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MODULE iom_nf90
!!======================================================================
!! *** MODULE iom_nf90 ***
!! Input/Output manager : Library to read input files with NF90 (only fliocom module)
!!======================================================================
!! History : 9.0 ! 05 12 (J. Belier) Original code
!! 9.0 ! 06 02 (S. Masson) Adaptation to NEMO
!! " ! 07 07 (D. Storkey) Changes to iom_nf90_gettime
!! 3.6 ! 2015-15 (J. Harle) Added procedure to read REAL attributes
!! 4.0 ! 2017-11 (M. Andrejczuk) Extend IOM interface to write any 3D fields
!!----------------------------------------------------------------------
!!----------------------------------------------------------------------
!! iom_open : open a file read only
!! iom_close : close a file or all files opened by iom
!! iom_get : read a field (interfaced to several routines)
!! iom_varid : get the id of a variable in a file
!! iom_rstput : write a field in a restart file (interfaced to several routines)
!!----------------------------------------------------------------------
USE dom_oce ! ocean space and time domain
USE sbc_oce, ONLY: ght_abl ! abl vertical level number and height
USE lbclnk ! lateal boundary condition / mpp exchanges
USE iom_def ! iom variables definitions
USE netcdf ! NetCDF library
USE in_out_manager ! I/O manager
USE lib_mpp ! MPP library
IMPLICIT NONE
PRIVATE
PUBLIC iom_nf90_open , iom_nf90_close, iom_nf90_varid, iom_nf90_get, iom_nf90_rstput
PUBLIC iom_nf90_chkatt, iom_nf90_getatt, iom_nf90_putatt
PUBLIC iom_nf90_check
INTERFACE iom_nf90_get
MODULE PROCEDURE iom_nf90_g0d_sp
MODULE PROCEDURE iom_nf90_g0d_dp, iom_nf90_g123d
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END INTERFACE
!!----------------------------------------------------------------------
!! NEMO/OCE 4.0 , NEMO Consortium (2018)
!! $Id: iom_nf90.F90 14433 2021-02-11 08:06:49Z smasson $
!! Software governed by the CeCILL license (see ./LICENSE)
!!----------------------------------------------------------------------
CONTAINS
SUBROUTINE iom_nf90_open( cdname, kiomid, ldwrt, ldok, kdlev, cdcomp )
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_open ***
!!
!! ** Purpose : open an input file with NF90
!!---------------------------------------------------------------------
CHARACTER(len=*) , INTENT(inout) :: cdname ! File name
INTEGER , INTENT( out) :: kiomid ! nf90 identifier of the opened file
LOGICAL , INTENT(in ) :: ldwrt ! read or write the file?
LOGICAL , INTENT(in ) :: ldok ! check the existence
INTEGER , INTENT(in ), OPTIONAL :: kdlev ! size of the ice/abl third dimension
CHARACTER(len=3) , INTENT(in ), OPTIONAL :: cdcomp ! name of component calling iom_nf90_open
CHARACTER(LEN=256) :: clinfo ! info character
CHARACTER(LEN=256) :: cltmp ! temporary character
CHARACTER(LEN=12 ) :: clfmt ! writing format
CHARACTER(LEN=3 ) :: clcomp ! name of component calling iom_nf90_open
INTEGER :: idg ! number of digits
INTEGER :: iln ! lengths of character
INTEGER :: istop ! temporary storage of nstop
INTEGER :: if90id ! nf90 identifier of the opened file
INTEGER :: idmy ! dummy variable
INTEGER :: jl ! loop variable
INTEGER :: ichunk ! temporary storage of nn_chunksz
INTEGER :: imode ! creation mode flag: NF90_CLOBBER or NF90_NOCLOBBER or NF90_HDF5
INTEGER :: ihdf5 ! local variable for retrieval of value for NF90_HDF5
LOGICAL :: llclobber ! local definition of ln_clobber
!---------------------------------------------------------------------
!
clinfo = ' iom_nf90_open ~~~ '
istop = nstop ! store the actual value of nstop
!
! !number of vertical levels
IF( PRESENT(cdcomp) ) THEN
IF( .NOT. PRESENT(kdlev) ) CALL ctl_stop( 'iom_nf90_open: cdcomp and kdlev must both be present' )
clcomp = cdcomp ! use input value
ELSE
clcomp = 'OCE' ! by default
ENDIF
!
IF( nn_chunksz > 0 ) THEN ; ichunk = nn_chunksz
ELSE ; ichunk = NF90_SIZEHINT_DEFAULT
ENDIF
!
llclobber = ldwrt .AND. ln_clobber
IF( ldok .AND. .NOT. llclobber ) THEN !== Open existing file ==!
! !=========================!
IF( ldwrt ) THEN ! ... in write mode
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' open existing file: '//TRIM(cdname)//' in WRITE mode'
IF( snc4set%luse ) THEN
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id ), clinfo)
ELSE
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id, chunksize = ichunk ), clinfo)
ENDIF
CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo)
ELSE ! ... in read mode
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' open existing file: '//TRIM(cdname)//' in READ mode'
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_NOWRITE, if90id, chunksize = ichunk ), clinfo)
ENDIF
ELSE !== the file doesn't exist ==! (or we overwrite it)
! !============================!
iln = INDEX( cdname, '.nc' )
IF( ldwrt ) THEN !* the file should be open in write mode so we create it...
IF( jpnij > 1 ) THEN
idg = MAX( INT(LOG10(REAL(MAX(1,jpnij-1),wp))) + 1, 4 ) ! how many digits to we need to write? min=4, max=9
WRITE(clfmt, "('(a,a,i', i1, '.', i1, ',a)')") idg, idg ! '(a,a,ix.x,a)'
WRITE(cltmp,clfmt) cdname(1:iln-1), '_', narea-1, '.nc'
cdname = TRIM(cltmp)
ENDIF
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' create new file: '//TRIM(cdname)//' in WRITE mode'
IF( llclobber ) THEN ; imode = IOR( NF90_64BIT_OFFSET, NF90_CLOBBER )
ELSE ; imode = IOR( NF90_64BIT_OFFSET, NF90_NOCLOBBER )
ENDIF
IF( snc4set%luse ) THEN
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' creating file: '//TRIM(cdname)//' in hdf5 (netcdf4) mode'
CALL GET_NF90_SYMBOL("NF90_HDF5", ihdf5)
IF( llclobber ) THEN ; imode = IOR(ihdf5, NF90_CLOBBER)
ELSE ; imode = IOR(ihdf5, NF90_NOCLOBBER)
ENDIF
CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id ), clinfo)
ELSE
CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id, chunksize = ichunk ), clinfo)
ENDIF
CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo)
! define dimensions
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'x', Ni_0, idmy ), clinfo)
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'y', Nj_0, idmy ), clinfo)
SELECT CASE (clcomp)
CASE ('OCE') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'nav_lev', jpk, idmy ), clinfo)
CASE ('ICE') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'numcat', kdlev, idmy ), clinfo)
CASE ('ABL') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'nav_lev', kdlev, idmy ), clinfo)
CASE ('SED') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'numsed', kdlev, idmy ), clinfo)
CASE DEFAULT ; CALL ctl_stop( 'iom_nf90_open unknown component type' )
END SELECT
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'time_counter', NF90_UNLIMITED, idmy ), clinfo)
! global attributes
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_number_total' , jpnij ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_number' , narea-1 ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_dimensions_ids' , (/ 1 , 2 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_size_global' , (/ Ni0glo , Nj0glo /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_size_local' , (/ Ni_0 , Nj_0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_position_first' , (/ mig0(Nis0), mjg0(Njs0) /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_position_last' , (/ mig0(Nie0), mjg0(Nje0) /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_halo_size_start', (/ 0 , 0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_halo_size_end' , (/ 0 , 0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_type' , 'BOX' ), clinfo)
ELSE !* the file should be open for read mode so it must exist...
CALL ctl_stop( TRIM(clinfo), ' should be impossible case...' )
ENDIF
ENDIF
!
! start to fill file informations
! =============
IF( istop == nstop ) THEN ! no error within this routine
!does not work with some compilers kiomid = MINLOC(iom_file(:)%nfid, dim = 1)
kiomid = 0
DO jl = jpmax_files, 1, -1
IF( iom_file(jl)%nfid == 0 ) kiomid = jl
ENDDO
iom_file(kiomid)%name = TRIM(cdname)
iom_file(kiomid)%comp = clcomp
iom_file(kiomid)%nfid = if90id
iom_file(kiomid)%nvars = 0
iom_file(kiomid)%irec = -1 ! useless for NetCDF files, used to know if the file is in define mode
CALL iom_nf90_check(NF90_Inquire(if90id, unlimitedDimId = iom_file(kiomid)%iduld), clinfo)
IF( iom_file(kiomid)%iduld .GE. 0 ) THEN
CALL iom_nf90_check(NF90_Inquire_Dimension(if90id, iom_file(kiomid)%iduld, &
& name = iom_file(kiomid)%uldname, &
& len = iom_file(kiomid)%lenuld ), clinfo )
ENDIF
IF(lwp) WRITE(numout,*) ' ---> '//TRIM(cdname)//' OK'
ELSE
kiomid = 0 ! return error flag
ENDIF
!
END SUBROUTINE iom_nf90_open
SUBROUTINE iom_nf90_close( kiomid )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_close ***
!!
!! ** Purpose : close an input file with NF90
!!--------------------------------------------------------------------
INTEGER, INTENT(in) :: kiomid ! iom identifier of the file to be closed
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = ' iom_nf90_close , file: '//TRIM(iom_file(kiomid)%name)
CALL iom_nf90_check(NF90_CLOSE(iom_file(kiomid)%nfid), clinfo)
END SUBROUTINE iom_nf90_close
FUNCTION iom_nf90_varid ( kiomid, cdvar, kiv, kdimsz, kndims, lduld )
!!-----------------------------------------------------------------------
!! *** FUNCTION iom_varid ***
!!
!! ** Purpose : get the id of a variable in a file with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! file Identifier
CHARACTER(len=*) , INTENT(in ) :: cdvar ! name of the variable
INTEGER , INTENT(in ) :: kiv !
INTEGER, DIMENSION(:), INTENT( out), OPTIONAL :: kdimsz ! size of each dimension
INTEGER , INTENT( out), OPTIONAL :: kndims ! number of dimensions
LOGICAL , INTENT( out), OPTIONAL :: lduld ! true if the last dimension is unlimited (time)
!
INTEGER :: iom_nf90_varid ! iom variable Id
INTEGER :: if90id ! nf90 file identifier
INTEGER :: ji ! dummy loop index
INTEGER :: ivarid ! NetCDF variable Id
INTEGER :: i_nvd ! number of dimension of the variable
INTEGER, DIMENSION(jpmax_dims) :: idimid ! dimension ids of the variable
LOGICAL :: llok ! ok test
CHARACTER(LEN=100) :: clinfo ! info character
!!-----------------------------------------------------------------------
clinfo = ' iom_nf90_varid, file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(cdvar)
iom_nf90_varid = 0 ! default definition
IF( PRESENT(kdimsz) ) kdimsz(:) = 0 ! default definition
if90id = iom_file(kiomid)%nfid ! get back NetCDF file id
!
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr ! does the variable exist in the file
IF( llok ) THEN
iom_nf90_varid = kiv
iom_file(kiomid)%nvars = kiv
iom_file(kiomid)%nvid(kiv) = ivarid
iom_file(kiomid)%cn_var(kiv) = TRIM(cdvar)
CALL iom_nf90_check(NF90_Inquire_Variable(if90id, ivarid, ndims = i_nvd), clinfo) ! number of dimensions
iom_file(kiomid)%ndims(kiv) = i_nvd
CALL iom_nf90_check(NF90_Inquire_Variable(if90id, ivarid, dimids = idimid(1:i_nvd)), clinfo) ! dimensions ids
iom_file(kiomid)%luld(kiv) = .FALSE. ! default value
iom_file(kiomid)%dimsz(:,kiv) = 0 ! reset dimsz in case previously used
DO ji = 1, i_nvd ! dimensions size
CALL iom_nf90_check(NF90_Inquire_Dimension(if90id, idimid(ji), len = iom_file(kiomid)%dimsz(ji,kiv)), clinfo)
IF( idimid(ji) == iom_file(kiomid)%iduld ) iom_file(kiomid)%luld(kiv) = .TRUE. ! unlimited dimension?
END DO
!---------- Deal with scale_factor and add_offset
llok = NF90_Inquire_attribute(if90id, ivarid, 'scale_factor') == nf90_noerr
IF( llok) THEN
CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, 'scale_factor', iom_file(kiomid)%scf(kiv)), clinfo)
ELSE
iom_file(kiomid)%scf(kiv) = 1.
END IF
llok = NF90_Inquire_attribute(if90id, ivarid, 'add_offset') == nf90_noerr
IF( llok ) THEN
CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, 'add_offset', iom_file(kiomid)%ofs(kiv)), clinfo)
ELSE
iom_file(kiomid)%ofs(kiv) = 0.
END IF
! return the simension size
IF( PRESENT(kdimsz) ) THEN
IF( i_nvd <= SIZE(kdimsz) ) THEN
kdimsz(1:i_nvd) = iom_file(kiomid)%dimsz(1:i_nvd,kiv)
ELSE
WRITE(ctmp1,*) i_nvd, SIZE(kdimsz)
CALL ctl_stop( TRIM(clinfo), 'error in kdimsz size'//TRIM(ctmp1) )
ENDIF
ENDIF
IF( PRESENT(kndims) ) kndims = iom_file(kiomid)%ndims(kiv)
IF( PRESENT( lduld) ) lduld = iom_file(kiomid)%luld(kiv)
ELSE
iom_nf90_varid = -1 ! variable not found, return error code: -1
ENDIF
!
END FUNCTION iom_nf90_varid
!!----------------------------------------------------------------------
!! INTERFACE iom_nf90_get
!!----------------------------------------------------------------------
SUBROUTINE iom_nf90_g0d_sp( kiomid, kvid, pvar, kstart )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g0d ***
!!
!! ** Purpose : read a scalar with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
INTEGER , INTENT(in ) :: kvid ! variable id
REAL(sp), INTENT( out) :: pvar ! read field
INTEGER , DIMENSION(1), INTENT(in ), OPTIONAL :: kstart ! start position of the reading in each axis
!
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g0d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
CALL iom_nf90_check(NF90_GET_VAR(iom_file(kiomid)%nfid, iom_file(kiomid)%nvid(kvid), pvar, start = kstart), clinfo )
END SUBROUTINE iom_nf90_g0d_sp
SUBROUTINE iom_nf90_g0d_dp( kiomid, kvid, pvar, kstart )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g0d ***
!!
!! ** Purpose : read a scalar with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
INTEGER , INTENT(in ) :: kvid ! variable id
REAL(dp), INTENT( out) :: pvar ! read field
INTEGER , DIMENSION(1), INTENT(in ), OPTIONAL :: kstart ! start position of the reading in each axis
!
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g0d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
CALL iom_nf90_check(NF90_GET_VAR(iom_file(kiomid)%nfid, iom_file(kiomid)%nvid(kvid), pvar, start = kstart), clinfo )
END SUBROUTINE iom_nf90_g0d_dp
SUBROUTINE iom_nf90_g123d( kiomid, kvid, knbdim, kstart, kcount, kx1, kx2, ky1, ky2, &
& pvsp1d, pvsp2d, pvsp3d, pvdp1d, pvdp2d, pvdp3d )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g123d ***
!!
!! ** Purpose : read a 1D/2D/3D variable with NF90
!!
!! ** Method : read ONE record at each CALL
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! iom identifier of the file
INTEGER , INTENT(in ) :: kvid ! Name of the variable
INTEGER , INTENT(in ) :: knbdim ! number of dimensions of the variable
INTEGER , DIMENSION(:) , INTENT(in ) :: kstart ! start position of the reading in each axis
INTEGER , DIMENSION(:) , INTENT(in ) :: kcount ! number of points to be read in each axis
INTEGER , INTENT(in ) :: kx1, kx2, ky1, ky2 ! subdomain indexes
REAL(sp), DIMENSION(:) , INTENT( out), OPTIONAL :: pvsp1d ! read field (1D case), single precision
REAL(sp), DIMENSION(:,:) , INTENT( out), OPTIONAL :: pvsp2d ! read field (2D case), single precision
REAL(sp), DIMENSION(:,:,:) , INTENT( out), OPTIONAL :: pvsp3d ! read field (3D case), single precision
REAL(dp), DIMENSION(:) , INTENT( out), OPTIONAL :: pvdp1d ! read field (1D case), double precision
REAL(dp), DIMENSION(:,:) , INTENT( out), OPTIONAL :: pvdp2d ! read field (2D case), double precision
REAL(dp), DIMENSION(:,:,:) , INTENT( out), OPTIONAL :: pvdp3d ! read field (3D case), double precision
!
CHARACTER(LEN=100) :: clinfo ! info character
INTEGER :: if90id ! nf90 identifier of the opened file
INTEGER :: ivid ! nf90 variable id
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g123d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
if90id = iom_file(kiomid)%nfid ! get back NetCDF file id
ivid = iom_file(kiomid)%nvid(kvid) ! get back NetCDF var id
!
IF( PRESENT(pvsp1d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvsp1d(: ), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ELSEIF( PRESENT(pvdp1d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvdp1d(: ), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ELSEIF( PRESENT(pvsp2d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvsp2d(kx1:kx2,ky1:ky2 ), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ELSEIF( PRESENT(pvdp2d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvdp2d(kx1:kx2,ky1:ky2 ), start = kstart(1:knbdim), &
ELSEIF( PRESENT(pvsp3d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvsp3d(kx1:kx2,ky1:ky2,:), start = kstart(1:knbdim), &
ELSEIF( PRESENT(pvdp3d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pvdp3d(kx1:kx2,ky1:ky2,:), start = kstart(1:knbdim), &
END SUBROUTINE iom_nf90_g123d
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SUBROUTINE iom_nf90_chkatt( kiomid, cdatt, llok, ksize, cdvar )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_chkatt ***
!!
!! ** Purpose : check existence of attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*), INTENT(in ) :: cdatt ! attribute name
LOGICAL , INTENT( out) :: llok ! error code
INTEGER , INTENT( out), OPTIONAL &
& :: ksize ! attribute size
CHARACTER(len=*), INTENT(in ), OPTIONAL &
& :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: isize ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
! check the variable exists in the file
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr
IF( llok ) &
! check the variable has the attribute required
llok = NF90_Inquire_attribute(if90id, ivarid, cdatt, len=isize ) == nf90_noerr
ELSE
llok = NF90_Inquire_attribute(if90id, NF90_GLOBAL, cdatt, len=isize ) == nf90_noerr
ENDIF
!
IF( PRESENT(ksize) ) ksize = isize
!
IF( .not. llok) &
CALL ctl_warn('iom_nf90_chkatt: no attribute '//cdatt//' found')
!
END SUBROUTINE iom_nf90_chkatt
!!----------------------------------------------------------------------
!! INTERFACE iom_nf90_getatt
!!----------------------------------------------------------------------
SUBROUTINE iom_nf90_getatt( kiomid, cdatt, katt0d, katt1d, patt0d, patt1d, cdatt0d, cdvar)
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_getatt ***
!!
!! ** Purpose : read an attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in ) :: cdatt ! attribute name
INTEGER , INTENT( out), OPTIONAL :: katt0d ! read scalar integer
INTEGER, DIMENSION(:) , INTENT( out), OPTIONAL :: katt1d ! read 1d array integer
REAL(wp) , INTENT( out), OPTIONAL :: patt0d ! read scalar real
REAL(wp), DIMENSION(:), INTENT( out), OPTIONAL :: patt1d ! read 1d array real
CHARACTER(len=*) , INTENT( out), OPTIONAL :: cdatt0d ! read character
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
LOGICAL :: llok ! temporary logical
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
! check the variable exists in the file
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr
IF( llok ) THEN
! check the variable has the attribute required
llok = NF90_Inquire_attribute(if90id, ivarid, cdatt) == nf90_noerr
ELSE
CALL ctl_warn('iom_nf90_getatt: no variable '//TRIM(cdvar)//' found')
ENDIF
ELSE
llok = NF90_Inquire_attribute(if90id, NF90_GLOBAL, cdatt) == nf90_noerr
ivarid = NF90_GLOBAL
ENDIF
!
IF( llok) THEN
clinfo = 'iom_nf90_getatt, file: '//TRIM(iom_file(kiomid)%name)//', att: '//TRIM(cdatt)
IF(PRESENT( katt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = katt0d), clinfo)
IF(PRESENT( katt1d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = katt1d), clinfo)
IF(PRESENT( patt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = patt0d), clinfo)
IF(PRESENT( patt1d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = patt1d), clinfo)
IF(PRESENT(cdatt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = cdatt0d), clinfo)
ELSE
IF(PRESENT( katt0d)) katt0d = -999
IF(PRESENT( katt1d)) katt1d(:) = -999
IF(PRESENT( patt0d)) patt0d = -999._wp
IF(PRESENT( patt1d)) patt1d(:) = -999._wp
IF(PRESENT(cdatt0d)) cdatt0d = 'UNKNOWN'
ENDIF
!
END SUBROUTINE iom_nf90_getatt
SUBROUTINE iom_nf90_putatt( kiomid, cdatt, katt0d, katt1d, patt0d, patt1d, cdatt0d, cdvar)
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_putatt ***
!!
!! ** Purpose : write an attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in ) :: cdatt ! attribute name
INTEGER , INTENT(in ), OPTIONAL :: katt0d ! read scalar integer
INTEGER, DIMENSION(:) , INTENT(in ), OPTIONAL :: katt1d ! read 1d array integer
REAL(wp) , INTENT(in ), OPTIONAL :: patt0d ! read scalar real
REAL(wp), DIMENSION(:), INTENT(in ), OPTIONAL :: patt1d ! read 1d array real
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdatt0d ! read character
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
INTEGER :: isize ! Attribute size
INTEGER :: itype ! Attribute type
LOGICAL :: llok ! temporary logical
LOGICAL :: llatt ! temporary logical
LOGICAL :: lldata ! temporary logical
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr ! is the variable in the file?
IF( .NOT. llok ) THEN
CALL ctl_warn('iom_nf90_putatt: no variable '//TRIM(cdvar)//' found' &
& , ' no attribute '//cdatt//' written' )
RETURN
ENDIF
ELSE
ivarid = NF90_GLOBAL
ENDIF
llatt = NF90_Inquire_attribute(if90id, ivarid, cdatt, len = isize, xtype = itype ) == nf90_noerr
!
! trick: irec used to know if the file is in define mode or not
lldata = iom_file(kiomid)%irec /= -1 ! default: go back in define mode if in data mode
IF( lldata .AND. llatt ) THEN ! attribute already there. Do we really need to go back in define mode?
! do we have the appropriate type?
IF(PRESENT( katt0d) .OR. PRESENT( katt1d)) llok = itype == NF90_INT
IF(PRESENT( patt0d) .OR. PRESENT( patt1d)) llok = itype == NF90_DOUBLE
IF(PRESENT(cdatt0d) ) llok = itype == NF90_CHAR
! and do we have the appropriate size?
IF(PRESENT( katt0d)) llok = llok .AND. isize == 1
IF(PRESENT( katt1d)) llok = llok .AND. isize == SIZE(katt1d)
IF(PRESENT( patt0d)) llok = llok .AND. isize == 1
IF(PRESENT( patt1d)) llok = llok .AND. isize == SIZE(patt1d)
IF(PRESENT(cdatt0d)) llok = llok .AND. isize == LEN_TRIM(cdatt0d)
!
lldata = .NOT. llok
ENDIF
!
clinfo = 'iom_nf90_putatt, file: '//TRIM(iom_file(kiomid)%name)//', att: '//TRIM(cdatt)
IF(lldata) CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ! leave data mode to define mode
!
IF(PRESENT( katt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = katt0d) , clinfo)
IF(PRESENT( katt1d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = katt1d) , clinfo)
IF(PRESENT( patt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = patt0d) , clinfo)
IF(PRESENT( patt1d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = patt1d) , clinfo)
IF(PRESENT(cdatt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = trim(cdatt0d)), clinfo)
!
IF(lldata) CALL iom_nf90_check(NF90_ENDDEF( if90id ), clinfo) ! leave define mode to data mode
!
END SUBROUTINE iom_nf90_putatt
SUBROUTINE iom_nf90_rstput( kt, kwrite, kiomid, cdvar , kvid , ktype , &
& pvsp0d, pvsp1d, pvsp2d, pvsp3d, &
& pvdp0d, pvdp1d, pvdp2d, pvdp3d )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_rstput ***
!!
!! ** Purpose : read the time axis cdvar in the file
!!--------------------------------------------------------------------
INTEGER , INTENT(in) :: kt ! ocean time-step
INTEGER , INTENT(in) :: kwrite ! writing time-step
INTEGER , INTENT(in) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in) :: cdvar ! variable name
INTEGER , INTENT(in) :: kvid ! variable id
INTEGER , INTENT(in), OPTIONAL :: ktype ! variable type (default R8)
REAL(sp) , INTENT(in), OPTIONAL :: pvsp0d ! written Od field
REAL(sp), DIMENSION( :), INTENT(in), OPTIONAL :: pvsp1d ! written 1d field
REAL(sp), DIMENSION(:, : ), INTENT(in), OPTIONAL :: pvsp2d ! written 2d field
REAL(sp), DIMENSION(:, :, :), INTENT(in), OPTIONAL :: pvsp3d ! written 3d field
REAL(dp) , INTENT(in), OPTIONAL :: pvdp0d ! written Od field
REAL(dp), DIMENSION( :), INTENT(in), OPTIONAL :: pvdp1d ! written 1d field
REAL(dp), DIMENSION(:, : ), INTENT(in), OPTIONAL :: pvdp2d ! written 2d field
REAL(dp), DIMENSION(:, :, :), INTENT(in), OPTIONAL :: pvdp3d ! written 3d field
!
INTEGER :: idims ! number of dimension
INTEGER :: idvar ! variable id
INTEGER :: jd ! dimension loop counter
INTEGER :: ix1, ix2, iy1, iy2 ! subdomain indexes
INTEGER, DIMENSION(4) :: idimsz ! dimensions size
INTEGER, DIMENSION(4) :: idimid ! dimensions id
CHARACTER(LEN=256) :: clinfo ! info character
INTEGER :: if90id ! nf90 file identifier
INTEGER :: itype ! variable type
INTEGER, DIMENSION(4) :: ichunksz ! NetCDF4 chunk sizes. Will be computed using
! ! nn_nchunks_[i,j,k,t] namelist parameters
INTEGER :: ichunkalg, ishuffle, ideflate, ideflate_level
! ! NetCDF4 internally fixed parameters
INTEGER :: idlv ! local variable
LOGICAL :: lchunk ! logical switch to activate chunking and compression
! ! when appropriate (currently chunking is applied to 4d fields only)
LOGICAL :: llis0d, llis1d, llis2d, llis3d
CHARACTER(LEN=256) :: ccname ! local variable
!---------------------------------------------------------------------
!
llis0d = PRESENT(pvsp0d) .OR. PRESENT(pvdp0d)
llis1d = PRESENT(pvsp1d) .OR. PRESENT(pvdp1d)
llis2d = PRESENT(pvsp2d) .OR. PRESENT(pvdp2d)
llis3d = PRESENT(pvsp3d) .OR. PRESENT(pvdp3d)
!
clinfo = ' iom_nf90_rp0123d, file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(cdvar)
if90id = iom_file(kiomid)%nfid
!
! define dimension variables if it is not already done
! ==========================
IF( iom_file(kiomid)%nvars == 0 ) THEN
! are we in define mode?
IF( iom_file(kiomid)%irec /= -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = -1
ENDIF
! define the dimension variables if it is not already done
DO jd = 1, 2
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION(if90id,jd,iom_file(kiomid)%cn_var(jd),iom_file(kiomid)%dimsz(jd,jd)),clinfo)
ccname = TRIM(iom_file(kiomid)%cn_var(jd))
IF ( ccname == 'x') ccname = 'nav_lon'
IF ( ccname == 'y') ccname = 'nav_lat'
CALL iom_nf90_check(NF90_DEF_VAR( if90id, ccname, NF90_FLOAT , (/ 1, 2 /), &
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& iom_file(kiomid)%nvid(jd) ), clinfo)
END DO
iom_file(kiomid)%dimsz(2,1) = iom_file(kiomid)%dimsz(2,2) ! second dim of first variable
iom_file(kiomid)%dimsz(1,2) = iom_file(kiomid)%dimsz(1,1) ! first dim of second variable
DO jd = 3, 4
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION(if90id,jd,iom_file(kiomid)%cn_var(jd),iom_file(kiomid)%dimsz(1,jd)), clinfo)
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(iom_file(kiomid)%cn_var(jd)), NF90_FLOAT , (/ jd /), &
& iom_file(kiomid)%nvid(jd) ), clinfo)
END DO
! update informations structure related the dimension variable we just added...
iom_file(kiomid)%nvars = 4
iom_file(kiomid)%luld(1:4) = (/ .FALSE., .FALSE., .FALSE., .TRUE. /)
iom_file(kiomid)%ndims(1:4) = (/ 2, 2, 1, 1 /)
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' define dimension variables done'
ENDIF
! define the data if it is not already done
! ===============
IF( kvid <= 0 ) THEN
!
! NetCDF4 chunking and compression fixed settings
ichunkalg = 0
ishuffle = 1
ideflate = 1
ideflate_level = 1
!
idvar = iom_file(kiomid)%nvars + 1
! are we in define mode?
IF( iom_file(kiomid)%irec /= -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = -1
ENDIF
! variable definition
IF( llis0d ) THEN ; idims = 0
ELSEIF( llis1d ) THEN
idims = 2 ; idimid(1:idims) = (/3,4/)
ELSEIF( llis2d ) THEN ; idims = 3 ; idimid(1:idims) = (/1,2,4/)
ELSEIF( llis3d ) THEN
idims = 4 ; idimid(1:idims) = (/1,2,3,4/)
ENDIF
IF( PRESENT(ktype) ) THEN ! variable external type
SELECT CASE (ktype)
CASE (jp_r8) ; itype = NF90_DOUBLE
CASE (jp_r4) ; itype = NF90_FLOAT
CASE (jp_i4) ; itype = NF90_INT
CASE (jp_i2) ; itype = NF90_SHORT
CASE (jp_i1) ; itype = NF90_BYTE
CASE DEFAULT ; CALL ctl_stop( TRIM(clinfo)//' unknown variable type' )
END SELECT
ELSE
itype = NF90_DOUBLE
ENDIF
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(cdvar), itype, &
& iom_file(kiomid)%nvid(idvar) ), clinfo )
ELSE
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(cdvar), itype, idimid(1:idims), &
& iom_file(kiomid)%nvid(idvar) ), clinfo )
ENDIF
lchunk = .false.
IF( snc4set%luse .AND. idims == 4 ) lchunk = .true.
! update informations structure related the new variable we want to add...
iom_file(kiomid)%nvars = idvar
iom_file(kiomid)%cn_var(idvar) = TRIM(cdvar)
iom_file(kiomid)%scf(idvar) = 1.
iom_file(kiomid)%ofs(idvar) = 0.
iom_file(kiomid)%ndims(idvar) = idims
iom_file(kiomid)%luld(idvar) = .NOT. llis0d
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DO jd = 1, idims
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION( if90id, idimid(jd), len = iom_file(kiomid)%dimsz(jd,idvar) ), clinfo)
IF ( lchunk ) ichunksz(jd) = iom_file(kiomid)%dimsz(jd,idvar)
END DO
IF ( lchunk ) THEN
! Calculate chunk sizes by partitioning each dimension as requested in namnc4 namelist
! Disallow very small chunk sizes and prevent chunk sizes larger than each individual dimension
ichunksz(1) = MIN( ichunksz(1),MAX( (ichunksz(1)-1)/snc4set%ni + 1 ,16 ) ) ! Suggested default nc4set%ni=4
ichunksz(2) = MIN( ichunksz(2),MAX( (ichunksz(2)-1)/snc4set%nj + 1 ,16 ) ) ! Suggested default nc4set%nj=2
ichunksz(3) = MIN( ichunksz(3),MAX( (ichunksz(3)-1)/snc4set%nk + 1 , 1 ) ) ! Suggested default nc4set%nk=6
ichunksz(4) = 1 ! Do not allow chunks to span the
! ! unlimited dimension
CALL iom_nf90_check(SET_NF90_DEF_VAR_CHUNKING(if90id, idvar, ichunkalg, ichunksz), clinfo)
CALL iom_nf90_check(SET_NF90_DEF_VAR_DEFLATE(if90id, idvar, ishuffle, ideflate, ideflate_level), clinfo)
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' chunked ok. Chunks sizes: ', ichunksz
ENDIF
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' defined ok'
ELSE
idvar = kvid
ENDIF
!
! time step kwrite : write the variable
IF( kt == kwrite ) THEN
! are we in write mode?
IF( iom_file(kiomid)%irec == -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_ENDDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = 0
ENDIF
! on what kind of domain must the data be written?
IF( llis2d .OR. llis3d ) THEN
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idimsz(1:2) = iom_file(kiomid)%dimsz(1:2,idvar)
IF( idimsz(1) == Ni_0 .AND. idimsz(2) == Nj_0 ) THEN
ix1 = Nis0 ; ix2 = Nie0 ; iy1 = Njs0 ; iy2 = Nje0
ELSEIF( idimsz(1) == jpi .AND. idimsz(2) == jpj ) THEN
ix1 = 1 ; ix2 = jpi ; iy1 = 1 ; iy2 = jpj
ELSEIF( idimsz(1) == jpi .AND. idimsz(2) == jpj ) THEN
ix1 = 1 ; ix2 = jpi ; iy1 = 1 ; iy2 = jpj
ELSE
CALL ctl_stop( 'iom_nf90_rp0123d: should have been an impossible case...' )
ENDIF
! write dimension variables if it is not already done
! =============
! trick: is defined to 0 => dimension variable are defined but not yet written
IF( iom_file(kiomid)%dimsz(1, 4) == 0 ) THEN ! time_counter = 0
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 1, glamt(ix1:ix2, iy1:iy2) ), clinfo )
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 2, gphit(ix1:ix2, iy1:iy2) ), clinfo )
SELECT CASE (iom_file(kiomid)%comp)
CASE ('OCE')
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, gdept_1d ), clinfo )
CASE ('ABL')
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, ght_abl ), clinfo )
CASE DEFAULT
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, (/ (idlv, idlv = 1,iom_file(kiomid)%dimsz(1,3)) /) ), clinfo )
END SELECT
! "wrong" value: to be improved but not really useful...
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 4, kt ), clinfo )
! update the size of the variable corresponding to the unlimited dimension
iom_file(kiomid)%dimsz(1, 4) = 1 ! so we don't enter this IF case any more...
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' write dimension variables done'
ENDIF
ENDIF
! write the data
! =============
IF( PRESENT(pvsp0d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvsp0d ), clinfo )
ELSEIF( PRESENT(pvdp0d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvdp0d ), clinfo )
ELSEIF( PRESENT(pvsp1d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvsp1d(:) ), clinfo )
ELSEIF( PRESENT(pvdp1d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvdp1d(:) ), clinfo )
ELSEIF( PRESENT(pvsp2d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvsp2d(ix1:ix2,iy1:iy2) ), clinfo )
ELSEIF( PRESENT(pvdp2d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvdp2d(ix1:ix2,iy1:iy2) ), clinfo )
ELSEIF( PRESENT(pvsp3d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvsp3d(ix1:ix2,iy1:iy2,:) ), clinfo )
ELSEIF( PRESENT(pvdp3d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pvdp3d(ix1:ix2,iy1:iy2,:) ), clinfo )
ENDIF
! add 1 to the size of the temporal dimension (not really useful...)
IF( iom_file(kiomid)%luld(idvar) ) iom_file(kiomid)%dimsz(iom_file(kiomid)%ndims(idvar), idvar) &
& = iom_file(kiomid)%dimsz(iom_file(kiomid)%ndims(idvar), idvar) + 1
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' written ok'
ENDIF
!
END SUBROUTINE iom_nf90_rstput
SUBROUTINE iom_nf90_check( kstatus, cdinfo )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_check ***
!!
!! ** Purpose : check nf90 errors
!!--------------------------------------------------------------------
INTEGER, INTENT(in) :: kstatus
CHARACTER(LEN=*), INTENT(in) :: cdinfo
!---------------------------------------------------------------------
IF(kstatus /= nf90_noerr) CALL ctl_stop( 'iom_nf90_check : '//TRIM(nf90_strerror(kstatus)), TRIM(cdinfo) )
END SUBROUTINE iom_nf90_check
!!======================================================================
END MODULE iom_nf90