- Timestamp:
- 2018-09-24T11:47:08+02:00 (6 years ago)
- Location:
- branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA
- Files:
-
- 8 edited
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air_sea.F90 (modified) (4 diffs)
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bio_medusa_fin.F90 (modified) (3 diffs)
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bio_medusa_init.F90 (modified) (2 diffs)
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plankton.F90 (modified) (3 diffs)
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sms_medusa.F90 (modified) (6 diffs)
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trcbio_medusa.F90 (modified) (3 diffs)
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trcini_medusa.F90 (modified) (1 diff)
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trcnam_medusa.F90 (modified) (7 diffs)
Legend:
- Unmodified
- Added
- Removed
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branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/air_sea.F90
r10020 r10149 74 74 jriver_alk, jriver_c, & 75 75 jriver_n, jriver_si, & 76 ln_foam_medusa, & 76 77 riv_alk, riv_c, riv_n, riv_si, & 77 78 zn_dms_chd, zn_dms_chn, zn_dms_din, & 78 79 zn_dms_mld, zn_dms_qsr, & 80 f2_pco2w, f2_fco2w, & 79 81 xnln, xnld 80 82 USE trc, ONLY: med_diag … … 87 89 # else 88 90 USE trcco2_medusa, ONLY: trc_co2_medusa 91 USE mocsy_mainmod, ONLY: p2fCO2 89 92 # endif 90 93 USE trcdms_medusa, ONLY: trc_dms_medusa … … 327 330 iters, ' AT (', ji, ', ', jj, ', 1) AT ', kt 328 331 endif 332 IF ( ln_foam_medusa ) THEN 333 !! DAF (Aug 2017): calculate fCO2 for observation operator 334 CALL p2fCO2( f_pco2w, ztmp, f_pp0, 0.0, 1, f_fco2w ) 335 ENDIF 329 336 ENDIF 330 337 ENDDO … … 506 513 CO2flux_conv 507 514 !! ENDIF 515 IF ( ln_foam_medusa ) THEN 516 !! DAF (Aug 2017): Save pCO2 and fCO2 for observation operator 517 f2_pco2w(ji,jj) = f_pco2w(ji,jj) 518 f2_fco2w(ji,jj) = f_pco2w(ji,jj) 519 ENDIF 508 520 IF ( lk_iomput ) THEN 509 521 IF( med_diag%ATM_PCO2%dgsave ) THEN -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_fin.F90
r10020 r10149 46 46 f3_co3, f3_h2co3, f3_hco3, & 47 47 f3_omarg, f3_omcal, f3_pH, & 48 ln_foam_medusa, mld_max, pgrow_avg, & 49 ploss_avg, phyt_avg, & 48 50 za_sed_c, za_sed_ca, za_sed_fe, & 49 51 za_sed_n, za_sed_si, & … … 55 57 USE trc, ONLY: med_diag, nittrc000, trn 56 58 USE trcnam_trp, ONLY: ln_trcadv_cen2, ln_trcadv_tvd 59 USE zdfmxl, ONLY: hmld 57 60 58 61 !! time (integer timestep) … … 113 116 # endif 114 117 118 IF ( ln_foam_medusa ) THEN 119 !!---------------------------------------------------------------------- 120 !! Diagnostics required for ocean colour assimilation: 121 !! Mixed layer average phytoplankton growth, loss and concentration 122 !! Maximum mixed layer depth 123 !!---------------------------------------------------------------------- 124 !! 125 DO jj = 2,jpjm1 126 DO ji = 2,jpim1 127 IF ( hmld(ji,jj) .GT. 0.0 ) THEN 128 pgrow_avg(ji,jj) = pgrow_avg(ji,jj) / hmld(ji,jj) 129 ploss_avg(ji,jj) = ploss_avg(ji,jj) / hmld(ji,jj) 130 phyt_avg(ji,jj) = phyt_avg(ji,jj) / hmld(ji,jj) 131 IF ( hmld(ji,jj) .GT. mld_max(ji,jj) ) THEN 132 mld_max(ji,jj) = hmld(ji,jj) 133 ENDIF 134 ENDIF 135 END DO 136 END DO 137 ENDIF 138 115 139 # if defined key_debug_medusa 116 140 !! AXY (12/07/17) -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/bio_medusa_init.F90
r10020 r10149 35 35 USE bio_medusa_mod 36 36 USE par_oce, ONLY: jpi, jpj, jpk 37 USE sms_medusa, ONLY: jdms 37 USE sms_medusa, ONLY: jdms, pgrow_avg, ploss_avg, phyt_avg, mld_max 38 38 USE trc, ONLY: ln_diatrc, med_diag, nittrc000 39 39 USE in_out_manager, ONLY: lwp, numout … … 195 195 fslowsinkc(:,:) = 0.0 196 196 # endif 197 !! 198 pgrow_avg(:,:) = 0.0 199 ploss_avg(:,:) = 0.0 200 phyt_avg(:,:) = 0.0 201 IF( kt == nittrc000 ) THEN 202 mld_max(:,:) = 0.0 203 ENDIF 197 204 !! 198 205 !! allocate and initiate 2D diag -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/plankton.F90
r8441 r10149 36 36 fdpn, fdpn2, fdzme, fdzme2, & 37 37 fdzmi, fdzmi2, fsdiss, fsin, & 38 fdep1, fprn, fprd, & 39 fgmepd, fgmepn, fgmipn, & 38 40 zphd, zphn, zpds, zzme, zzmi 39 USE dom_oce, ONLY: tmask 41 USE dom_oce, ONLY: e3t_0, e3t_n, gdepw_0, gdepw_n, tmask 42 USE par_kind, ONLY: wp 40 43 USE par_oce, ONLY: jpim1, jpjm1 41 44 USE phytoplankton_mod, ONLY: phytoplankton 42 45 USE sms_medusa, ONLY: jmpd, jmpn, jmzme, jmzmi, & 46 ln_foam_medusa, & 47 pgrow_avg, ploss_avg, phyt_avg, & 43 48 xkphd, xkphn, xkzme, xkzmi, & 44 49 xmetapd, xmetapn, xmetazme, xmetazmi, & 45 50 xmpd, xmpn, xmzme, xmzmi, xsdiss 51 USE zdfmxl, ONLY: hmld 46 52 USE zooplankton_mod, ONLY: zooplankton 53 54 !!* Substitution 55 # include "domzgr_substitute.h90" 47 56 48 57 !! Level … … 50 59 51 60 INTEGER :: ji, jj 61 62 REAL(wp) :: fq0 52 63 53 64 !!------------------------------------------------------------------- … … 188 199 ENDDO 189 200 201 IF ( ln_foam_medusa ) THEN 202 !! Mixed layer averages for ocean colour assimilation 203 !! 204 DO jj = 2,jpjm1 205 DO ji = 2,jpim1 206 IF (tmask(ji,jj,jk) == 1) THEN 207 if (fdep1(ji,jj).le.hmld(ji,jj)) then 208 !! this level is entirely in the mixed layer 209 fq0 = 1.0 210 elseif (fsdepw(ji,jj,jk).ge.hmld(ji,jj)) then 211 !! this level is entirely below the mixed layer 212 fq0 = 0.0 213 else 214 !! this level straddles the mixed layer 215 fq0 = (hmld(ji,jj) - fsdepw(ji,jj,jk)) / fse3t(ji,jj,jk) 216 endif 217 !! 218 pgrow_avg(ji,jj) = pgrow_avg(ji,jj) + & 219 (((fprn(ji,jj) * zphn(ji,jj)) + & 220 (fprd(ji,jj) * zphd(ji,jj)) ) * & 221 fse3t(ji,jj,jk) * fq0) 222 ploss_avg(ji,jj) = ploss_avg(ji,jj) + & 223 ((fgmepd(ji,jj) + fdpd(ji,jj) + & 224 fdpd2(ji,jj) + & 225 fgmepn(ji,jj) + fdpn(ji,jj) + & 226 fdpn2(ji,jj) + fgmipn(ji,jj) ) * & 227 fse3t(ji,jj,jk) * fq0) 228 phyt_avg(ji,jj) = phyt_avg(ji,jj) + & 229 ((zphn(ji,jj) + zphd(ji,jj)) * & 230 fse3t(ji,jj,jk) * fq0) 231 ENDIF 232 ENDDO 233 ENDDO 234 ENDIF 235 190 236 END SUBROUTINE plankton 191 237 -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/sms_medusa.F90
r9385 r10149 212 212 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: f2_ccd_arg !: 2D aragonite CCD depth 213 213 !! 214 !! 2D fields of pCO2 and fCO2 for observation operator 215 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: f2_pco2w !: 2D pCO2 216 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: f2_fco2w !: 2D fCO2 217 !! 214 218 !! 2D fields of organic and inorganic material sedimented on the seafloor 215 219 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: zb_sed_n !: 2D organic nitrogen (before) … … 289 293 INTEGER :: co2_rec 290 294 REAL(wp) :: co2_yinit, co2_yend !: First and Last year read in the xCO2.atm file 295 REAL(wp) :: xobs_xco2a !: Observed atmospheric xCO2, from namelist 291 296 #endif 292 297 … … 349 354 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: cmask !: ??? 350 355 356 !!---------------------------------------------------------------------- 357 !! Parameters required for ocean colour assimilation 358 !!---------------------------------------------------------------------- 359 !! 360 LOGICAL :: ln_foam_medusa !: Flag to calculate and save diagnostics 361 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: pgrow_avg !: Mixed layer average phytoplankton growth 362 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: ploss_avg !: Mixed layer average phytoplankton loss 363 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: phyt_avg !: Mixed layer average phytoplankton 364 REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: mld_max !: Maximum mixed layer depth 365 !! 366 351 367 !!---------------------------------------------------------------------- 352 368 !! NEMO/TOP 3.3 , NEMO Consortium (2010) … … 361 377 !!---------------------------------------------------------------------- 362 378 USE lib_mpp , ONLY: ctl_warn 363 INTEGER :: ierr( 8) ! Local variables379 INTEGER :: ierr(9) ! Local variables 364 380 !!---------------------------------------------------------------------- 365 381 ierr(:) = 0 … … 371 387 !* 2D and 3D fields of carbonate system parameters 372 388 ALLOCATE( f2_ccd_cal(jpi,jpj) , f2_ccd_arg(jpi,jpj) , & 389 f2_pco2w(jpi,jpj) , f2_fco2w(jpi,jpj) , & 373 390 & f3_pH(jpi,jpj,jpk) , f3_h2co3(jpi,jpj,jpk), & 374 391 & f3_hco3(jpi,jpj,jpk) , f3_co3(jpi,jpj,jpk) , & … … 419 436 & ffln(jpi,jpj,jpk) , fflf(jpi,jpj,jpk) , & 420 437 & ffls(jpi,jpj,jpk) , cmask(jpi,jpj) , STAT=ierr(8) ) 438 !* Fields for ocean colour data assimilation 439 ALLOCATE( pgrow_avg(jpi,jpj) , ploss_avg(jpi,jpj) , & 440 & phyt_avg(jpi,jpj) , mld_max(jpi,jpj) , STAT=ierr(9) ) 421 441 #endif 422 442 ! -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcbio_medusa.F90
r10020 r10149 105 105 USE sbc_oce, ONLY: lk_oasis 106 106 USE sms_medusa, ONLY: hist_pco2, co2_yinit, co2_yend, & 107 lk_pi_co2 107 # if defined key_roam 108 xobs_xco2a, & 109 # endif 110 pgrow_avg, & 111 ploss_avg, phyt_avg, mld_max, & 112 lk_pi_co2, ln_foam_medusa 108 113 USE trc, ONLY: ln_rsttr, nittrc000, trn 109 114 USE bio_medusa_init_mod, ONLY: bio_medusa_init … … 330 335 !! f_xco2a(:,:) = 284.725 !! CMIP5 pre-industrial pCO2 331 336 f_xco2a(:,:) = 284.317 !! CMIP6 pre-industrial pCO2 337 ELSEIF ( xobs_xco2a > 0.0 ) THEN 338 IF(lwp) WRITE(numout,*) ' using observed atm pCO2 = ', xobs_xco2a 339 f_xco2a(:,:) = xobs_xco2a 332 340 ELSE 333 341 !! xCO2 from file … … 418 426 !! now use the NEMO calendar tool : nsec_month to be sure to call 419 427 !! at the beginning of a new month . 428 !! DAF: For FOAM we want to run daily 420 429 IF ( (kt == nittrc000 .AND. .NOT.ln_rsttr) .OR. & 421 ( nsec_month .LE. INT(rdt) ) ) THEN 430 ( nsec_month .LE. INT(rdt) ) .OR. & 431 ( nsec_day .LE. INT(rdt) .AND. ln_foam_medusa ) ) THEN 422 432 IF ( lwp ) WRITE(numout,*) & 423 433 ' *** 3D carb chem call *** -- kt:', kt, & -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcini_medusa.F90
r9385 r10149 330 330 !!---------------------------------------------------------------------- 331 331 !! 332 IF( ( .NOT.lk_oasis ) .AND. ( .NOT.lk_pi_co2 ) ) THEN332 IF( ( .NOT.lk_oasis ) .AND. ( .NOT.lk_pi_co2 ) .AND. ( xobs_xco2a <= 0.0 ) ) THEN 333 333 IF(lwp) WRITE(numout,*) ' trc_ini_medusa: initialisating atm CO2 record' 334 334 CALL trc_ini_medusa_co2atm -
branches/UKMO/dev_r5518_GO6_package/NEMOGCM/NEMO/TOP_SRC/MEDUSA/trcnam_medusa.F90
r9258 r10149 87 87 & xsdiss, & 88 88 & sedlam,sedlostpoc,jpkb,jdms,jdms_input,jdms_model, & 89 & scl_chl, chl_out, dmsmin, dmscut, dmsslp 89 & scl_chl, chl_out, dmsmin, dmscut, dmsslp, & 90 & ln_foam_medusa 90 91 #if defined key_roam 91 92 NAMELIST/natroam/ xthetaphy,xthetazoo,xthetanit, & 93 & xobs_xco2a, & 92 94 & xthetarem,xo2min 93 95 #endif … … 255 257 dmscut = 1.72 !! Anderson DMS default 256 258 dmsslp = 8.24 !! Anderson DMS default 259 !! 260 ln_foam_medusa = .FALSE. 257 261 258 262 !REWIND(numnatm) … … 415 419 !! chl_out : select the chl field to send at the UM: 416 420 !! 1- Surf Chl ; 2- MLD Chl 421 !! 422 !! FOAM - observation operator and data assimilation 423 !! ln_foam_medusa : calculate required diagnostics 417 424 418 425 IF(lwp) THEN … … 975 982 ENDIF 976 983 ENDIF ! IF lk_oasis=true 984 !! FOAM 985 WRITE(numout,*) '=== FOAM-related parameters' 986 WRITE(numout,*) & 987 & ' calculate diagnostics for data assimilation, ln_foam_medusa = ', ln_foam_medusa 977 988 !! 978 989 ENDIF … … 1030 1041 xthetarem = 0. 1031 1042 xo2min = 0. 1043 xobs_xco2a = 0. 1032 1044 1033 1045 !READ(numnatm,natroam) … … 1049 1061 !! xthetarem : oxygen consumption by carbon remineralisation 1050 1062 !! xo2min : oxygen minimum concentration 1063 !! xobs_xco2a : observed atmospheric xCO2 (not used if <= 0) 1051 1064 1052 1065 IF(lwp) THEN … … 1066 1079 WRITE(numout,*) & 1067 1080 & ' oxygen minimum concentration xo2min = ', xo2min 1081 WRITE(numout,*) & 1082 & ' observed atmospheric xCO2 (not used if <= 0) xobs_xco2a = ', xobs_xco2a 1068 1083 ENDIF 1069 1084
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