ROMS-TOPAZ diagnostic 2d, 3d 변수 배열 등록 및 write 모듈 등록

HyunChaeJung commented 1 year ago

~/ROMS1158/ROMS/Modules/mod_diags.F

.....
!!add TOPAZ, hcjung 20230508
#  elif defined TOPAZ
      real(r8), pointer :: DiaBio2d(:,:,:)
      real(r8), pointer :: DiaBio3d(:,:,:,:)
#  endif
.....
!!add TOPAZ, hcjung 20230508
#  elif defined TOPAZ
  IF (NDbio2d.gt.0) THEN
    allocate ( DIAGS(ng) % DiaBio2d(LBi:UBi,LBj:UBj,NDbio2d) )
    Dmem(ng)=Dmem(ng)+REAL(NDbio2d,r8)*size2d
  END IF
  IF (NDbio3d.gt.0) THEN
    allocate ( DIAGS(ng) % DiaBio3d(LBi:UBi,LBj:UBj,N(ng),NDbio3d) )
    Dmem(ng)=Dmem(ng)+REAL(N(ng)*NDbio3d,r8)*size2d
  END IF
#  endif
......
!!add TOPAZ, hcjung 20230508
#   elif defined TOPAZ
  IF (NDbio2d.gt.0) THEN
    IF (.not.destroy(ng, DIAGS(ng)%DiaBio2d, MyFile,                &
 &                   __LINE__, 'DIAGS(ng)%DiaBio2d')) RETURN
  END IF

  IF (NDbio3d.gt.0) THEN
    IF (.not.destroy(ng, DIAGS(ng)%DiaBio3d, MyFile,                &
 &                   __LINE__, 'DIAGS(ng)%DiaBio3d')) RETURN
  END IF
#   endif
......
!!add TOPAZ, hcjung 20230508
#  elif defined TOPAZ
    IF (NDbio2d.gt.0) THEN
      DO idiag=1,NDbio2d
        DO i=Imin,Imax
          DIAGS(ng) % DiaBio2d(i,j,idiag) = IniVal
        END DO
      END DO
    END IF
    IF (NDbio3d.gt.0) THEN
      DO idiag=1,NDbio3d
        DO k=1,N(ng)
          DO i=Imin,Imax
            DIAGS(ng) % DiaBio3d(i,j,k,idiag) = IniVal
          END DO
        END DO
      END DO
    END IF
#  endif
......

HyunChaeJung commented 1 year ago

./Utility/set_diags.F

......
!!add TOPAZ, hcjung 20230508
#  elif defined TOPAZ
    DO idiag=1,NDbio2d
!          IF (idiag.ne.ipCO2) THEN
        DO j=JstrR,JendR
          DO i=IstrR,IendR
            DIAGS(ng)%DiaBio2d(i,j,idiag)=rfac(i,j)*                &
 &                    DIAGS(ng)%DiaBio2d(i,j,idiag)
          END DO
        END DO
!          END IF
    END DO
    DO idiag=1,NDbio3d
      DO k=1,N(ng)
        DO j=JstrR,JendR
          DO i=IstrR,IendR
            DIAGS(ng)%DiaBio3d(i,j,k,idiag)=rfac(i,j)*              &
 &                    DIAGS(ng)%DiaBio3d(i,j,k,idiag)
          END DO
        END DO
      END DO
    END DO
#  endif
......
!!add TOPAZ, hcjung 20230508
#   elif defined TOPAZ
!
!  Biological terms 2D diagnostics.
!
    DO idiag=1,NDbio2d
      CALL bc_r2d_tile (ng, tile,                                   &
 &                      LBi, UBi, LBj, UBj,                         &
 &                      DIAGS(ng)%DiaBio2d(:,:,idiag))
    END DO
#    ifdef DISTRIBUTE
    CALL mp_exchange3d (ng, tile, iNLM, 1,                          &
 &                      LBi, UBi, LBj, UBj, 1, NDbio2d,             &
 &                      NghostPoints,                               &
 &                      EWperiodic(ng), NSperiodic(ng),             &
 &                      DIAGS(ng)%DiaBio2d)
#    endif
!
!  Biological terms 3D diagnostics.
!
    DO idiag=1,NDbio3d
      CALL bc_r3d_tile (ng, tile,                                   &
 &                      LBi, UBi, LBj, UBj, 1, N(ng),               &
 &                      DIAGS(ng)%DiaBio3d(:,:,:,idiag))
    END DO
#    ifdef DISTRIBUTE
    CALL mp_exchange4d (ng, tile, iNLM, 1,                          &
 &                      LBi, UBi, LBj, UBj, 1, N(ng), 1, NDbio3d,   &
 &                      NghostPoints,                               &
 &                      EWperiodic(ng), NSperiodic(ng),             &
 &                      DIAGS(ng)%DiaBio3d)
#    endif
.....

HyunChaeJung commented 1 year ago

./Utility/wrt_diags.F

......
#  elif defined TOPAZ
!
!  Write out 2D biological diagnostic fields.
!

  DO ivar=1,NDbio2d
    ifield=iDbio2(ivar)
    IF (Dout(ifield,ng)) THEN
       scale=1.0_dp

      gtype=gfactor*r2dvar
      status=nf_fwrite2d(ng, iNLM, DIA(ng)%ncid,                    &
 &                       DIA(ng)%Vid(ifield),                       &
 &                       DIA(ng)%Rindex, gtype,                     &
 &                       LBi, UBi, LBj, UBj, scale,                 &
#   ifdef MASKING
 &                       GRID(ng) % rmask,                          &
#   endif
 &                       DIAGS(ng) % DiaBio2d(:,:,ivar),            &
 &                       SetFillVal = .FALSE.)
      IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
        IF (Master) THEN
          WRITE (stdout,10) TRIM(Vname(1,ifield)), DIA(ng)%Rindex
        END IF
        exit_flag=3
        ioerror=status
        RETURN
      END IF
    END IF
  END DO
!
!  Write out 3D biological diagnostic fields.
!
  DO ivar=1,NDbio3d
    ifield=iDbio3(ivar)
    IF (Dout(ifield,ng)) THEN
      scale=1.0_dp
      gtype=gfactor*r3dvar
      status=nf_fwrite3d(ng, iNLM, DIA(ng)%ncid,                    &
 &                       DIA(ng)%Vid(ifield),                       &
 &                       DIA(ng)%Rindex, gtype,                     &
 &                       LBi, UBi, LBj, UBj, 1, N(ng), scale,       &
#   ifdef MASKING
 &                       GRID(ng) % rmask,                          &
#   endif
 &                       DIAGS(ng) % DiaBio3d(:,:,:,ivar),          &
 &                       SetFillVal = .FALSE.)
      IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
        IF (Master) THEN
          WRITE (stdout,10) TRIM(Vname(1,ifield)), DIA(ng)%Rindex
        END IF
        exit_flag=3
        ioerror=status
        RETURN
      END IF
    END IF
  END DO
......
!!add TOPAZ, hcjung 20230508
#   elif defined TOPAZ
!
!  Write out 2D biological diagnostic fields.
!
  DO ivar=1,NDbio2d
    ifield=iDbio2(ivar)
    IF (Dout(ifield,ng)) THEN
        scale=1.0_dp

      IF (DIA(ng)%pioVar(ifield)%dkind.eq.PIO_double) THEN
        ioDesc => ioDesc_dp_r2dvar(ng)
      ELSE
        ioDesc => ioDesc_sp_r2dvar(ng)
      END IF
      status=nf_fwrite2d(ng, iNLM, DIA(ng)%pioFile,                 &
 &                       DIA(ng)%pioVar(ifield),                    &
 &                       DIA(ng)%Rindex,                            &
 &                       ioDesc,                                    &
 &                       LBi, UBi, LBj, UBj, scale,                 &
#    ifdef MASKING
 &                       GRID(ng) % rmask,                          &
#    endif
 &                       DIAGS(ng) % DiaBio2d(:,:,ivar),            &
 &                       SetFillVal = .FALSE.)
      IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
        IF (Master) THEN
          WRITE (stdout,10) TRIM(Vname(1,ifield)), DIA(ng)%Rindex
        END IF
        exit_flag=3
        ioerror=status
        RETURN
      END IF
    END IF
  END DO
!
!  Write out 3D biological diagnostic fields.
!
  DO ivar=1,NDbio3d
    ifield=iDbio3(ivar)
    IF (Dout(ifield,ng)) THEN
      scale=1.0_dp
      IF (DIA(ng)%pioVar(ifield)%dkind.eq.PIO_double) THEN
        ioDesc => ioDesc_dp_r3dvar(ng)
      ELSE
        ioDesc => ioDesc_sp_r3dvar(ng)
      END IF
      status=nf_fwrite3d(ng, iNLM, DIA(ng)%pioFile,                 &
 &                       DIA(ng)%pioVar(ifield),                    &
 &                       DIA(ng)%Rindex,                            &
 &                       ioDesc,                                    &
 &                       LBi, UBi, LBj, UBj, 1, N(ng), scale,       &
#    ifdef MASKING
 &                       GRID(ng) % rmask,                          &
#    endif
 &                       DIAGS(ng) % DiaBio3d(:,:,:,ivar),          &
 &                       SetFillVal = .FALSE.)
      IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
        IF (Master) THEN
          WRITE (stdout,10) TRIM(Vname(1,ifield)), DIA(ng)%Rindex
        END IF
        exit_flag=3
        ioerror=status
        RETURN
      END IF
    END IF
  END DO
.......

HyunChaeJung commented 1 year ago

./Utility/def_diags.F

!
!  Define 2D biological diagnostic fields.
!
    DO ivar=1,NDbio2d
      ifield=iDbio2(ivar)
      IF (Dout(ifield,ng)) THEN
        Vinfo( 1)=Vname(1,ifield)
        WRITE (Vinfo( 2),'(a,1x,a)') Prefix, TRIM(Vname(2,ifield))
        Vinfo( 3)=Vname(3,ifield)
        Vinfo(14)=Vname(4,ifield)
        Vinfo(16)=Vname(1,idtime)
#   if defined WRITE_WATER && defined MASKING
        Vinfo(20)='mask_rho'
#   endif
        Vinfo(21)=Vname(6,ifield)
        Vinfo(22)='coordinates'
        Aval(5)=REAL(r2dvar,r8)
        status=def_var(ng, iNLM, DIA(ng)%ncid, DIA(ng)%Vid(ifield), &
 &                     NF_FOUT, nvd3, t2dgrd, Aval, Vinfo, ncname)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
      END IF
    END DO
!
!  Define 3D biological diagnostic fields.
!
    DO ivar=1,NDbio3d
      ifield=iDbio3(ivar)
      IF (Dout(ifield,ng)) THEN
        Vinfo( 1)=Vname(1,ifield)
        WRITE (Vinfo( 2),'(a,1x,a)') Prefix, TRIM(Vname(2,ifield))
        Vinfo( 3)=Vname(3,ifield)
        Vinfo(14)=Vname(4,ifield)
        Vinfo(16)=Vname(1,idtime)
#   if defined WRITE_WATER && defined MASKING
        Vinfo(20)='mask_rho'
#   endif
        Vinfo(21)=Vname(6,ifield)
        Vinfo(22)='coordinates'
        Aval(5)=REAL(r3dvar,r8)
        status=def_var(ng, iNLM, DIA(ng)%ncid, DIA(ng)%Vid(ifield), &
 &                     NF_FOUT, nvd4, t3dgrd, Aval, Vinfo, ncname)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
      END IF
    END DO

HCJung-jbnu commented 1 year ago

bio_topaz.in


! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! biological processes diagnostics terms into DIAGNOSTIC output file [Ngrids].

Dout(iIRRM) == T !Irradiance Memory mol/kg Dout(iHTTL) == T !H+ ion Concentration mol/kg Dout(iSBTF) == T !SiO2 flux to Sediments mol/kg Dout(iPBTF) == T !P flux to Sediments mol/kg Dout(iNBTF) == T !N flux to Sediments mol/kg Dout(iLBTF) == T !Lith flux to Sediments mol/kg Dout(iCCBF) == T !Calcite flux to Sediments mol/kg Dout(iCABF) == T !Aragonite flux to Sediments mol/kg Dout(iCION) == T !Carbonate ion Concentration mol/kg Dout(iCHL_) == T !Chlorophyll Concentration mol/kg Dout(iCASD) == T !Sediment CaCO3 mol/kg

Dout(iCOAL) == T !Solubility of CO2 for air mol/kg/atm Dout(iCOSC) == T !Schmidt number for CO2 none Dout(iCOCS) == T !Ocean surface gas concentration of CO2 mol/kg Dout(iO2AL) == T !Solubility of O2 for air mol/kg/atm Dout(iO2SC) == T !Schmidt number for O2 none Dout(iO2CS) == T !Ocean surface gas concentration of O2 mol/kg

HCJung-jbnu / ROMS-TOPAZ

ROMS-TOPAZ diagnostic 2d, 3d 변수 배열 등록 및 write 모듈 등록 #19