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Changeset 13489 for branches/UKMO/AMM15_v3_6_STABLE_package_collate_utils366_fabmv1_v2/NEMOGCM/NEMO/TOP_SRC/FABM/trcsms_fabm.F90 – NEMO

Ignore:
Timestamp:
2020-09-17T19:13:57+02:00 (4 years ago)
Author:
dford
Message:

Merge in previous branch.

File:
1 edited

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  • branches/UKMO/AMM15_v3_6_STABLE_package_collate_utils366_fabmv1_v2/NEMOGCM/NEMO/TOP_SRC/FABM/trcsms_fabm.F90

    r10728 r13489  
    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 
     41   USE par_fabm, ONLY: jp_fabm_swr 
    3842 
    3943   !USE fldread         !  time interpolation 
    40  
    41    USE fabm 
    4244 
    4345   IMPLICIT NONE 
     
    4850   PRIVATE 
    4951 
    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 
     52   PUBLIC   trc_sms_fabm            ! called by trcsms.F90 module 
     53   PUBLIC   trc_sms_fabm_alloc      ! called by trcini_fabm.F90 module 
     54   PUBLIC   trc_sms_fabm_check_mass ! called by trcwri_fabm.F90 
     55   PUBLIC   nemo_fabm_start 
     56 
     57   ! Work arrays 
     58   REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: flux          ! Cross-interface flux of pelagic variables (# m-2 s-1) 
     59   REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: current_total ! Totals of conserved quantities 
     60 
     61   ! Arrays for environmental variables that are computed by the coupler 
     62   REAL(wp), PUBLIC, TARGET, ALLOCATABLE, DIMENSION(:,:,:) :: prn,rho 
     63   REAL(wp), PUBLIC, TARGET, ALLOCATABLE, DIMENSION(:,:) :: taubot 
     64   REAL(wp), PUBLIC, TARGET :: daynumber_in_year 
     65 
     66   ! State repair counters 
     67   INTEGER, SAVE :: repair_interior_count = 0 
     68   INTEGER, SAVE :: repair_surface_count  = 0 
     69   INTEGER, SAVE :: repair_bottom_count   = 0 
     70 
     71   ! Coupler parameters 
     72   INTEGER, PUBLIC :: nn_adv  ! Vertical advection scheme for sinking/floating/movement 
     73                              ! (1: 1st order upwind, 3: 3rd order TVD) 
     74 
     75   ! Flag indicating whether model%start has been called (will be done on-demand) 
     76   LOGICAL, SAVE :: started = .false. 
    8077 
    8178   !!---------------------------------------------------------------------- 
     
    9693      ! 
    9794      INTEGER, INTENT(in) ::   kt   ! ocean time-step index 
    98       INTEGER :: jn 
    99       REAL(wp), POINTER, DIMENSION(:,:,:) :: ztrfabm 
     95      INTEGER :: jn, jk 
     96      REAL(wp), POINTER, DIMENSION(:,:,:) :: ztrfabm, pdat 
     97      REAL(wp), DIMENSION(jpi,jpj)    :: vint 
    10098 
    10199!!---------------------------------------------------------------------- 
     
    109107      IF(lwp) WRITE(numout,*) ' ~~~~~~~~~~~~~~' 
    110108 
     109      IF (.NOT. started) CALL nemo_fabm_start 
     110 
    111111      CALL update_inputs( kt ) 
    112112 
    113       CALL compute_fabm 
    114  
    115       CALL compute_vertical_movement( kt ) 
     113      CALL compute_fabm( kt ) 
     114 
     115      CALL compute_vertical_movement( kt, nn_adv ) 
    116116 
    117117      CALL st2d_fabm_nxt( kt ) 
     
    123123      CALL trc_bc_read  ( kt )       ! tracers: surface and lateral Boundary Conditions 
    124124      CALL trc_rnf_fabm ( kt ) ! River forcings 
     125 
     126      ! Send 3D diagnostics to output (these apply to time "n") 
     127      DO jn = 1, size(model%interior_diagnostic_variables) 
     128         IF (model%interior_diagnostic_variables(jn)%save) THEN 
     129            ! Save 3D field 
     130            pdat => model%get_interior_diagnostic_data(jn) 
     131            CALL iom_put(model%interior_diagnostic_variables(jn)%name, pdat) 
     132 
     133            ! Save depth integral if selected for output in XIOS 
     134            IF (iom_use(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT')) THEN 
     135               vint = 0._wp 
     136               DO jk = 1, jpkm1 
     137                  vint = vint + pdat(:,:,jk) * fse3t(:,:,jk) * tmask(:,:,jk) 
     138               END DO 
     139               CALL iom_put(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT', vint) 
     140            END IF 
     141         END IF 
     142      END DO 
     143 
     144      ! Send 2D diagnostics to output (these apply to time "n") 
     145      DO jn = 1, size(model%horizontal_diagnostic_variables) 
     146         IF (model%horizontal_diagnostic_variables(jn)%save) & 
     147             CALL iom_put( model%horizontal_diagnostic_variables(jn)%name, model%get_horizontal_diagnostic_data(jn)) 
     148      END DO 
    125149 
    126150      IF( l_trdtrc ) THEN      ! Save the trends in the mixed layer 
     
    139163      INTEGER, INTENT(IN) :: kt 
    140164      INTEGER :: ji,jj,jk,jkmax 
    141       REAL(wp), DIMENSION(jpi,jpj,jpk) :: pgrow_3d, ploss_3d, zmld 
     165      REAL(wp), DIMENSION(jpi,jpj) :: zmld 
     166      REAL(wp), DIMENSION(jpi,jpj,jpk) :: pgrow_3d, ploss_3d 
    142167       
    143168      IF (kt == nittrc000) THEN 
     
    148173      PHYT_AVG(:,:)  = 0.0 
    149174         
    150       pgrow_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_pgrow) 
    151       ploss_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_ploss) 
     175      pgrow_3d(:,:,:) = model%get_interior_diagnostic_data(jp_fabm_pgrow) 
     176      ploss_3d(:,:,:) = model%get_interior_diagnostic_data(jp_fabm_ploss) 
    152177       
    153178      SELECT CASE( mld_choice_bgc ) 
     
    220245   END SUBROUTINE asmdiags_fabm 
    221246 
    222    SUBROUTINE compute_fabm() 
     247   SUBROUTINE compute_fabm( kt ) 
     248      INTEGER, INTENT(in) :: kt   ! ocean time-step index 
     249 
    223250      INTEGER :: ji,jj,jk,jn 
    224       TYPE(type_state) :: valid_state 
     251      LOGICAL :: valid, repaired 
    225252      REAL(wp) :: zalfg,zztmpx,zztmpy 
    226253 
    227254      ! Validate current model state (setting argument to .TRUE. enables repair=clipping) 
    228       valid_state = check_state(.TRUE.) 
    229       IF (.NOT.valid_state%valid) THEN 
     255      CALL check_state(.TRUE., valid, repaired) 
     256      IF (.NOT. valid) THEN 
    230257         WRITE(numout,*) "Invalid value in FABM encountered in area ",narea,"!!!" 
    231258#if defined key_iomput 
     
    240267#endif 
    241268      END IF 
    242       IF (valid_state%repaired) THEN 
     269      IF (repaired) THEN 
    243270         WRITE(numout,*) "Total interior repairs up to now on process",narea,":",repair_interior_count 
    244271         WRITE(numout,*) "Total surface repairs up to now on process",narea,":",repair_surface_count 
     
    246273      ENDIF 
    247274 
     275      daynumber_in_year = fjulday - fjulstartyear + 1 
     276 
    248277      ! Compute the now hydrostatic pressure 
    249278      ! copied from istate.F90 
    250279      ! ------------------------------------ 
    251280 
    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 
     281      IF (ALLOCATED(rho)) rho = rau0 * ( 1._wp + rhd ) 
     282 
     283      IF (ALLOCATED(prn)) THEN 
     284         zalfg = 0.5e-4_wp * grav ! FABM wants dbar, convert from Pa (and multiply with 0.5 to average 2 cell thicknesses below) 
     285         prn(:,:,1) = 10.1325_wp + zalfg * fse3t(:,:,1) * rho(:,:,1) 
     286         DO jk = 2, jpkm1                                              ! Vertical integration from the surface 
     287            prn(:,:,jk) = prn(:,:,jk-1) + zalfg * ( & 
     288                        fse3t(:,:,jk-1) * rho(:,:,jk-1)  & 
     289                        + fse3t(:,:,jk) * rho(:,:,jk) ) 
     290         END DO 
     291      END IF 
     292 
     293      ! Compute the bottom stress 
     294      ! copied from diawri.F90 
     295      ! ------------------------------------ 
     296 
     297      IF (ALLOCATED(taubot)) THEN 
     298         taubot(:,:) = 0._wp 
     299         DO jj = 2, jpjm1 
     300            DO ji = fs_2, fs_jpim1   ! vector opt. 
     301                  zztmpx = (  bfrua(ji  ,jj) * un(ji  ,jj,mbku(ji  ,jj))  & 
     302                        &  + bfrua(ji-1,jj) * un(ji-1,jj,mbku(ji-1,jj))  ) 
     303                  zztmpy = (  bfrva(ji,  jj) * vn(ji,jj  ,mbkv(ji,jj  ))  & 
     304                        &  + bfrva(ji,jj-1) * vn(ji,jj-1,mbkv(ji,jj-1))  ) 
     305                  taubot(ji,jj) = 0.5_wp * rau0 * SQRT( zztmpx * zztmpx + zztmpy * zztmpy ) * tmask(ji,jj,1) 
     306                  ! 
     307            END DO 
     308         END DO 
     309      END IF 
     310 
     311      CALL model%prepare_inputs(real(kt, wp),nyear,nmonth,nday,REAL(nsec_day,wp)) 
     312 
     313      ! Retrieve 3D shortwave and store in etot3 
     314      IF (ln_qsr_spec) THEN 
     315         etot3(:,:,:) = model%get_interior_diagnostic_data(jp_fabm_swr) 
     316      ENDIF 
    293317 
    294318      ! Zero rate array of interface-attached state variables 
     
    296320 
    297321      ! 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) 
     322      DO jj=2,jpjm1 
     323         ! Process bottom (get_bottom_sources increments rather than sets, so zero flux array first) 
    300324         flux = 0._wp 
    301          CALL fabm_do_bottom(model,1,jpi,jj,flux,fabm_st2Da(:,jj,jp_fabm_surface+1:)) 
     325         CALL model%get_bottom_sources(fs_2,fs_jpim1,jj,flux,fabm_st2Da(fs_2:fs_jpim1,jj,jp_fabm_surface+1:)) 
    302326         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) 
     327            ! Divide bottom fluxes by height of bottom layer and add to source terms. 
     328            DO ji=fs_2,fs_jpim1 
     329               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)) 
     330            END DO 
     331         END DO 
     332 
     333         ! Process surface (get_surface_sources increments rather than sets, so zero flux array first) 
    311334         flux = 0._wp 
    312          CALL fabm_do_surface(model,1,jpi,jj,flux,fabm_st2Da(:,jj,1:jp_fabm_surface)) 
     335         CALL model%get_surface_sources(fs_2,fs_jpim1,jj,flux,fabm_st2Da(fs_2:fs_jpim1,jj,1:jp_fabm_surface)) 
     336         ! Divide surface fluxes by height of surface layer and add to source terms. 
    313337         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 
     338            DO ji=fs_2,fs_jpim1 
     339               tra(ji,jj,1,jp_fabm_m1+jn) = tra(ji,jj,1,jp_fabm_m1+jn) + flux(ji,jn)/fse3t(ji,jj,1) 
     340            END DO 
     341         END DO 
     342      END DO 
     343 
     344      ! Compute interior source terms (NB get_interior_sources increments rather than sets) 
     345      DO jk=1,jpkm1 
     346         DO jj=2,jpjm1 
     347            CALL model%get_interior_sources(fs_2,fs_jpim1,jj,jk,tra(fs_2:fs_jpim1,jj,jk,jp_fabm0:jp_fabm1)) 
     348         END DO 
     349      END DO 
     350 
     351      CALL model%finalize_outputs() 
    325352   END SUBROUTINE compute_fabm 
    326353 
    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 
     354   SUBROUTINE check_state(repair, valid, repaired) 
     355      LOGICAL, INTENT(IN)  :: repair 
     356      LOGICAL, INTENT(OUT) :: valid, repaired 
     357 
     358      INTEGER :: jj, jk 
     359      LOGICAL :: valid_int, valid_sf, valid_bt 
     360 
     361      valid = .TRUE.     ! Whether the model state is valid after this subroutine returns 
     362      repaired = .FALSE. ! Whether the model state has been repaired by this subroutine 
     363      DO jk=1,jpkm1 
     364         DO jj=2,jpjm1 
     365            CALL model%check_interior_state(fs_2, fs_jpim1, jj, jk, repair, valid_int) 
     366            IF (repair .AND. .NOT. valid_int) THEN 
    340367               repair_interior_count = repair_interior_count + 1 
    341                exit_state%repaired = .TRUE. 
     368               repaired = .TRUE. 
    342369            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 
     370            IF (.NOT. (valid_int .OR. repair)) valid = .FALSE. 
     371         END DO 
     372      END DO 
     373      DO jj=2,jpjm1 
     374         CALL model%check_surface_state(fs_2, fs_jpim1, jj, repair, valid_sf) 
     375         IF (repair .AND. .NOT. valid_sf) THEN 
    349376            repair_surface_count = repair_surface_count + 1 
    350             exit_state%repaired = .TRUE. 
     377            repaired = .TRUE. 
    351378         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 
     379         IF (.NOT. (valid_sf .AND. valid_bt) .AND. .NOT. repair) valid = .FALSE. 
     380         CALL model%check_bottom_state(fs_2, fs_jpim1, jj, repair, valid_bt) 
     381         IF (repair .AND. .NOT. valid_bt) THEN 
    355382            repair_bottom_count = repair_bottom_count + 1 
    356             exit_state%repaired = .TRUE. 
     383            repaired = .TRUE. 
    357384         END IF 
    358          IF (.NOT.(valid_sf.AND.valid_bt).AND..NOT.repair) exit_state%valid = .FALSE. 
    359       END DO 
    360    END FUNCTION 
     385         IF (.NOT. (valid_sf .AND. valid_bt) .AND. .NOT. repair) valid = .FALSE. 
     386      END DO 
     387   END SUBROUTINE 
    361388 
    362389   SUBROUTINE trc_sms_fabm_check_mass() 
    363390      REAL(wp) :: total(SIZE(model%conserved_quantities)) 
    364       INTEGER :: jk,jj,jn 
     391      INTEGER :: ji,jk,jj,jn 
    365392 
    366393      total = 0._wp 
    367394 
    368       DO jk=1,jpk 
    369          DO jj=1,jpj 
    370             CALL fabm_get_conserved_quantities(model,1,jpi,jj,jk,current_total) 
     395      IF (.NOT. started) CALL nemo_fabm_start 
     396 
     397      DO jk=1,jpkm1 
     398         DO jj=2,jpjm1 
     399            CALL model%get_interior_conserved_quantities(fs_2,fs_jpim1,jj,jk,current_total) 
    371400            DO jn=1,SIZE(model%conserved_quantities) 
    372                total(jn) = total(jn) + SUM(cvol(:,jj,jk)*current_total(:,jn)*tmask_i(:,jj)) 
     401               DO ji=fs_2,fs_jpim1 
     402                  total(jn) = total(jn) + cvol(ji,jj,jk) * current_total(ji,jn) * tmask_i(ji,jj) 
     403               END DO 
    373404            END DO 
    374405         END DO 
    375406      END DO 
    376407 
    377       DO jj=1,jpj 
    378          CALL fabm_get_horizontal_conserved_quantities(model,1,jpi,jj,current_total) 
     408      DO jj=2,jpjm1 
     409         CALL model%get_horizontal_conserved_quantities(fs_2,fs_jpim1,jj,current_total) 
    379410         DO jn=1,SIZE(model%conserved_quantities) 
    380             total(jn) = total(jn) + SUM(e1e2t(:,jj)*current_total(:,jn)*tmask_i(:,jj)) 
     411            DO ji=fs_2,fs_jpim1 
     412               total(jn) = total(jn) + e1e2t(ji,jj) * current_total(ji,jn) * tmask_i(ji,jj) 
     413            END DO 
    381414         END DO 
    382415      END DO 
     
    434467 
    435468   INTEGER FUNCTION trc_sms_fabm_alloc() 
    436       INTEGER :: jj,jk,jn 
     469      INTEGER :: jn 
    437470      !!---------------------------------------------------------------------- 
    438471      !!              ***  ROUTINE trc_sms_fabm_alloc  *** 
     
    441474      ! ALLOCATE here the arrays specific to FABM 
    442475      ALLOCATE( lk_rad_fabm(jp_fabm)) 
    443       ALLOCATE( prn(jpi, jpj, jpk)) 
    444       ALLOCATE( rho(jpi, jpj, jpk)) 
    445       ALLOCATE( taubot(jpi, jpj)) 
     476      IF (model%variable_needs_values(fabm_standard_variables%pressure)) ALLOCATE(prn(jpi, jpj, jpk)) 
     477      IF (ALLOCATED(prn) .or. model%variable_needs_values(fabm_standard_variables%density)) ALLOCATE(rho(jpi, jpj, jpk)) 
     478      IF (model%variable_needs_values(fabm_standard_variables%bottom_stress)) ALLOCATE(taubot(jpi, jpj)) 
    446479      ! ALLOCATE( tab(...) , STAT=trc_sms_fabm_alloc ) 
    447480 
     
    452485 
    453486      ! 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 
     487      ALLOCATE(flux(fs_2:fs_jpim1,jp_fabm)) 
    459488 
    460489      ! 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))) 
     490      ALLOCATE(w_ct(fs_2:fs_jpim1,1:jpkm1,jp_fabm)) 
     491      ALLOCATE(current_total(fs_2:fs_jpim1,SIZE(model%conserved_quantities))) 
    466492#if defined key_trdtrc && defined key_iomput 
    467493      IF( lk_trdtrc ) ALLOCATE(tr_vmv(jpi,jpj,jpk,jp_fabm)) 
     
    474500      ! 
    475501 
    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 
     502      ! Provide FABM with domain extents 
     503      CALL model%set_domain(jpi, jpj, jpk, rdt) 
     504      CALL model%set_domain_start(fs_2, 2, 1) 
     505      CALL model%set_domain_stop(fs_jpim1, jpjm1, jpkm1) 
     506 
     507      ! Provide FABM with the vertical indices of the bottom, and the land-sea mask. 
     508      CALL model%set_bottom_index(mbkt)  ! NB mbkt extents should match dimension lengths provided to set_domain 
     509      CALL model%set_mask(tmask,tmask(:,:,1)) ! NB tmask extents should match dimension lengths provided to set_domain 
     510 
     511      ! Initialize state and send pointers to state data to FABM 
     512      ! We mask land points in states with zeros, as per with NEMO "convention" 
     513      ! NB we cannot call model%initialize_*_state at this point, because model%start has not been called yet. 
     514      DO jn=1,jp_fabm 
     515         trn(:,:,:,jp_fabm_m1+jn) = model%interior_state_variables(jn)%initial_value * tmask 
     516         CALL model%link_interior_state_data(jn,trn(:,:,:,jp_fabm_m1+jn)) 
     517      END DO 
    496518      DO jn=1,jp_fabm_surface 
    497          CALL fabm_link_surface_state_data(model,jn,fabm_st2Dn(:,:,jn)) 
     519         fabm_st2Dn(:,:,jn) = model%surface_state_variables(jn)%initial_value * tmask(:,:,1) 
     520         CALL model%link_surface_state_data(jn,fabm_st2Dn(:,:,jn)) 
    498521      END DO 
    499522      DO jn=1,jp_fabm_bottom 
    500          CALL fabm_link_bottom_state_data(model,jn,fabm_st2Dn(:,:,jp_fabm_surface+jn)) 
     523         fabm_st2Dn(:,:,jp_fabm_surface+jn) = model%bottom_state_variables(jn)%initial_value * tmask(:,:,1) 
     524         CALL model%link_bottom_state_data(jn,fabm_st2Dn(:,:,jp_fabm_surface+jn)) 
    501525      END DO 
    502526 
    503527      ! 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) 
     528      CALL model%link_interior_data(fabm_standard_variables%depth, fsdept(:,:,:)) 
     529      CALL model%link_interior_data(fabm_standard_variables%temperature, tsn(:,:,:,jp_tem)) 
     530      CALL model%link_interior_data(fabm_standard_variables%practical_salinity, tsn(:,:,:,jp_sal)) 
     531      IF (ALLOCATED(rho)) CALL model%link_interior_data(fabm_standard_variables%density, rho(:,:,:)) 
     532      IF (ALLOCATED(prn)) CALL model%link_interior_data(fabm_standard_variables%pressure, prn) 
     533      IF (ALLOCATED(taubot)) CALL model%link_horizontal_data(fabm_standard_variables%bottom_stress, taubot(:,:)) 
     534      CALL model%link_interior_data(fabm_standard_variables%cell_thickness, fse3t(:,:,:)) 
     535      CALL model%link_horizontal_data(fabm_standard_variables%latitude, gphit) 
     536      CALL model%link_horizontal_data(fabm_standard_variables%longitude, glamt) 
     537      CALL model%link_scalar(fabm_standard_variables%number_of_days_since_start_of_the_year, daynumber_in_year) 
     538      CALL model%link_horizontal_data(fabm_standard_variables%wind_speed, wndm(:,:)) 
     539      CALL model%link_horizontal_data(fabm_standard_variables%surface_downwelling_shortwave_flux, qsr(:,:)) 
     540      CALL model%link_horizontal_data(fabm_standard_variables%bottom_depth_below_geoid, bathy(:,:)) 
     541      CALL model%link_horizontal_data(fabm_standard_variables%ice_area_fraction, fr_i(:,:)) 
    523542 
    524543      ! 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 
     544      CALL link_inputs 
     545      CALL update_inputs(nit000, .FALSE.) 
    541546 
    542547      ! Set mask for negativity corrections to the relevant states 
    543       lk_rad_fabm = .FALSE. 
     548      lk_rad_fabm(:) = .FALSE. 
    544549      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.' 
     550        IF (model%interior_state_variables(jn)%minimum >= 0._wp) THEN 
     551          lk_rad_fabm(jn) = .TRUE. 
     552          IF(lwp) WRITE(numout,*) 'FABM clipping for '//TRIM(model%interior_state_variables(jn)%name)//' activated.' 
    548553        END IF 
    549554      END DO 
    550555 
    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 
    563556 
    564557      ! Copy initial condition for interface-attached state variables to "previous" state field 
     
    566559      fabm_st2Db = fabm_st2Dn 
    567560 
    568       ! Initialise repair counters 
    569       repair_interior_count = 0 
    570       repair_surface_count = 0 
    571       repair_bottom_count = 0 
    572  
    573561   END FUNCTION trc_sms_fabm_alloc 
     562 
     563   SUBROUTINE nemo_fabm_start() 
     564      INTEGER :: jn 
     565 
     566      ! Make FABM aware of diagnostics that are not needed [not included in output] 
     567      ! This works only after iom has completely initialised, because it depends on iom_use 
     568      DO jn=1,size(model%interior_diagnostic_variables) 
     569         model%interior_diagnostic_variables(jn)%save = iom_use(model%interior_diagnostic_variables(jn)%name) & 
     570            .or. iom_use(TRIM(model%interior_diagnostic_variables(jn)%name)//'_VINT') & 
     571            .or. iom_use(TRIM(model%interior_diagnostic_variables(jn)%name)//'25h') & 
     572            .or. iom_use('top_'//TRIM(model%interior_diagnostic_variables(jn)%name)) & 
     573            .or. iom_use('mid_'//TRIM(model%interior_diagnostic_variables(jn)%name)) & 
     574            .or. iom_use('bot_'//TRIM(model%interior_diagnostic_variables(jn)%name)) 
     575      END DO 
     576      model%interior_diagnostic_variables(jp_fabm_o3ta)%save = .TRUE. 
     577      model%interior_diagnostic_variables(jp_fabm_o3ph)%save = .TRUE. 
     578      model%interior_diagnostic_variables(jp_fabm_o3pc)%save = .TRUE. 
     579      model%interior_diagnostic_variables(jp_fabm_xeps)%save = .TRUE. 
     580      model%interior_diagnostic_variables(jp_fabm_pgrow)%save = .TRUE. 
     581      model%interior_diagnostic_variables(jp_fabm_ploss)%save = .TRUE. 
     582      IF( ln_qsr_spec ) THEN 
     583         model%interior_diagnostic_variables(jp_fabm_swr)%save = .TRUE. 
     584      ENDIF 
     585      DO jn=1,size(model%horizontal_diagnostic_variables) 
     586         model%horizontal_diagnostic_variables(jn)%save = iom_use(model%horizontal_diagnostic_variables(jn)%name) & 
     587            .or. iom_use(TRIM(model%horizontal_diagnostic_variables(jn)%name)//'25h') 
     588      END DO 
     589 
     590      ! Check whether FABM has all required data 
     591      ! [after this, the save attribute of diagnostic variables can no longer change!] 
     592      CALL model%start() 
     593 
     594      started = .TRUE. 
     595 
     596   END SUBROUTINE 
    574597 
    575598#else 
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