source: trunk/NEMOGCM/NEMO/SAO_SRC/sao_read.F90 @ 6140

MODULE sao_read
   !!==================================================================
   !!                    *** MODULE sao_read ***
   !! Read routines : I/O for Stand Alone Observation operator
   !!==================================================================
   USE mppini
   USE lib_mpp
   USE in_out_manager
   USE par_kind, ONLY: lc
   USE netcdf
   USE oce,     ONLY: tsn, sshn
   USE dom_oce, ONLY: nlci, nlcj, nimpp, njmpp, tmask
   USE par_oce, ONLY: jpi, jpj, jpk
   USE obs_fbm, ONLY: fbimdi, fbrmdi, fbsp, fbdp
   USE sao_data

   IMPLICIT NONE
   PRIVATE

   PUBLIC sao_rea_dri

CONTAINS
   SUBROUTINE sao_rea_dri(kfile)
      !!------------------------------------------------------------------------
      !!             *** sao_rea_dri ***
      !!
      !! Purpose : To choose appropriate read method
      !! Method  :
      !!
      !! Author  : A. Ryan Oct 2013
      !!
      !!------------------------------------------------------------------------
      INTEGER, INTENT(IN) :: &
              & kfile         !: File number
      CHARACTER(len=lc) :: &
              & cdfilename    !: File name
      INTEGER :: &
              & kindex        !: File index to read

      cdfilename = TRIM(sao_files(kfile))
      kindex = nn_sao_idx(kfile)
      CALL sao_read_file(TRIM(cdfilename), kindex)

   END SUBROUTINE sao_rea_dri

   SUBROUTINE sao_read_file(filename, ifcst)
      !!------------------------------------------------------------------------
      !!             *** sao_read_file ***
      !!
      !! Purpose : To fill tn and sn with dailymean field from netcdf files
      !! Method  : Use subdomain indices to create start and count matrices
      !!           for netcdf read.
      !!
      !! Author  : A. Ryan Oct 2010
      !!------------------------------------------------------------------------

      INTEGER,          INTENT(IN) :: ifcst
      CHARACTER(len=*), INTENT(IN) :: filename
      INTEGER                      :: ncid, &
                                    & varid,&
                                    & istat,&
                                    & ntimes,&
                                    & tdim, &
                                    & xdim, &
                                    & ydim, &
                                    & zdim
      INTEGER                      :: ii, ij, ik
      INTEGER, DIMENSION(4)        :: start_n, &
                                    & count_n
      INTEGER, DIMENSION(3)        :: start_s, &
                                    & count_s
      REAL(fbdp), DIMENSION(:,:,:),ALLOCATABLE :: temp_tn, &
                                              & temp_sn
      REAL(fbdp), DIMENSION(:,:),  ALLOCATABLE :: temp_sshn
      REAL(fbdp)                     :: fill_val

      ! DEBUG
      INTEGER :: istage

      IF (TRIM(filename) == 'nofile') THEN
         tsn(:,:,:,:) = fbrmdi
         sshn(:,:) = fbrmdi
      ELSE
         WRITE(numout,*) "Opening :", TRIM(filename)
         ! Open Netcdf file to find dimension id
         istat = nf90_open(path=TRIM(filename), mode=nf90_nowrite, ncid=ncid)
         IF ( istat /= nf90_noerr ) THEN
             WRITE(numout,*) "WARNING: Could not open ", trim(filename)
             WRITE(numout,*) "ERROR: ", nf90_strerror(istat)
         ENDIF
         istat = nf90_inq_dimid(ncid,'x',xdim)
         istat = nf90_inq_dimid(ncid,'y',ydim)
         istat = nf90_inq_dimid(ncid,'deptht',zdim)
         istat = nf90_inq_dimid(ncid,'time_counter',tdim)
         istat = nf90_inquire_dimension(ncid, tdim, len=ntimes)
         IF (ifcst .LE. ntimes) THEN
            ! Allocate temporary temperature array
            ALLOCATE(temp_tn(nlci,nlcj,jpk))
            ALLOCATE(temp_sn(nlci,nlcj,jpk))
            ALLOCATE(temp_sshn(nlci,nlcj))

            ! Set temp_tn, temp_sn to 0.
            temp_tn(:,:,:) = fbrmdi
            temp_sn(:,:,:) = fbrmdi
            temp_sshn(:,:) = fbrmdi

            ! Create start and count arrays
            start_n = (/ nimpp, njmpp, 1,   ifcst /)
            count_n = (/ nlci,  nlcj,  jpk, 1     /)
            start_s = (/ nimpp, njmpp, ifcst /)
            count_s = (/ nlci,  nlcj,  1     /)

            ! Read information into temporary arrays
            ! retrieve varid and read in temperature
            istat = nf90_inq_varid(ncid,'votemper',varid)
            istat = nf90_get_att(ncid, varid, '_FillValue', fill_val)
            istat = nf90_get_var(ncid, varid, temp_tn, start_n, count_n)
            WHERE(temp_tn(:,:,:) == fill_val) temp_tn(:,:,:) = fbrmdi

            ! retrieve varid and read in salinity
            istat = nf90_inq_varid(ncid,'vosaline',varid)
            istat = nf90_get_att(ncid, varid, '_FillValue', fill_val)
            istat = nf90_get_var(ncid, varid, temp_sn, start_n, count_n)
            WHERE(temp_sn(:,:,:) == fill_val) temp_sn(:,:,:) = fbrmdi

            ! retrieve varid and read in SSH
            istat = nf90_inq_varid(ncid,'sossheig',varid)
            IF (istat /= nf90_noerr) THEN
               ! Altimeter bias
               istat = nf90_inq_varid(ncid,'altbias',varid)
            END IF

            istat = nf90_get_att(ncid, varid, '_FillValue', fill_val)
            istat = nf90_get_var(ncid, varid, temp_sshn, start_s, count_s)
            WHERE(temp_sshn(:,:) == fill_val) temp_sshn(:,:) = fbrmdi

            ! Initialise tsn, sshn to fbrmdi
            tsn(:,:,:,:) = fbrmdi
            sshn(:,:) = fbrmdi

            ! Mask out missing data index
            tsn(1:nlci,1:nlcj,1:jpk,1) = temp_tn(:,:,:) * tmask(1:nlci,1:nlcj,1:jpk)
            tsn(1:nlci,1:nlcj,1:jpk,2) = temp_sn(:,:,:) * tmask(1:nlci,1:nlcj,1:jpk)
            sshn(1:nlci,1:nlcj)        = temp_sshn(:,:) * tmask(1:nlci,1:nlcj,1)

            ! Remove halo from tmask, tsn, sshn to prevent double obs counting
            IF (jpi > nlci) THEN
                tmask(nlci+1:,:,:) = 0
                tsn(nlci+1:,:,:,1) = 0
                tsn(nlci+1:,:,:,2) = 0
                sshn(nlci+1:,:) = 0
            END IF
            IF (jpj > nlcj) THEN
                tmask(:,nlcj+1:,:) = 0
                tsn(:,nlcj+1:,:,1) = 0
                tsn(:,nlcj+1:,:,2) = 0
                sshn(:,nlcj+1:) = 0
            END IF

            ! Deallocate arrays
            DEALLOCATE(temp_tn, temp_sn, temp_sshn)
         ELSE
            ! Mark all as missing data
            tsn(:,:,:,:) = fbrmdi
            sshn(:,:) = fbrmdi
         ENDIF
         ! Close netcdf file
         WRITE(numout,*) "Closing :", TRIM(filename)
         istat = nf90_close(ncid)
      END IF
   END SUBROUTINE sao_read_file
END MODULE sao_read