Ignore:
Timestamp:
2020-07-03T14:42:49+02:00 (3 months ago)
Author:
dford
Message:

Update NEMO-FABM coupler for compatability with FABM v1.0.

File:
1 edited

Legend:

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  • branches/UKMO/AMM15_v3_6_STABLE_package_collate_utils366_fabmv1/NEMOGCM/NEMO/TOP_SRC/FABM/trcsms_fabm.F90

    r10728 r13241  
    55   !!====================================================================== 
    66   !! History :   1.0  !  2015-04  (PML) Original code 
     7   !! History :   1.1  !  2020-06  (PML) Update to FABM 1.0, improved performance 
    78   !!---------------------------------------------------------------------- 
    89#if defined key_fabm 
     
    1920   USE trd_oce 
    2021   USE trdtrc 
     22   USE traqsr,only: ln_qsr_spec 
    2123#if defined key_trdtrc && defined key_iomput 
    2224   USE trdtrc_oce 
     
    2426 
    2527   USE oce, only: tsn  ! Needed? 
    26    USE sbc_oce, only: lk_oasis 
     28   USE sbc_oce, only: lk_oasis,fr_i 
    2729   USE dom_oce 
    2830   USE zdf_oce 
    29    !USE iom 
     31   USE iom 
    3032   USE xios 
    3133   USE cpl_oasis3 
     
    3638   USE asmbgc, ONLY: mld_choice_bgc 
    3739   USE lbclnk 
     40   USE fabm_types, ONLY: standard_variables 
    3841 
    3942   !USE fldread         !  time interpolation 
    40  
    41    USE fabm 
    4243 
    4344   IMPLICIT NONE 
     
    4849   PRIVATE 
    4950 
    50    PUBLIC   trc_sms_fabm       ! called by trcsms.F90 module 
    51    PUBLIC   trc_sms_fabm_alloc ! called by trcini_fabm.F90 module 
    52    PUBLIC   trc_sms_fabm_check_mass 
    53    PUBLIC   st2d_fabm_nxt ! 2D state intergration 
    54    PUBLIC   compute_fabm ! Compute FABM sources, sinks and diagnostics 
    55  
    56    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:) :: flux    ! Cross-interface flux of pelagic variables (# m-2 s-1) 
    57  
    58    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:)   :: ext     ! Light extinction coefficient (m-1) 
    59  
    60    ! Work array for mass aggregation 
    61    REAL(wp), ALLOCATABLE, SAVE, TARGET, DIMENSION(:,:)   :: current_total 
    62  
    63  
    64    ! Arrays for environmental variables 
    65    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, TARGET, DIMENSION(:,:,:) :: prn,rho 
    66    REAL(wp), PUBLIC, ALLOCATABLE, SAVE, TARGET, DIMENSION(:,:) :: taubot 
    67  
    68    ! repair counters 
    69    INTEGER :: repair_interior_count,repair_surface_count,repair_bottom_count 
    70  
    71    ! state check type 
    72    TYPE type_state 
    73       LOGICAL             :: valid 
    74       LOGICAL             :: repaired 
    75    END TYPE 
    76  
    77    REAL(wp), PUBLIC :: daynumber_in_year 
    78  
    79    TYPE (type_bulk_variable_id),SAVE :: swr_id 
     51   PUBLIC   trc_sms_fabm            ! called by trcsms.F90 module 
     52   PUBLIC   trc_sms_fabm_alloc      ! called by trcini_fabm.F90 module 
     53   PUBLIC   trc_sms_fabm_check_mass ! called by trcwri_fabm.F90 
     54 
     55   ! Work arrays 
     56   REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: flux          ! Cross-interface flux of pelagic variables (# m-2 s-1) 
     57   REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: current_total ! Totals of conserved quantities 
     58 
     59   ! Arrays for environmental variables that are computed by the coupler 
     60   REAL(wp), PUBLIC, TARGET, ALLOCATABLE, DIMENSION(:,:,:) :: prn,rho 
     61   REAL(wp), PUBLIC, TARGET, ALLOCATABLE, DIMENSION(:,:) :: taubot 
     62   REAL(wp), PUBLIC, TARGET :: daynumber_in_year 
     63   REAL(wp), PUBLIC, POINTER :: swrad(:,:,:)  ! pointer to ERSEM spectral heating term 
     64 
     65   ! State repair counters 
     66   INTEGER, SAVE :: repair_interior_count = 0 
     67   INTEGER, SAVE :: repair_surface_count  = 0 
     68   INTEGER, SAVE :: repair_bottom_count   = 0 
     69 
     70   ! Coupler parameters 
     71   INTEGER, PUBLIC :: nn_adv  ! Vertical advection scheme for sinking/floating/movement 
     72                              ! (1: 1st order upwind, 3: 3rd order TVD) 
     73 
     74   ! Flag indicating whether model%start has been called (will be done on-demand) 
     75   LOGICAL, SAVE :: started = .false. 
    8076 
    8177   !!---------------------------------------------------------------------- 
     
    9692      ! 
    9793      INTEGER, INTENT(in) ::   kt   ! ocean time-step index 
    98       INTEGER :: jn 
    99       REAL(wp), POINTER, DIMENSION(:,:,:) :: ztrfabm 
     94      INTEGER :: jn, jk 
     95      REAL(wp), POINTER, DIMENSION(:,:,:) :: ztrfabm, pdat 
     96      REAL(wp), DIMENSION(jpi,jpj)    :: vint 
    10097 
    10198!!---------------------------------------------------------------------- 
     
    109106      IF(lwp) WRITE(numout,*) ' ~~~~~~~~~~~~~~' 
    110107 
     108      IF (.NOT. started) CALL nemo_fabm_start 
     109 
    111110      CALL update_inputs( kt ) 
    112111 
    113       CALL compute_fabm 
    114  
    115       CALL compute_vertical_movement( kt ) 
     112      CALL compute_fabm( kt ) 
     113 
     114      CALL compute_vertical_movement( kt, nn_adv ) 
    116115 
    117116      CALL st2d_fabm_nxt( kt ) 
     
    123122      CALL trc_bc_read  ( kt )       ! tracers: surface and lateral Boundary Conditions 
    124123      CALL trc_rnf_fabm ( kt ) ! River forcings 
     124 
     125      ! Send 3D diagnostics to output (these apply to time "n") 
     126      DO jn = 1, size(model%interior_diagnostic_variables) 
     127         IF (model%interior_diagnostic_variables(jn)%save) THEN 
     128            ! Save 3D field 
     129            pdat => model%get_interior_diagnostic_data(jn) 
     130            CALL iom_put(model%interior_diagnostic_variables(jn)%name, pdat) 
     131 
     132            ! Save depth integral if selected for output in XIOS 
     133            IF (iom_use(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT')) THEN 
     134               vint = 0._wp 
     135               DO jk = 1, jpkm1 
     136                  vint = vint + pdat(:,:,jk) * fse3t(:,:,jk) * tmask(:,:,jk) 
     137               END DO 
     138               CALL iom_put(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT', vint) 
     139            END IF 
     140         END IF 
     141      END DO 
     142 
     143      ! Send 2D diagnostics to output (these apply to time "n") 
     144      DO jn = 1, size(model%horizontal_diagnostic_variables) 
     145         IF (model%horizontal_diagnostic_variables(jn)%save) & 
     146             CALL iom_put( model%horizontal_diagnostic_variables(jn)%name, model%get_horizontal_diagnostic_data(jn)) 
     147      END DO 
    125148 
    126149      IF( l_trdtrc ) THEN      ! Save the trends in the mixed layer 
     
    139162      INTEGER, INTENT(IN) :: kt 
    140163      INTEGER :: ji,jj,jk,jkmax 
    141       REAL(wp), DIMENSION(jpi,jpj,jpk) :: pgrow_3d, ploss_3d, zmld 
     164      REAL(wp), DIMENSION(jpi,jpj) :: zmld 
     165      REAL(wp), DIMENSION(jpi,jpj,jpk) :: pgrow_3d, ploss_3d 
    142166       
    143167      IF (kt == nittrc000) THEN 
     
    148172      PHYT_AVG(:,:)  = 0.0 
    149173         
    150       pgrow_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_pgrow) 
    151       ploss_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_ploss) 
     174      pgrow_3d(:,:,:) = model%get_interior_diagnostic_data(jp_fabm_pgrow) 
     175      ploss_3d(:,:,:) = model%get_interior_diagnostic_data(jp_fabm_ploss) 
    152176       
    153177      SELECT CASE( mld_choice_bgc ) 
     
    220244   END SUBROUTINE asmdiags_fabm 
    221245 
    222    SUBROUTINE compute_fabm() 
     246   SUBROUTINE compute_fabm( kt ) 
     247      INTEGER, INTENT(in) :: kt   ! ocean time-step index 
     248 
    223249      INTEGER :: ji,jj,jk,jn 
    224       TYPE(type_state) :: valid_state 
     250      LOGICAL :: valid, repaired 
    225251      REAL(wp) :: zalfg,zztmpx,zztmpy 
    226252 
    227253      ! Validate current model state (setting argument to .TRUE. enables repair=clipping) 
    228       valid_state = check_state(.TRUE.) 
    229       IF (.NOT.valid_state%valid) THEN 
     254      CALL check_state(.TRUE., valid, repaired) 
     255      IF (.NOT. valid) THEN 
    230256         WRITE(numout,*) "Invalid value in FABM encountered in area ",narea,"!!!" 
    231257#if defined key_iomput 
     
    240266#endif 
    241267      END IF 
    242       IF (valid_state%repaired) THEN 
     268      IF (repaired) THEN 
    243269         WRITE(numout,*) "Total interior repairs up to now on process",narea,":",repair_interior_count 
    244270         WRITE(numout,*) "Total surface repairs up to now on process",narea,":",repair_surface_count 
     
    246272      ENDIF 
    247273 
     274      daynumber_in_year = fjulday - fjulstartyear + 1 
     275 
    248276      ! Compute the now hydrostatic pressure 
    249277      ! copied from istate.F90 
    250278      ! ------------------------------------ 
    251279 
    252       zalfg = 0.5e-4 * grav ! FABM wants dbar, convert from Pa 
    253  
    254       rho = rau0 * ( 1. + rhd ) 
    255  
    256       prn(:,:,1) = 10.1325 + zalfg * fse3t(:,:,1) * rho(:,:,1) 
    257  
    258       daynumber_in_year=(fjulday-fjulstartyear+1)*1._wp 
    259  
    260       DO jk = 2, jpk                                              ! Vertical integration from the surface 
    261          prn(:,:,jk) = prn(:,:,jk-1) + zalfg * ( & 
    262                      fse3t(:,:,jk-1) * rho(:,:,jk-1)  & 
    263                      + fse3t(:,:,jk) * rho(:,:,jk) ) 
    264       END DO 
    265  
    266       ! Bottom stress 
    267       taubot(:,:) = 0._wp 
    268       DO jj = 2, jpjm1 
    269          DO ji = fs_2, fs_jpim1   ! vector opt. 
    270                zztmpx = (  bfrua(ji  ,jj) * un(ji  ,jj,mbku(ji  ,jj))  & 
    271                       &  + bfrua(ji-1,jj) * un(ji-1,jj,mbku(ji-1,jj))  ) 
    272                zztmpy = (  bfrva(ji,  jj) * vn(ji,jj  ,mbkv(ji,jj  ))  & 
    273                       &  + bfrva(ji,jj-1) * vn(ji,jj-1,mbkv(ji,jj-1))  ) 
    274                taubot(ji,jj) = 0.5_wp * rau0 * SQRT( zztmpx * zztmpx + zztmpy * zztmpy ) * tmask(ji,jj,1) 
    275                ! 
    276          ENDDO 
    277       ENDDO 
    278       ! Compute light extinction 
    279       DO jk=1,jpk 
    280           DO jj=1,jpj 
    281             call fabm_get_light_extinction(model,1,jpi,jj,jk,ext) 
    282          END DO 
    283       END DO 
    284  
    285       ! Compute light field (stored among FABM's internal diagnostics) 
    286       DO jj=1,jpj 
    287           DO ji=1,jpi 
    288             call fabm_get_light(model,1,jpk,ji,jj) 
    289          END DO 
    290       END DO 
    291  
    292       ! TODO: retrieve 3D shortwave and store in etot3 
     280      IF (ALLOCATED(rho)) rho = rau0 * ( 1._wp + rhd ) 
     281 
     282      IF (ALLOCATED(prn)) THEN 
     283         zalfg = 0.5e-4_wp * grav ! FABM wants dbar, convert from Pa (and multiply with 0.5 to average 2 cell thicknesses below) 
     284         prn(:,:,1) = 10.1325_wp + zalfg * fse3t(:,:,1) * rho(:,:,1) 
     285         DO jk = 2, jpkm1                                              ! Vertical integration from the surface 
     286            prn(:,:,jk) = prn(:,:,jk-1) + zalfg * ( & 
     287                        fse3t(:,:,jk-1) * rho(:,:,jk-1)  & 
     288                        + fse3t(:,:,jk) * rho(:,:,jk) ) 
     289         END DO 
     290      END IF 
     291 
     292      ! Compute the bottom stress 
     293      ! copied from diawri.F90 
     294      ! ------------------------------------ 
     295 
     296      IF (ALLOCATED(taubot)) THEN 
     297         taubot(:,:) = 0._wp 
     298         DO jj = 2, jpjm1 
     299            DO ji = fs_2, fs_jpim1   ! vector opt. 
     300                  zztmpx = (  bfrua(ji  ,jj) * un(ji  ,jj,mbku(ji  ,jj))  & 
     301                        &  + bfrua(ji-1,jj) * un(ji-1,jj,mbku(ji-1,jj))  ) 
     302                  zztmpy = (  bfrva(ji,  jj) * vn(ji,jj  ,mbkv(ji,jj  ))  & 
     303                        &  + bfrva(ji,jj-1) * vn(ji,jj-1,mbkv(ji,jj-1))  ) 
     304                  taubot(ji,jj) = 0.5_wp * rau0 * SQRT( zztmpx * zztmpx + zztmpy * zztmpy ) * tmask(ji,jj,1) 
     305                  ! 
     306            END DO 
     307         END DO 
     308      END IF 
     309 
     310      CALL model%prepare_inputs(real(kt, wp),nyear,nmonth,nday,REAL(nsec_day,wp)) 
     311 
     312      ! Retrieve 3D shortwave and store in etot3 
     313      IF (ln_qsr_spec) etot3(:,:,:) = swrad(:,:,:) 
    293314 
    294315      ! Zero rate array of interface-attached state variables 
     
    296317 
    297318      ! Compute interfacial source terms and fluxes 
    298       DO jj=1,jpj 
    299          ! Process bottom (fabm_do_bottom increments rather than sets, so zero flux array first) 
     319      DO jj=2,jpjm1 
     320         ! Process bottom (get_bottom_sources increments rather than sets, so zero flux array first) 
    300321         flux = 0._wp 
    301          CALL fabm_do_bottom(model,1,jpi,jj,flux,fabm_st2Da(:,jj,jp_fabm_surface+1:)) 
     322         CALL model%get_bottom_sources(fs_2,fs_jpim1,jj,flux,fabm_st2Da(fs_2:fs_jpim1,jj,jp_fabm_surface+1:)) 
    302323         DO jn=1,jp_fabm 
    303              DO ji=1,jpi 
    304                  ! Divide bottom fluxes by height of bottom layer and add to source terms. 
    305                  ! TODO: is there perhaps an existing variable for fse3t(ji,jj,mbkt(ji,jj))?? 
    306                  tra(ji,jj,mbkt(ji,jj),jp_fabm_m1+jn) = tra(ji,jj,mbkt(ji,jj),jp_fabm_m1+jn) + flux(ji,jn)/fse3t(ji,jj,mbkt(ji,jj)) 
    307              END DO 
    308          END DO 
    309  
    310          ! Process surface (fabm_do_surface increments rather than sets, so zero flux array first) 
     324            ! Divide bottom fluxes by height of bottom layer and add to source terms. 
     325            DO ji=fs_2,fs_jpim1 
     326               tra(ji,jj,mbkt(ji,jj),jp_fabm_m1+jn) = tra(ji,jj,mbkt(ji,jj),jp_fabm_m1+jn) + flux(ji,jn)/fse3t(ji,jj,mbkt(ji,jj)) 
     327            END DO 
     328         END DO 
     329 
     330         ! Process surface (get_surface_sources increments rather than sets, so zero flux array first) 
    311331         flux = 0._wp 
    312          CALL fabm_do_surface(model,1,jpi,jj,flux,fabm_st2Da(:,jj,1:jp_fabm_surface)) 
     332         CALL model%get_surface_sources(fs_2,fs_jpim1,jj,flux,fabm_st2Da(fs_2:fs_jpim1,jj,1:jp_fabm_surface)) 
     333         ! Divide surface fluxes by height of surface layer and add to source terms. 
    313334         DO jn=1,jp_fabm 
    314              ! Divide surface fluxes by height of surface layer and add to source terms. 
    315              tra(:,jj,1,jp_fabm_m1+jn) = tra(:,jj,1,jp_fabm_m1+jn) + flux(:,jn)/fse3t(:,jj,1) 
    316          END DO 
    317       END DO 
    318  
    319       ! Compute interior source terms (NB fabm_do increments rather than sets) 
    320       DO jk=1,jpk 
    321           DO jj=1,jpj 
    322               CALL fabm_do(model,1,jpi,jj,jk,tra(:,jj,jk,jp_fabm0:jp_fabm1)) 
    323           END DO 
    324       END DO 
     335            DO ji=fs_2,fs_jpim1 
     336               tra(ji,jj,1,jp_fabm_m1+jn) = tra(ji,jj,1,jp_fabm_m1+jn) + flux(ji,jn)/fse3t(ji,jj,1) 
     337            END DO 
     338         END DO 
     339      END DO 
     340 
     341      ! Compute interior source terms (NB get_interior_sources increments rather than sets) 
     342      DO jk=1,jpkm1 
     343         DO jj=2,jpjm1 
     344            CALL model%get_interior_sources(fs_2,fs_jpim1,jj,jk,tra(fs_2:fs_jpim1,jj,jk,jp_fabm0:jp_fabm1)) 
     345         END DO 
     346      END DO 
     347 
     348      CALL model%finalize_outputs() 
    325349   END SUBROUTINE compute_fabm 
    326350 
    327    FUNCTION check_state(repair) RESULT(exit_state) 
    328       LOGICAL, INTENT(IN) :: repair 
    329       TYPE(type_state) :: exit_state 
    330  
    331       INTEGER             :: jj,jk 
    332       LOGICAL             :: valid_int,valid_sf,valid_bt 
    333  
    334       exit_state%valid = .TRUE. 
    335       exit_state%repaired =.FALSE. 
    336       DO jk=1,jpk 
    337          DO jj=1,jpj 
    338             CALL fabm_check_state(model,1,jpi,jj,jk,repair,valid_int) 
    339             IF (repair.AND..NOT.valid_int) THEN 
     351   SUBROUTINE check_state(repair, valid, repaired) 
     352      LOGICAL, INTENT(IN)  :: repair 
     353      LOGICAL, INTENT(OUT) :: valid, repaired 
     354 
     355      INTEGER :: jj, jk 
     356      LOGICAL :: valid_int, valid_sf, valid_bt 
     357 
     358      valid = .TRUE.     ! Whether the model state is valid after this subroutine returns 
     359      repaired = .FALSE. ! Whether the model state has been repaired by this subroutine 
     360      DO jk=1,jpkm1 
     361         DO jj=2,jpjm1 
     362            CALL model%check_interior_state(fs_2, fs_jpim1, jj, jk, repair, valid_int) 
     363            IF (repair .AND. .NOT. valid_int) THEN 
    340364               repair_interior_count = repair_interior_count + 1 
    341                exit_state%repaired = .TRUE. 
     365               repaired = .TRUE. 
    342366            END IF 
    343             IF (.NOT.(valid_int.OR.repair)) exit_state%valid = .FALSE. 
    344          END DO 
    345       END DO 
    346       DO jj=1,jpj 
    347          CALL fabm_check_surface_state(model,1,jpi,jj,repair,valid_sf) 
    348          IF (repair.AND..NOT.valid_sf) THEN 
     367            IF (.NOT. (valid_int .OR. repair)) valid = .FALSE. 
     368         END DO 
     369      END DO 
     370      DO jj=2,jpjm1 
     371         CALL model%check_surface_state(fs_2, fs_jpim1, jj, repair, valid_sf) 
     372         IF (repair .AND. .NOT. valid_sf) THEN 
    349373            repair_surface_count = repair_surface_count + 1 
    350             exit_state%repaired = .TRUE. 
     374            repaired = .TRUE. 
    351375         END IF 
    352          IF (.NOT.(valid_sf.AND.valid_bt).AND..NOT.repair) exit_state%valid = .FALSE. 
    353          CALL fabm_check_bottom_state(model,1,jpi,jj,repair,valid_bt) 
    354          IF (repair.AND..NOT.valid_bt) THEN 
     376         IF (.NOT. (valid_sf .AND. valid_bt) .AND. .NOT. repair) valid = .FALSE. 
     377         CALL model%check_bottom_state(fs_2, fs_jpim1, jj, repair, valid_bt) 
     378         IF (repair .AND. .NOT. valid_bt) THEN 
    355379            repair_bottom_count = repair_bottom_count + 1 
    356             exit_state%repaired = .TRUE. 
     380            repaired = .TRUE. 
    357381         END IF 
    358          IF (.NOT.(valid_sf.AND.valid_bt).AND..NOT.repair) exit_state%valid = .FALSE. 
    359       END DO 
    360    END FUNCTION 
     382         IF (.NOT. (valid_sf .AND. valid_bt) .AND. .NOT. repair) valid = .FALSE. 
     383      END DO 
     384   END SUBROUTINE 
    361385 
    362386   SUBROUTINE trc_sms_fabm_check_mass() 
    363387      REAL(wp) :: total(SIZE(model%conserved_quantities)) 
    364       INTEGER :: jk,jj,jn 
     388      INTEGER :: ji,jk,jj,jn 
    365389 
    366390      total = 0._wp 
    367391 
    368       DO jk=1,jpk 
    369          DO jj=1,jpj 
    370             CALL fabm_get_conserved_quantities(model,1,jpi,jj,jk,current_total) 
     392      IF (.NOT. started) CALL nemo_fabm_start 
     393 
     394      DO jk=1,jpkm1 
     395         DO jj=2,jpjm1 
     396            CALL model%get_interior_conserved_quantities(fs_2,fs_jpim1,jj,jk,current_total) 
    371397            DO jn=1,SIZE(model%conserved_quantities) 
    372                total(jn) = total(jn) + SUM(cvol(:,jj,jk)*current_total(:,jn)*tmask_i(:,jj)) 
    373             END DO 
    374          END DO 
    375       END DO 
    376  
    377       DO jj=1,jpj 
    378          CALL fabm_get_horizontal_conserved_quantities(model,1,jpi,jj,current_total) 
     398               DO ji=fs_2,fs_jpim1 
     399                  total(jn) = total(jn) + cvol(ji,jj,jk) * current_total(ji,jn) * tmask_i(ji,jj) 
     400               END DO 
     401            END DO 
     402         END DO 
     403      END DO 
     404 
     405      DO jj=2,jpjm1 
     406         CALL model%get_horizontal_conserved_quantities(fs_2,fs_jpim1,jj,current_total) 
    379407         DO jn=1,SIZE(model%conserved_quantities) 
    380             total(jn) = total(jn) + SUM(e1e2t(:,jj)*current_total(:,jn)*tmask_i(:,jj)) 
     408            DO ji=fs_2,fs_jpim1 
     409               total(jn) = total(jn) + e1e2t(ji,jj) * current_total(ji,jn) * tmask_i(ji,jj) 
     410            END DO 
    381411         END DO 
    382412      END DO 
     
    434464 
    435465   INTEGER FUNCTION trc_sms_fabm_alloc() 
    436       INTEGER :: jj,jk,jn 
     466      INTEGER :: jn 
    437467      !!---------------------------------------------------------------------- 
    438468      !!              ***  ROUTINE trc_sms_fabm_alloc  *** 
     
    441471      ! ALLOCATE here the arrays specific to FABM 
    442472      ALLOCATE( lk_rad_fabm(jp_fabm)) 
    443       ALLOCATE( prn(jpi, jpj, jpk)) 
    444       ALLOCATE( rho(jpi, jpj, jpk)) 
    445       ALLOCATE( taubot(jpi, jpj)) 
     473      IF (model%variable_needs_values(fabm_standard_variables%pressure)) ALLOCATE(prn(jpi, jpj, jpk)) 
     474      IF (ALLOCATED(prn) .or. model%variable_needs_values(fabm_standard_variables%density)) ALLOCATE(rho(jpi, jpj, jpk)) 
     475      IF (model%variable_needs_values(fabm_standard_variables%bottom_stress)) ALLOCATE(taubot(jpi, jpj)) 
    446476      ! ALLOCATE( tab(...) , STAT=trc_sms_fabm_alloc ) 
    447477 
     
    452482 
    453483      ! Work array to hold surface and bottom fluxes 
    454       ALLOCATE(flux(jpi,jp_fabm)) 
    455  
    456       ! Work array to hold extinction coefficients 
    457       ALLOCATE(ext(jpi)) 
    458       ext=0._wp 
     484      ALLOCATE(flux(fs_2:fs_jpim1,jp_fabm)) 
    459485 
    460486      ! Allocate work arrays for vertical movement 
    461       ALLOCATE(w_ct(jpi,jpk,jp_fabm)) 
    462       ALLOCATE(w_if(jpk,jp_fabm)) 
    463       ALLOCATE(zwgt_if(jpk,jp_fabm)) 
    464       ALLOCATE(flux_if(jpk,jp_fabm)) 
    465       ALLOCATE(current_total(jpi,SIZE(model%conserved_quantities))) 
     487      ALLOCATE(w_ct(fs_2:fs_jpim1,1:jpkm1,jp_fabm)) 
     488      ALLOCATE(current_total(fs_2:fs_jpim1,SIZE(model%conserved_quantities))) 
    466489#if defined key_trdtrc && defined key_iomput 
    467490      IF( lk_trdtrc ) ALLOCATE(tr_vmv(jpi,jpj,jpk,jp_fabm)) 
     
    474497      ! 
    475498 
    476       ! Make FABM aware of diagnostics that are not needed [not included in output] 
    477       DO jn=1,size(model%diagnostic_variables) 
    478           !model%diagnostic_variables(jn)%save = iom_use(model%diagnostic_variables(jn)%name) 
    479       END DO 
    480       DO jn=1,size(model%horizontal_diagnostic_variables) 
    481           !model%horizontal_diagnostic_variables(jn)%save = iom_use(model%horizontal_diagnostic_variables(jn)%name) 
    482       END DO 
    483  
    484       ! Provide FABM with domain extents [after this, the save attribute of diagnostic variables can no longe change!] 
    485       call fabm_set_domain(model,jpi, jpj, jpk) 
    486  
    487       ! Provide FABM with the vertical indices of the surface and bottom, and the land-sea mask. 
    488       call model%set_bottom_index(mbkt)  ! NB mbkt extents should match dimension lengths provided to fabm_set_domain 
    489       call model%set_surface_index(1) 
    490       call fabm_set_mask(model,tmask,tmask(:,:,1)) ! NB tmask extents should match dimension lengths provided to fabm_set_domain 
    491  
    492       ! Send pointers to state data to FABM 
    493       do jn=1,jp_fabm 
    494          call fabm_link_bulk_state_data(model,jn,trn(:,:,:,jp_fabm_m1+jn)) 
    495       end do 
     499      ! Provide FABM with domain extents 
     500      CALL model%set_domain(jpi, jpj, jpk, rdt) 
     501      CALL model%set_domain_start(fs_2, 2, 1) 
     502      CALL model%set_domain_stop(fs_jpim1, jpjm1, jpkm1) 
     503 
     504      ! Provide FABM with the vertical indices of the bottom, and the land-sea mask. 
     505      CALL model%set_bottom_index(mbkt)  ! NB mbkt extents should match dimension lengths provided to set_domain 
     506      CALL model%set_mask(tmask,tmask(:,:,1)) ! NB tmask extents should match dimension lengths provided to set_domain 
     507 
     508      ! Initialize state and send pointers to state data to FABM 
     509      ! We mask land points in states with zeros, as per with NEMO "convention" 
     510      ! NB we cannot call model%initialize_*_state at this point, because model%start has not been called yet. 
     511      DO jn=1,jp_fabm 
     512         trn(:,:,:,jp_fabm_m1+jn) = model%interior_state_variables(jn)%initial_value * tmask 
     513         CALL model%link_interior_state_data(jn,trn(:,:,:,jp_fabm_m1+jn)) 
     514      END DO 
    496515      DO jn=1,jp_fabm_surface 
    497          CALL fabm_link_surface_state_data(model,jn,fabm_st2Dn(:,:,jn)) 
     516         fabm_st2Dn(:,:,jn) = model%surface_state_variables(jn)%initial_value * tmask(:,:,1) 
     517         CALL model%link_surface_state_data(jn,fabm_st2Dn(:,:,jn)) 
    498518      END DO 
    499519      DO jn=1,jp_fabm_bottom 
    500          CALL fabm_link_bottom_state_data(model,jn,fabm_st2Dn(:,:,jp_fabm_surface+jn)) 
     520         fabm_st2Dn(:,:,jp_fabm_surface+jn) = model%bottom_state_variables(jn)%initial_value * tmask(:,:,1) 
     521         CALL model%link_bottom_state_data(jn,fabm_st2Dn(:,:,jp_fabm_surface+jn)) 
    501522      END DO 
    502523 
    503524      ! Send pointers to environmental data to FABM 
    504       call fabm_link_bulk_data(model,standard_variables%temperature,tsn(:,:,:,jp_tem)) 
    505       call fabm_link_bulk_data(model,standard_variables%practical_salinity,tsn(:,:,:,jp_sal)) 
    506       call fabm_link_bulk_data(model,standard_variables%density,rho(:,:,:)) 
    507       call fabm_link_bulk_data(model,standard_variables%pressure,prn) 
    508       call fabm_link_horizontal_data(model,standard_variables%bottom_stress,taubot(:,:)) 
    509       ! correct target for cell thickness depends on NEMO configuration: 
    510 #ifdef key_vvl 
    511       call fabm_link_bulk_data(model,standard_variables%cell_thickness,e3t_n) 
    512 #else 
    513       call fabm_link_bulk_data(model,standard_variables%cell_thickness,e3t_0) 
    514 #endif 
    515       call fabm_link_horizontal_data(model,standard_variables%latitude,gphit) 
    516       call fabm_link_horizontal_data(model,standard_variables%longitude,glamt) 
    517       call fabm_link_scalar_data(model,standard_variables%number_of_days_since_start_of_the_year,daynumber_in_year) 
    518       call fabm_link_horizontal_data(model,standard_variables%wind_speed,wndm(:,:)) 
    519       call fabm_link_horizontal_data(model,standard_variables%surface_downwelling_shortwave_flux,qsr(:,:)) 
    520       call fabm_link_horizontal_data(model,standard_variables%bottom_depth_below_geoid,bathy(:,:)) 
    521  
    522       swr_id = model%get_bulk_variable_id(standard_variables%downwelling_shortwave_flux) 
     525      CALL model%link_interior_data(fabm_standard_variables%depth, fsdept(:,:,:)) 
     526      CALL model%link_interior_data(fabm_standard_variables%temperature, tsn(:,:,:,jp_tem)) 
     527      CALL model%link_interior_data(fabm_standard_variables%practical_salinity, tsn(:,:,:,jp_sal)) 
     528      IF (ALLOCATED(rho)) CALL model%link_interior_data(fabm_standard_variables%density, rho(:,:,:)) 
     529      IF (ALLOCATED(prn)) CALL model%link_interior_data(fabm_standard_variables%pressure, prn) 
     530      IF (ALLOCATED(taubot)) CALL model%link_horizontal_data(fabm_standard_variables%bottom_stress, taubot(:,:)) 
     531      CALL model%link_interior_data(fabm_standard_variables%cell_thickness, fse3t(:,:,:)) 
     532      CALL model%link_horizontal_data(fabm_standard_variables%latitude, gphit) 
     533      CALL model%link_horizontal_data(fabm_standard_variables%longitude, glamt) 
     534      CALL model%link_scalar(fabm_standard_variables%number_of_days_since_start_of_the_year, daynumber_in_year) 
     535      CALL model%link_horizontal_data(fabm_standard_variables%wind_speed, wndm(:,:)) 
     536      CALL model%link_horizontal_data(fabm_standard_variables%surface_downwelling_shortwave_flux, qsr(:,:)) 
     537      CALL model%link_horizontal_data(fabm_standard_variables%bottom_depth_below_geoid, bathy(:,:)) 
     538      CALL model%link_horizontal_data(fabm_standard_variables%ice_area_fraction, fr_i(:,:)) 
    523539 
    524540      ! Obtain user-specified input variables (read from NetCDF file) 
    525       call link_inputs 
    526       call update_inputs( nit000, .false. ) 
    527  
    528       ! Check whether FABM has all required data 
    529       call fabm_check_ready(model) 
    530  
    531       ! Initialize state 
    532       DO jj=1,jpj 
    533          CALL fabm_initialize_surface_state(model,1,jpi,jj) 
    534          CALL fabm_initialize_bottom_state(model,1,jpi,jj) 
    535       END DO 
    536       DO jk=1,jpk 
    537          DO jj=1,jpj 
    538             CALL fabm_initialize_state(model,1,jpi,jj,jk) 
    539          END DO 
    540       END DO 
     541      CALL link_inputs 
     542      CALL update_inputs(nit000, .FALSE.) 
    541543 
    542544      ! Set mask for negativity corrections to the relevant states 
    543       lk_rad_fabm = .FALSE. 
     545      lk_rad_fabm(:) = .FALSE. 
    544546      DO jn=1,jp_fabm 
    545         IF (model%state_variables(jn)%minimum.ge.0) THEN 
    546           lk_rad_fabm(jn)=.TRUE. 
    547           IF(lwp) WRITE(numout,*) 'FABM clipping for '//TRIM(model%state_variables(jn)%name)//' activated.' 
     547        IF (model%interior_state_variables(jn)%minimum >= 0._wp) THEN 
     548          lk_rad_fabm(jn) = .TRUE. 
     549          IF(lwp) WRITE(numout,*) 'FABM clipping for '//TRIM(model%interior_state_variables(jn)%name)//' activated.' 
    548550        END IF 
    549551      END DO 
    550552 
    551       ! Mask land points in states with zeros, not nice, but coherent 
    552       ! with NEMO "convention": 
    553       DO jn=jp_fabm0,jp_fabm1 
    554         WHERE (tmask==0._wp) 
    555           trn(:,:,:,jn)=0._wp 
    556         END WHERE 
    557       END DO 
    558       DO jn=1,jp_fabm_surface+jp_fabm_bottom 
    559         WHERE (tmask(:,:,1)==0._wp) 
    560           fabm_st2Dn(:,:,jn)=0._wp 
    561         END WHERE 
    562       END DO 
    563553 
    564554      ! Copy initial condition for interface-attached state variables to "previous" state field 
     
    566556      fabm_st2Db = fabm_st2Dn 
    567557 
    568       ! Initialise repair counters 
    569       repair_interior_count = 0 
    570       repair_surface_count = 0 
    571       repair_bottom_count = 0 
     558      ! Pointer to spectral heating term 
     559      swrad => model%get_data(model%get_interior_variable_id(standard_variables%net_rate_of_absorption_of_shortwave_energy_in_layer)) 
     560 
    572561 
    573562   END FUNCTION trc_sms_fabm_alloc 
     563 
     564   SUBROUTINE nemo_fabm_start() 
     565      INTEGER :: jn 
     566 
     567      ! Make FABM aware of diagnostics that are not needed [not included in output] 
     568      ! This works only after iom has completely initialised, because it depends on iom_use 
     569      DO jn=1,size(model%interior_diagnostic_variables) 
     570         model%interior_diagnostic_variables(jn)%save = iom_use(model%interior_diagnostic_variables(jn)%name) & 
     571            .or. iom_use(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT') 
     572      END DO 
     573      DO jn=1,size(model%horizontal_diagnostic_variables) 
     574         model%horizontal_diagnostic_variables(jn)%save = iom_use(model%horizontal_diagnostic_variables(jn)%name) 
     575      END DO 
     576 
     577      ! Check whether FABM has all required data 
     578      ! [after this, the save attribute of diagnostic variables can no longer change!] 
     579      CALL model%start() 
     580 
     581      started = .TRUE. 
     582   END SUBROUTINE 
    574583 
    575584#else 
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