_ca(:,:) + ( zfact * za_sed_ca(:,:) ) 132 !! endif 133 !! ENDIF 134 !! 135 !! Time filter and swap of arrays 136 IF( ln_trcadv_cen2 .OR. ln_trcadv_tvd ) THEN ! centred or tvd scheme 137 IF( neuler == 0 .AND. kt == nittrc000 ) THEN 138 if (jorgben.eq.1) then 139 zb_sed_n(:,:) = zn_sed_n(:,:) 140 zn_sed_n(:,:) = za_sed_n(:,:) 141 za_sed_n(:,:) = 0.0 142 !! 143 zb_sed_fe(:,:) = zn_sed_fe(:,:) 144 zn_sed_fe(:,:) = za_sed_fe(:,:) 145 za_sed_fe(:,:) = 0.0 146 !! 147 zb_sed_c(:,:) = zn_sed_c(:,:) 148 zn_sed_c(:,:) = za_sed_c(:,:) 149 za_sed_c(:,:) = 0.0 150 endif 151 if (jinorgben.eq.1) then 152 zb_sed_si(:,:) = zn_sed_si(:,:) 153 zn_sed_si(:,:) = za_sed_si(:,:) 154 za_sed_si(:,:) = 0.0 155 !! 156 zb_sed_ca(:,:) = zn_sed_ca(:,:) 157 zn_sed_ca(:,:) = za_sed_ca(:,:) 158 za_sed_ca(:,:) = 0.0 159 endif 160 ELSE 161 if (jorgben.eq.1) then 162 zb_sed_n(:,:) = (atfp * & 163 ( zb_sed_n(:,:) + za_sed_n(:,:) )) + & 164 (atfp1 * zn_sed_n(:,:) ) 165 zn_sed_n(:,:) = za_sed_n(:,:) 166 za_sed_n(:,:) = 0.0 167 !! 168 zb_sed_fe(:,:) = (atfp * & 169 ( zb_sed_fe(:,:) + za_sed_fe(:,:) )) + & 170 (atfp1 * zn_sed_fe(:,:)) 171 zn_sed_fe(:,:) = za_sed_fe(:,:) 172 za_sed_fe(:,:) = 0.0 173 !! 174 zb_sed_c(:,:) = (atfp * & 175 ( zb_sed_c(:,:) + za_sed_c(:,:) )) + & 176 (atfp1 * zn_sed_c(:,:) ) 177 zn_sed_c(:,:) = za_sed_c(:,:) 178 za_sed_c(:,:) = 0.0 179 endif 180 if (jinorgben.eq.1) then 181 zb_sed_si(:,:) = (atfp * & 182 ( zb_sed_si(:,:) + za_sed_si(:,:) )) + & 183 (atfp1 * zn_sed_si(:,:)) 184 zn_sed_si(:,:) = za_sed_si(:,:) 185 za_sed_si(:,:) = 0.0 186 !! 187 zb_sed_ca(:,:) = (atfp * & 188 ( zb_sed_ca(:,:) + za_sed_ca(:,:) )) + & 189 (atfp1 * zn_sed_ca(:,:)) 190 zn_sed_ca(:,:) = za_sed_ca(:,:) 191 za_sed_ca(:,:) = 0.0 192 endif 193 ENDIF 194 ELSE ! case of smolar scheme or muscl 195 if (jorgben.eq.1) then 196 zb_sed_n(:,:) = za_sed_n(:,:) 197 zn_sed_n(:,:) = za_sed_n(:,:) 198 za_sed_n(:,:) = 0.0 199 !! 200 zb_sed_fe(:,:) = za_sed_fe(:,:) 201 zn_sed_fe(:,:) = za_sed_fe(:,:) 202 za_sed_fe(:,:) = 0.0 203 !! 204 zb_sed_c(:,:) = za_sed_c(:,:) 205 zn_sed_c(:,:) = za_sed_c(:,:) 206 za_sed_c(:,:) = 0.0 207 endif 208 if (jinorgben.eq.1) then 209 zb_sed_si(:,:) = za_sed_si(:,:) 210 zn_sed_si(:,:) = za_sed_si(:,:) 211 za_sed_si(:,:) = 0.0 212 !! 213 zb_sed_ca(:,:) = za_sed_ca(:,:) 214 zn_sed_ca(:,:) = za_sed_ca(:,:) 215 za_sed_ca(:,:) = 0.0 216 endif 217 ENDIF 218 endif 115 # endif 219 116 220 117 # if defined key_debug_medusa … … 253 150 fq1 = f_sbenin_n(ji,jj) + f_fbenin_n(ji,jj) 254 151 fq2 = fq0 + fq1 255 IF (lwp) write (numout,'(a,2i3,a,3f15.10)') & 256 'AXY N cons: (i,j)=',ji,jj,', (flx,ben,err)=', & 257 fq0,fq1,fq2 152 fq3 = f_benout_n(ji,jj) 153 if (lwp) write (numout,'a,2i3,a,4f15,5)') & 154 'AXY N cons: (i,j)=',ji,jj,', (flx,ben,err,out)=', & 155 fq0,fq1,fq2,fq3 258 156 ENDIF 259 157 ENDDO … … 266 164 fq1 = f_fbenin_si(ji,jj) 267 165 fq2 = fq0 + fq1 268 IF (lwp) write (numout,'(a,2i3,a,3f15.10)') & 269 'AXY Si cons: (i,j)=',ji,jj,', (flx,ben,err)=', & 270 fq0,fq1,fq2 166 fq3 = f_benout_si(ji,jj) 167 if (lwp) write (numout,'a,2i3,a,4f15,5)') & 168 'AXY Si cons: (i,j)=',ji,jj,', (flx,ben,err,out)=', & 169 fq0,fq1,fq2,fq3 271 170 ENDIF 272 171 ENDDO … … 278 177 fq0 = fflx_c(ji,jj) 279 178 fq1 = f_sbenin_c(ji,jj) + f_fbenin_c(ji,jj) + f_fbenin_ca(ji,jj) 280 fq2 = f_co2flux(ji,jj) * e3t_n(ji,jj,1)179 fq2 = f_co2flux(ji,jj) * fse3t(ji,jj,1) 281 180 fq3 = fq0 + fq1 282 IF (lwp) write (numout,'(a,2i3,a,4f15.10)') & 283 'AXY C cons: (i,j)=',ji,jj,', (flx,ben,asf,err)=', & 284 fq0,fq1,fq2,fq3 285 ENDIF 286 ENDDO 287 ENDDO 288 !! alkalinity 289 DO jj = 2,jpjm1 290 DO ji = 2,jpim1 291 if (tmask(ji,jj,1) == 1) then 292 fq0 = fflx_a(ji,jj) 293 fq1 = 2.0 * f_fbenin_ca(ji,jj) 294 fq2 = fq0 + fq1 295 IF (lwp) write (numout,'(a,2i3,a,3f15.10)') & 296 'AXY alk cons: (i,j)=',ji,jj,', (flx,ben,err)=', & 297 fq0,fq1,fq2 181 fq4 = f_benout_c(ji,jj) + f_benout_ca(ji,jj) 182 if (lwp) write (numout,'a,2i3,a,5f15,5)') & 183 'AXY C cons: (i,j)=',ji,jj,', (flx,ben,asf,err,out)=', & 184 fq0,fq1,fq2,fq3,fq4 185 ENDIF 186 ENDDO 187 ENDDO 188 !! alkalinity 189 DO jj = 2,jpjm1 190 DO ji = 2,jpim1 191 if (tmask(ji,jj,1) == 1) then 192 fq0 = fflx_a(ji,jj) 193 fq1 = 2.0 * f_fbenin_ca(ji,jj) 194 fq2 = fq0 + fq1 195 fq3 = 2.0 * f_benout_ca(ji,jj) 196 if (lwp) write (numout,'a,2i3,a,4f15,5)') & 197 'AXY alk cons: (i,j)=',ji,jj,', (flx,ben,err,out)=', & 198 fq0,fq1,fq2,fq3 298 199 ENDIF 299 200 ENDDO … … 333 234 ENDDO 334 235 ENDDO 236 237 !!!--------------------------------------------------------------- 238 !! Calculates Chl diag for UM coupling 239 !!!--------------------------------------------------------------- 240 !! JPALM -- 02-06-2017 -- 241 !! add Chl surf coupling 242 !! no need to output, just pass to cpl var 243 IF (lk_oasis) THEN 244 IF (chl_out.eq.1) THEN 245 !! export and scale surface chl 246 zn_chl_srf(:,:) = MAX( 0.0, (trn(:,:,1,jpchd) + trn(:,:,1,jpchn)) * 1.0E-6 ) 247 !! surf Chl in Kg-chl/m3 as needed for cpl 248 ELSEIF (chl_out.eq.2) THEN 249 !! export and scale mld chl 250 zn_chl_srf(:,:) = MAX( 0.0, fchl_ml(:,:) * 1.0E-6 ) 251 !! mld Chl in Kg-chl/m3 as needed for cpl 252 ENDIF 253 chloro_out_cpl(:,:) = zn_chl_srf(:,:) * scl_chl !! Coupling Chl 254 END IF 255 335 256 !!---------------------------------------------------------------- 336 257 !! Add in XML diagnostics stuff … … 360 281 CALL iom_put( "OCAL_LVL" , fccd ) 361 282 ENDIF 283 IF ( med_diag%CHL_MLD%dgsave ) THEN 284 CALL iom_put( "CHL_MLD" , fchl_ml ) 285 ENDIF 286 IF (lk_oasis) THEN 287 IF ( med_diag%CHL_CPL%dgsave ) THEN 288 CALL iom_put( "CHL_CPL" , chloro_out_cpl ) 289 ENDIF 290 ENDIF 362 291 IF ( med_diag%PN_JLIM%dgsave ) THEN 363 292 CALL iom_put( "PN_JLIM" , fjln2d ) -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_init.F90
r9073 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Add slow-sinking detrius variables 8 9 !!---------------------------------------------------------------------- 9 10 #if defined key_medusa … … 161 162 fprn_ml(:,:) = 0.0 !! mixed layer PP diagnostics 162 163 fprd_ml(:,:) = 0.0 !! mixed layer PP diagnostics 164 !! AXY (16/08/17) 165 fchl_ml(:,:) = 0.0 !! mixed layer chlorophyll diagnostics 163 166 !! 164 167 fslownflux(:,:) = 0.0 … … 183 186 f_omarg(:,:) = 0.0 184 187 f_omcal(:,:) = 0.0 185 188 !! 189 !! AXY (08/08/17): zero slow detritus fluxes 190 fslowsink(:,:) = 0.0 191 # if defined key_roam 192 fslowsinkc(:,:) = 0.0 193 # endif 186 194 !! 187 195 !! allocate and initiate 2D diag -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_mod.F90
r9070 r9157 7 7 !! History : 8 8 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 9 !! - ! 2017-08 (A. Yool) Slow detritus, ML-avg chl variables 9 10 !!---------------------------------------------------------------------- 10 11 #if defined key_medusa … … 54 55 !! AXY (01/03/10): add in mixed layer PP diagnostics 55 56 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fprn_ml,fprd_ml 57 !! AXY (16/08/17): add in mixed layer chlorophyll diagnostic 58 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fchl_ml 56 59 !! 57 60 !! nutrient limiting factors … … 94 97 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fregenfastc 95 98 # endif 96 99 !! 100 !! AXY (08/08/17): sinking of detritus moved here 101 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fslowsink, fslowgain, fslowloss 102 # if defined key_roam 103 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fslowsinkc, fslowgainc, fslowlossc 104 # endif 105 !! 97 106 !! Particle flux 98 107 REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: fdep1 … … 287 296 fjlim_pn(jpi,jpj),fjlim_pd(jpi,jpj), & 288 297 fun_T(jpi,jpj),fun_Q10(jpi,jpj), & 289 fprn_ml(jpi,jpj),fprd_ml(jpi,jpj), 298 fprn_ml(jpi,jpj),fprd_ml(jpi,jpj),fchl_ml(jpi,jpj), & 290 299 fnln(jpi,jpj),ffln2(jpi,jpj), & 291 300 fnld(jpi,jpj),ffld(jpi,jpj),fsld(jpi,jpj), & … … 316 325 fregenfastc(jpi,jpj), & 317 326 # endif 327 fslowsink(jpi,jpj),fslowgain(jpi,jpj), & 328 fslowloss(jpi,jpj), & 329 # if defined key_roam 330 fslowsinkc(jpi,jpj),fslowgainc(jpi,jpj), & 331 fslowlossc(jpi,jpj), & 332 # endif 318 333 fdep1(jpi,jpj), & 319 334 ftempn(jpi,jpj),ftempsi(jpi,jpj),ftempfe(jpi,jpj), & -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_update.F90
r9070 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Amend slow-detritus bug 9 !! - ! 2017-08 (A. Yool) Reformatting for clarity 8 10 !!---------------------------------------------------------------------- 9 11 #if defined key_medusa … … 60 62 fsil_cons, fsil_prod, fsdiss, & 61 63 ftempca, fthetad, fthetan, & 64 fslowsink, fslowgain, fslowloss, & ! AXY (22/08/17) 65 f_sbenin_n, f_sbenin_c, & 62 66 # if defined key_roam 67 fslowsinkc, fslowgainc, fslowlossc, & ! AXY (22/08/17) 63 68 fcar_cons, fcar_prod, fcomm_resp, & 64 69 fddc, fflx_a, fflx_c, fflx_o2, zoxy, & … … 181 186 ENDDO 182 187 183 DO jj = 2,jpjm1 184 DO ji = 2,jpim1 185 if (tmask(ji,jj,jk) == 1) then 186 !! 187 !!---------------------------------------------------------- 188 !! detritus 189 btra(ji,jj,jpdet_lc) = b0 * & 190 ! mort. losses 191 (fdpn(ji,jj) + ((1.0 - xfdfrac1) * & 192 fdpd(ji,jj)) + & 193 fdzmi(ji,jj) + & 194 ((1.0 - xfdfrac2) * fdzme(ji,jj)) + & 195 ! assim. inefficiency 196 ((1.0 - xbetan) * (finmi(ji,jj) + & 197 finme(ji,jj))) - & 198 ! grazing and remin. 199 fgmid(ji,jj) - fgmed(ji,jj) - & 200 fdd(ji,jj) + & 201 ! seafloor fast->slow 202 ffast2slown(ji,jj)) 203 !! 188 !!---------------------------------------------------------- 189 !! detritus 190 DO jj = 2,jpjm1 191 DO ji = 2,jpim1 192 if (tmask(ji,jj,jk) == 1) then 193 !! 194 btra(ji,jj,jpdet_lc) = b0 * ( & 195 fdpn(ji,jj) & ! mort. losses 196 + ((1.0 - xfdfrac1) * fdpd(ji,jj)) & ! mort. losses 197 + fdzmi(ji,jj) & ! mort. losses 198 + ((1.0 - xfdfrac2) * fdzme(ji,jj)) & ! mort. losses 199 + ((1.0 - xbetan) * (finmi(ji,jj) + finme(ji,jj))) & ! assim. inefficiency 200 - fgmid(ji,jj) - fgmed(ji,jj) & ! grazing 201 - fdd(ji,jj) & ! remin. 202 + fslowgain(ji,jj) - fslowloss(ji,jj) & ! slow-sinking 203 - (f_sbenin_n(ji,jj) / fse3t(ji,jj,jk)) & ! slow-sinking loss to seafloor 204 + ffast2slown(ji,jj) ) ! seafloor fast->slow 204 205 ENDIF 205 206 ENDDO … … 305 306 ffetop(ji,jj) + ffebot(ji,jj) - & 306 307 ffescav(ji,jj) ) 308 ENDIF 309 ENDDO 310 ENDDO 311 307 312 # if defined key_roam 308 !! 309 !!---------------------------------------------------------- 310 !! AXY (26/11/08): implicit detrital carbon change 311 btra(ji,jj,jpdtc_lc) = b0 * ( & 312 ! mort. losses 313 (xthetapn * fdpn(ji,jj)) + & 314 ((1.0 - xfdfrac1) * & 315 (xthetapd * fdpd(ji,jj))) + & 316 (xthetazmi * fdzmi(ji,jj)) + & 317 ((1.0 - xfdfrac2) * & 318 (xthetazme * fdzme(ji,jj))) + & 319 ! assim. inefficiency 320 ((1.0 - xbetac) * & 321 (ficmi(ji,jj) + ficme(ji,jj))) - & 322 ! grazing and remin. 323 fgmidc(ji,jj) - fgmedc(ji,jj) - & 324 fddc(ji,jj) + & 325 ! seafloor fast->slow 326 ffast2slowc(ji,jj) ) 313 !!---------------------------------------------------------- 314 !! AXY (26/11/08): implicit detrital carbon change 315 DO jj = 2,jpjm1 316 DO ji = 2,jpim1 317 if (tmask(ji,jj,jk) == 1) then 318 !! 319 btra(ji,jj,jpdtc_lc) = b0 * ( & 320 (xthetapn * fdpn(ji,jj)) & ! mort. losses 321 + ((1.0 - xfdfrac1) * (xthetapd * fdpd(ji,jj))) & ! mort. losses 322 + (xthetazmi * fdzmi(ji,jj)) & ! mort. losses 323 + ((1.0 - xfdfrac2) * (xthetazme * fdzme(ji,jj))) & ! mort. losses 324 + ((1.0 - xbetac) * (ficmi(ji,jj) + ficme(ji,jj))) & ! assim. inefficiency 325 - fgmidc(ji,jj) - fgmedc(ji,jj) & ! grazing 326 - fddc(ji,jj) & ! remin. 327 + fslowgainc(ji,jj) - fslowlossc(ji,jj) & ! slow-sinking 328 - (f_sbenin_c(ji,jj) / fse3t(ji,jj,jk)) & ! slow-sinking loss to seafloor 329 + ffast2slowc(ji,jj) ) ! seafloor fast->slow 327 330 ENDIF 328 331 ENDDO … … 575 578 f_o2flux(ji,jj)) 576 579 endif 580 ENDIF 581 ENDDO 582 ENDDO 577 583 # endif 578 ENDIF579 ENDDO580 ENDDO581 584 582 585 # if defined key_debug_medusa -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/detritus.F90
r9070 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Revise slow-sinking of detritus 8 9 !!---------------------------------------------------------------------- 9 10 #if defined key_medusa … … 35 36 f_sbenin_n, fdd, & 36 37 idf, idfval, & 37 # if defined key_roam 38 fslowsink, & 39 fslowgain, fslowloss, & 40 # if defined key_roam 41 fslowsinkc, & 42 fslowgainc, fslowlossc, & 38 43 fddc, & 39 44 # endif 40 45 fun_T, fun_Q10, zdet, zdtc 41 46 USE detritus_fast_sink_mod, ONLY: detritus_fast_sink 42 USE dom_oce, ONLY: mbathy, tmask47 USE dom_oce, ONLY: mbathy, e3t_0, e3t_n, gphit, tmask 43 48 USE in_out_manager, ONLY: lwp, numout 44 49 USE par_oce, ONLY: jpim1, jpjm1 45 50 USE sms_medusa, ONLY: jmd, jorgben, jsfd, vsed, & 46 51 xrfn, xmd, xmdc, xthetad 52 53 !!* Substitution 54 # include "domzgr_substitute.h90" 47 55 48 56 !! Level … … 123 131 DO ji = 2,jpim1 124 132 if (tmask(ji,jj,jk) == 1) then 133 !!---------------------------------------------------------------------- 134 !! Detritus sinking (AXY, 08/08/18) 135 !! Replaces slow-sinking done in trcsed_medusa.F90 136 !! 137 !! Uses the fslowsink variable to carry slow-sinking detritus from one 138 !! grid level to the next, variable fslowgain to "add" detritus sinking 139 !! from above and variable fslowloss to "subtract" detritus sinking out 140 !! to below; these variables appear in the differential equations of 141 !! detrital nitrogen and carbon below 142 !!---------------------------------------------------------------------- 143 !! 144 fslowgain(ji,jj) = fslowsink(ji,jj) / fse3t(ji,jj,jk) ! = mmol N / m3 / d 145 if (jk.lt.mbathy(ji,jj)) then 146 fslowloss(ji,jj) = (zdet(ji,jj) * vsed * 86400.) / fse3t(ji,jj,jk) ! = mmol N / m3 / d 147 else 148 fslowloss(ji,jj) = 0. ! = mmol N / m3 / d 149 endif 150 fslowsink(ji,jj) = fslowloss(ji,jj) * fse3t(ji,jj,jk) ! = mmol N / m2 / d 151 !! 152 # if defined key_roam 153 fslowgainc(ji,jj) = fslowsinkc(ji,jj) / fse3t(ji,jj,jk) ! = mmol C / m3 / d 154 if (jk.lt.mbathy(ji,jj)) then 155 fslowlossc(ji,jj) = (zdtc(ji,jj) * vsed * 86400.) / fse3t(ji,jj,jk) ! = mmol C / m3 / d 156 else 157 fslowlossc(ji,jj) = 0. ! = mmol C / m3 / d 158 endif 159 fslowsinkc(ji,jj) = fslowlossc(ji,jj) * fse3t(ji,jj,jk) ! = mmol C / m2 / d 160 # endif 161 ENDIF 162 ENDDO 163 ENDDO 164 165 DO jj = 2,jpjm1 166 DO ji = 2,jpim1 167 if (tmask(ji,jj,jk) == 1) then 125 168 !!--------------------------------------------------------- 126 169 !! Detritus addition to benthos -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/phytoplankton.F90
r9070 r9157 6 6 !! History : 7 7 !! - ! 2017-04 (M. Stringer) Code taken from trcbio_medusa.F90 8 !! - ! 2017-08 (A. Yool) Mean mixed layer chlorophyll 8 9 !!---------------------------------------------------------------------- 9 10 #if defined key_medusa … … 42 43 zchd, zchn, zdet, zdin, zdtc, & 43 44 zfer, zpds, zphd, zphn, zsil, & 44 zzme, zzmi 45 zzme, zzmi, fchl_ml 45 46 USE dom_oce, ONLY: e3t_0, e3t_n, gdepw_0, gdepw_n, tmask 46 47 USE in_out_manager, ONLY: lwp, numout … … 55 56 xvpd, xvpn, xxi 56 57 USE zdfmxl, ONLY: hmld 58 USE lbclnk, ONLY: lbc_lnk 57 59 58 60 !!* Substitution … … 373 375 fprd_ml(ji,jj) = fprd_ml(ji,jj) + (fprd(ji,jj) * zphd(ji,jj) * & 374 376 fse3t(ji,jj,jk) * fq0) 375 ENDIF 376 ENDDO 377 ENDDO 377 !! AXY (16/08/17) 378 fchl_ml(ji,jj) = fchl_ml(ji,jj) + ((zchn(ji,jj) + zchd(ji,jj)) * & 379 (fse3t(ji,jj,jk) * fq0) / hmld(ji,jj)) 380 ENDIF 381 ENDDO 382 ENDDO 383 CALL lbc_lnk(fchl_ml(:,:),'T',1. ) 378 384 379 385 DO jj = 2,jpjm1 -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/sms_medusa.F90
r8132 r9157 177 177 INTEGER :: jdms_model !: choice of DMS model passed to atmosphere 178 178 !! 1 = ANDR, 2 = SIMO, 3 = ARAN, 4 = HALL 179 !! 179 !! FOR UKESM 180 REAL(wp) :: scl_chl !: scaling factor for tuned Chl passed to the UM 181 INTEGER :: chl_out !: select Chl field exported and scaled for UM: 182 !: 1- Surface Chl ; 2- MLD Chl 180 183 !! 181 184 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: remdmp !: depth dependent damping coefficient of passive tracers -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcini_medusa.F90
r8147 r9157 271 271 zn_dms_srf(:,:) = 0.0 272 272 za_dms_srf(:,:) = 0.0 273 zn_chl_srf(:,:) = 2.0E-8 !! Chl srf273 zn_chl_srf(:,:) = 2.0E-8 !! Chl cpl - set first as surf 274 274 !! 275 275 IF(lwp) WRITE(numout,*) ' trc_ini_medusa: DMS and CO2 flux (UKESM) initialised to zero' … … 278 278 CO2Flux_out_cpl(:,:) = zn_co2_flx(:,:) !! Coupling variable 279 279 DMS_out_cpl(:,:) = zn_dms_srf(:,:) !! Coupling variable 280 chloro_out_cpl(:,:) = zn_chl_srf(:,:) !! Coupling variable280 chloro_out_cpl(:,:) = zn_chl_srf(:,:) * scl_chl !! Coupling variable 281 281 END IF 282 282 !! -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcnam_medusa.F90
r9070 r9157 24 24 USE sms_medusa ! sms trends 25 25 USE iom ! I/O manager 26 USE sbc_oce, ONLY: lk_oasis 26 27 !!USE trc_nam_dia ! JPALM 13-11-2015 -- if iom_use for diag 27 28 … … 85 86 & jriver_n,jriver_si,jriver_c,jriver_alk,jriver_dep, & 86 87 & xsdiss, & 87 & sedlam,sedlostpoc,jpkb,jdms,jdms_input,jdms_model 88 & sedlam,sedlostpoc,jpkb,jdms,jdms_input,jdms_model, & 89 & scl_chl, chl_out 88 90 #if defined key_roam 89 91 NAMELIST/natroam/ xthetaphy,xthetazoo,xthetanit, & … … 246 248 jdms_input = 0 247 249 jdms_model = 0 250 scl_chl = 1. 251 chl_out = 1 248 252 249 253 !REWIND(numnatm) … … 400 404 !! 1 = ANDR, 2 = SIMO, 3 = ARAN, 4 = HALL, 5 = ANDM 401 405 !! 406 !! UKESM1 - exported Chl to UM 407 !! scl_chl : scaling factor to tune the chl field sent to the UM 408 !! chl_out : select the chl field to send at the UM: 409 !! 1- Surf Chl ; 2- MLD Chl 410 402 411 IF(lwp) THEN 403 412 !! … … 909 918 !! 910 919 !! UKESM1 - new diagnostics !! Jpalm; AXY (08/07/15) 911 WRITE(numout,*) '=== UKESM1-related parameters' 912 WRITE(numout,*) & 913 & ' include DMS diagnostic?, jdms = ', jdms 914 if (jdms_input .eq. 0) then 915 WRITE(numout,*) & 916 & ' use instant (0) or diel-avg (1) inputs, jdms_input = instantaneous' 917 else 918 WRITE(numout,*) & 919 & ' use instant (0) or diel-avg (1) inputs, jdms_input = diel-average' 920 endif 921 if (jdms_model .eq. 1) then 922 WRITE(numout,*) & 923 & ' choice of DMS model passed to atmosphere, jdms_model = Anderson et al. (2001)' 924 elseif (jdms_model .eq. 2) then 925 WRITE(numout,*) & 926 & ' choice of DMS model passed to atmosphere, jdms_model = Simo & Dachs (2002)' 927 elseif (jdms_model .eq. 3) then 928 WRITE(numout,*) & 929 & ' choice of DMS model passed to atmosphere, jdms_model = Aranami & Tsunogai (2004)' 930 elseif (jdms_model .eq. 4) then 931 WRITE(numout,*) & 932 & ' choice of DMS model passed to atmosphere, jdms_model = Halloran et al. (2010)' 933 elseif (jdms_model .eq. 5) then 934 WRITE(numout,*) & 935 & ' choice of DMS model passed to atmosphere, jdms_model = Anderson et al. (2001; modified)' 936 endif 920 WRITE(numout,*) '=== UKESM1-related parameters ===' 921 WRITE(numout,*) ' ---- --- ---' 922 923 IF (lk_oasis) THEN 924 WRITE(numout,*) '=== UKESM1 -- coupled DMS to the atmosphere' 925 WRITE(numout,*) & 926 & ' include DMS diagnostic?, jdms = ', jdms 927 if (jdms_input .eq. 0) then 928 WRITE(numout,*) & 929 & ' use instant (0) or diel-avg (1) inputs, jdms_input = instantaneous' 930 else 931 WRITE(numout,*) & 932 & ' use instant (0) or diel-avg (1) inputs, jdms_input = diel-average' 933 endif 934 if (jdms_model .eq. 1) then 935 WRITE(numout,*) & 936 & ' choice of DMS model passed to atmosphere, jdms_model = Anderson et al. (2001)' 937 elseif (jdms_model .eq. 2) then 938 WRITE(numout,*) & 939 & ' choice of DMS model passed to atmosphere, jdms_model = Simo & Dachs (2002)' 940 elseif (jdms_model .eq. 3) then 941 WRITE(numout,*) & 942 & ' choice of DMS model passed to atmosphere, jdms_model = Aranami & Tsunogai (2004)' 943 elseif (jdms_model .eq. 4) then 944 WRITE(numout,*) & 945 & ' choice of DMS model passed to atmosphere, jdms_model = Halloran et al. (2010)' 946 elseif (jdms_model .eq. 5) then 947 WRITE(numout,*) & 948 & ' choice of DMS model passed to atmosphere, jdms_model = Anderson et al. (2001; modified)' 949 endif 950 951 WRITE(numout,*) '=== UKESM1 -- coupled Chl to the atmosphere' 952 WRITE(numout,*) & 953 & ' Scaling factor to export tuned Chl to the atmosphere scl_chl = ', scl_chl 954 IF (chl_out .eq. 1) THEN 955 WRITE(numout,*) & 956 & ' Chl field to be scaled and sent to the atmosphere: chl_out = Surface Chl field ' 957 ELSEIF (chl_out .eq. 2) THEN 958 WRITE(numout,*) & 959 & ' Chl field to be scaled and sent to the atmosphere: chl_out = MLD Chl field ' 960 ENDIF 961 ENDIF ! IF lk_oasis=true 937 962 !! 938 963 ENDIF … … 2053 2078 med_diag%OCN_DPCO2%dgsave = .FALSE. 2054 2079 ENDIF 2055 !! 2080 !! UKESM additional 2081 IF (iom_use("CHL_MLD")) THEN 2082 med_diag%CHL_MLD%dgsave = .TRUE. 2083 ELSE 2084 med_diag%CHL_MLD%dgsave = .FALSE. 2085 ENDIF 2086 IF (iom_use("CHL_CPL")) THEN 2087 med_diag%CHL_CPL%dgsave = .TRUE. 2088 ELSE 2089 med_diag%CHL_CPL%dgsave = .FALSE. 2090 ENDIF 2091 !! 3D 2056 2092 IF (iom_use("TPP3")) THEN 2057 2093 med_diag%TPP3%dgsave = .TRUE. -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcsms_medusa.F90
r8074 r9157 8 8 !! - ! 2008-11 (A. Yool) continuing adaptation for MEDUSA 9 9 !! - ! 2010-03 (A. Yool) updated for branch inclusion 10 !! - ! 2017-08 (A. Yool) amend for slow detritus bug 10 11 !!---------------------------------------------------------------------- 11 12 #if defined key_medusa … … 88 89 # endif 89 90 90 CALL trc_sed_medusa( kt ) ! sedimentation model 91 # if defined key_debug_medusa 92 IF(lwp) WRITE(numout,*) ' MEDUSA done trc_sed_medusa' 93 CALL flush(numout) 94 # endif 91 !! AXY (08/08/2017): remove call to buggy subroutine (now handled by detritus.F90) 92 !! CALL trc_sed_medusa( kt ) ! sedimentation model 93 !! # if defined key_debug_medusa 94 !! IF(lwp) WRITE(numout,*) ' MEDUSA done trc_sed_medusa' 95 !! CALL flush(numout) 96 !! # endif 95 97 # endif 96 98 -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/trc.F90
r8280 r9157 134 134 OCN_KWCO2, OCN_K0, CO2STARAIR, OCN_DPCO2, & ! end of regular 2D 135 135 TPP3, DETFLUX3, REMIN3N, PH3, OM_CAL3, & ! end of regular 3D 136 ! JPALM (01/09/17): additional UKESM 2D diag 137 CHL_MLD, CHL_CPL, & 136 138 ! AXY (11/11/16): additional CMIP6 2D diagnostics 137 139 epC100, epCALC100, epN100, epSI100, & -
branches/NERC/dev_r5518_GO6_Carb_Fail_from_GO6_8356/NEMOGCM/NEMO/TOP_SRC/trcrst.F90
r9073 r9157 276 276 !! as proxy of org matter from the ocean 277 277 !! -- needed for the coupling with atm 278 !! 07-12-2017 -- To make things cleaner, we want to store an 279 !! unscaled Chl field in the restart and only 280 !! scale it when reading it in. 281 278 282 IF( iom_varid( numrtr, 'N_CHL_srf', ldstop = .FALSE. ) > 0 ) THEN 279 IF(lwp) WRITE(numout,*) 'Chl surf concentration - reading in ...'283 IF(lwp) WRITE(numout,*) 'Chl cpl concentration - reading in ... - scale by ', scl_chl 280 284 CALL iom_get( numrtr, jpdom_autoglo, 'N_CHL_srf', zn_chl_srf(:,:) ) 281 285 ELSE 282 IF(lwp) WRITE(numout,*) ' Chl surf concentration - setting to zero ...'283 zn_chl_srf(:,:) = (trn(:,:,1,jpchn) + trn(:,:,1,jpchd)) * 1.E-6286 IF(lwp) WRITE(numout,*) 'set Chl coupled concentration - scaled by ', scl_chl 287 zn_chl_srf(:,:) = MAX( 0.0, (trn(:,:,1,jpchn) + trn(:,:,1,jpchd)) * 1.E-6 ) 284 288 ENDIF 285 289 IF (lk_oasis) THEN 286 chloro_out_cpl(:,:) = zn_chl_srf(:,:) !! Coupling variable290 chloro_out_cpl(:,:) = zn_chl_srf(:,:) * scl_chl !! Coupling variable 287 291 END IF 288 292 !! … … 296 300 call trc_rst_dia_stat(zn_dms_srf(:,:), 'DMS surf') 297 301 call trc_rst_dia_stat(zn_co2_flx(:,:), 'CO2 flux') 298 call trc_rst_dia_stat(zn_chl_srf(:,:), 'CHL surf') 302 IF (lk_oasis) THEN 303 call trc_rst_dia_stat(chloro_out_cpl(:,:), 'CHL cpl') 304 END IF 299 305 !! 300 306 !! JPALM 14-06-2016 -- add Carbonate chenistry variables through the restart … … 456 462 CALL iom_rstput( kt, nitrst, numrtw, 'B_CO2_flx', zb_co2_flx(:,:) ) 457 463 CALL iom_rstput( kt, nitrst, numrtw, 'N_CO2_flx', zn_co2_flx(:,:) ) 464 !! JPALM 07-12-2017 -- To make things cleaner, we want to store an 465 !! unscaled Chl field in the restart and only 466 !! scale it when reading it in. 458 467 CALL iom_rstput( kt, nitrst, numrtw, 'N_CHL_srf', zn_chl_srf(:,:) ) 459 468 !! … … 467 476 call trc_rst_dia_stat(zn_dms_srf(:,:), 'DMS surf') 468 477 call trc_rst_dia_stat(zn_co2_flx(:,:), 'CO2 flux') 469 call trc_rst_dia_stat(zn_chl_srf(:,:), ' CHL surf')478 call trc_rst_dia_stat(zn_chl_srf(:,:), 'unscaled CHL cpl') 470 479 !! 471 480 IF(lwp) WRITE(numout,*) ' MEDUSA averaged prop. for dust and iron dep.'
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