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MODULE iom
!!======================================================================
!! *** MODULE iom ***
!! Input/Output manager : Library to read input files
!!======================================================================
!! History : 2.0 ! 2005-12 (J. Belier) Original code
!! 2.0 ! 2006-02 (S. Masson) Adaptation to NEMO
!! 3.0 ! 2007-07 (D. Storkey) Changes to iom_gettime
!! 3.4 ! 2012-12 (R. Bourdalle-Badie and G. Reffray) add C1D case
!! 3.6 ! 2014-15 DIMG format removed
!! 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 domutl !
USE flo_oce ! floats module declarations
USE lbclnk ! lateal boundary condition / mpp exchanges
USE iom_def ! iom variables definitions
USE iom_nf90 ! NetCDF format with native NetCDF library
USE in_out_manager ! I/O manager
USE lib_mpp ! MPP library
USE sbc_oce , ONLY : nn_fsbc, ght_abl, ghw_abl, e3t_abl, e3w_abl, jpka, jpkam1
USE icb_oce , ONLY : nclasses, class_num ! !: iceberg classes
#if defined key_si3
USE ice , ONLY : jpl
#endif
USE phycst ! physical constants
USE dianam ! build name of file
#if defined key_xios
USE xios
# endif
USE ioipsl, ONLY : ju2ymds ! for calendar
USE crs ! Grid coarsening
#if defined key_top
USE trc, ONLY : profsed
#endif
USE lib_fortran
USE diu_bulk, ONLY : ln_diurnal_only, ln_diurnal
USE iom_nf90
USE netcdf
IMPLICIT NONE
PUBLIC ! must be public to be able to access iom_def through iom
#if defined key_xios
LOGICAL, PUBLIC, PARAMETER :: lk_iomput = .TRUE. !: iom_put flag
#else
LOGICAL, PUBLIC, PARAMETER :: lk_iomput = .FALSE. !: iom_put flag
#endif
LOGICAL, PUBLIC :: l_iom = .TRUE. !: RK3 iom flag prevent writing at stage 1&2
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PUBLIC iom_init, iom_init_closedef, iom_swap, iom_open, iom_close, iom_setkt, iom_varid, iom_get, iom_get_var
PUBLIC iom_chkatt, iom_getatt, iom_putatt, iom_getszuld, iom_rstput, iom_delay_rst, iom_put
PUBLIC iom_use, iom_context_finalize, iom_update_file_name, iom_miss_val
PUBLIC iom_xios_setid
PRIVATE iom_rp0d_sp, iom_rp1d_sp, iom_rp2d_sp, iom_rp3d_sp
PRIVATE iom_rp0d_dp, iom_rp1d_dp, iom_rp2d_dp, iom_rp3d_dp
PRIVATE iom_get_123d
PRIVATE iom_g0d_sp, iom_g1d_sp, iom_g2d_sp, iom_g3d_sp
PRIVATE iom_g0d_dp, iom_g1d_dp, iom_g2d_dp, iom_g3d_dp
PRIVATE iom_p1d_sp, iom_p2d_sp, iom_p3d_sp, iom_p4d_sp
PRIVATE iom_p1d_dp, iom_p2d_dp, iom_p3d_dp, iom_p4d_dp
#if defined key_xios
PRIVATE iom_set_domain_attr, iom_set_axis_attr, iom_set_field_attr, iom_set_file_attr, iom_get_file_attr, iom_set_grid_attr
PRIVATE set_grid, set_grid_bounds, set_scalar, set_xmlatt, set_mooring, iom_sdate
PRIVATE iom_set_rst_context, iom_set_vars_active
# endif
PRIVATE set_xios_context
PRIVATE iom_set_rstw_active
INTERFACE iom_get
MODULE PROCEDURE iom_g0d_sp, iom_g1d_sp, iom_g2d_sp, iom_g3d_sp
MODULE PROCEDURE iom_g0d_dp, iom_g1d_dp, iom_g2d_dp, iom_g3d_dp
END INTERFACE
INTERFACE iom_getatt
MODULE PROCEDURE iom_g0d_iatt, iom_g1d_iatt, iom_g0d_ratt, iom_g1d_ratt, iom_g0d_catt
END INTERFACE
INTERFACE iom_putatt
MODULE PROCEDURE iom_p0d_iatt, iom_p1d_iatt, iom_p0d_ratt, iom_p1d_ratt, iom_p0d_catt
END INTERFACE
INTERFACE iom_rstput
MODULE PROCEDURE iom_rp0d_sp, iom_rp1d_sp, iom_rp2d_sp, iom_rp3d_sp
MODULE PROCEDURE iom_rp0d_dp, iom_rp1d_dp, iom_rp2d_dp, iom_rp3d_dp
END INTERFACE
INTERFACE iom_put
MODULE PROCEDURE iom_p0d_sp, iom_p1d_sp, iom_p2d_sp, iom_p3d_sp, iom_p4d_sp
MODULE PROCEDURE iom_p0d_dp, iom_p1d_dp, iom_p2d_dp, iom_p3d_dp, iom_p4d_dp
END INTERFACE iom_put
!! * Substitutions
# include "do_loop_substitute.h90"
!!----------------------------------------------------------------------
!! NEMO/OCE 4.0 , NEMO Consortium (2018)
!! $Id: iom.F90 15512 2021-11-15 17:22:03Z techene $
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!! Software governed by the CeCILL license (see ./LICENSE)
!!----------------------------------------------------------------------
CONTAINS
SUBROUTINE iom_init( cdname, kdid, ld_closedef )
!!----------------------------------------------------------------------
!! *** ROUTINE ***
!!
!! ** Purpose :
!!
!!----------------------------------------------------------------------
CHARACTER(len=*), INTENT(in) :: cdname
INTEGER , OPTIONAL, INTENT(in) :: kdid
LOGICAL , OPTIONAL, INTENT(in) :: ld_closedef
#if defined key_xios
!
TYPE(xios_duration) :: dtime = xios_duration(0, 0, 0, 0, 0, 0)
TYPE(xios_date) :: start_date
CHARACTER(len=lc) :: clname
INTEGER :: irefyear, irefmonth, irefday
INTEGER :: ji
LOGICAL :: llrst_context ! is context related to restart
LOGICAL :: llrstr, llrstw
INTEGER :: inum
!
REAL(wp), ALLOCATABLE, DIMENSION(:,:) :: zt_bnds, zw_bnds
REAL(wp), DIMENSION(2,jpkam1) :: za_bnds ! ABL vertical boundaries
LOGICAL :: ll_closedef
LOGICAL :: ll_exist
!!----------------------------------------------------------------------
!
ll_closedef = .TRUE.
IF ( PRESENT(ld_closedef) ) ll_closedef = ld_closedef
!
ALLOCATE( zt_bnds(2,jpk), zw_bnds(2,jpk) )
!
clname = cdname
IF( TRIM(Agrif_CFixed()) /= '0' ) clname = TRIM(Agrif_CFixed())//"_"//TRIM(cdname)
CALL xios_context_initialize(TRIM(clname), mpi_comm_oce)
CALL iom_swap( cdname )
llrstr = (cdname == cr_ocerst_cxt) .OR. (cdname == cr_icerst_cxt)
llrstr = llrstr .OR. (cdname == cr_ablrst_cxt)
llrstr = llrstr .OR. (cdname == cr_toprst_cxt)
llrstr = llrstr .OR. (cdname == cr_sedrst_cxt)
llrstw = (cdname == cw_ocerst_cxt) .OR. (cdname == cw_icerst_cxt)
llrstw = llrstw .OR. (cdname == cw_ablrst_cxt)
llrstw = llrstw .OR. (cdname == cw_toprst_cxt)
llrstw = llrstw .OR. (cdname == cw_sedrst_cxt)
llrst_context = llrstr .OR. llrstw
! Calendar type is now defined in xml file
IF (.NOT.(xios_getvar('ref_year' ,irefyear ))) irefyear = 1900
IF (.NOT.(xios_getvar('ref_month',irefmonth))) irefmonth = 01
IF (.NOT.(xios_getvar('ref_day' ,irefday ))) irefday = 01
SELECT CASE ( nleapy ) ! Choose calendar for IOIPSL
CASE ( 1) ; CALL xios_define_calendar( TYPE = "Gregorian", time_origin = xios_date(irefyear,irefmonth,irefday,0,0,0), &
& start_date = xios_date( nyear, nmonth, nday,0,0,0) )
CASE ( 0) ; CALL xios_define_calendar( TYPE = "NoLeap" , time_origin = xios_date(irefyear,irefmonth,irefday,0,0,0), &
& start_date = xios_date( nyear, nmonth, nday,0,0,0) )
CASE (30) ; CALL xios_define_calendar( TYPE = "D360" , time_origin = xios_date(irefyear,irefmonth,irefday,0,0,0), &
& start_date = xios_date( nyear, nmonth, nday,0,0,0) )
END SELECT
! horizontal grid definition
IF(.NOT.llrst_context) CALL set_scalar
!
IF( cdname == cxios_context ) THEN
CALL set_grid( "T", glamt, gphit, .FALSE., .FALSE. )
CALL set_grid( "U", glamu, gphiu, .FALSE., .FALSE. )
CALL set_grid( "V", glamv, gphiv, .FALSE., .FALSE. )
CALL set_grid( "W", glamt, gphit, .FALSE., .FALSE. )
CALL set_grid( "F", glamf, gphif, .FALSE., .FALSE. )
CALL set_grid_znl( gphit )
!
IF( ln_cfmeta ) THEN ! Add additional grid metadata
CALL iom_set_domain_attr("grid_T", area = real( e1e2t(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_U", area = real( e1e2u(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_V", area = real( e1e2v(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_W", area = REAL( e1e2t(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_F", area = real( e1e2f(Nis0:Nie0, Njs0:Nje0), dp))
CALL set_grid_bounds( "T", glamf, gphif, glamt, gphit )
CALL set_grid_bounds( "U", glamv, gphiv, glamu, gphiu )
CALL set_grid_bounds( "V", glamu, gphiu, glamv, gphiv )
CALL set_grid_bounds( "W", glamf, gphif, glamt, gphit )
CALL set_grid_bounds( "F", glamt, gphit, glamf, gphif )
ENDIF
ENDIF
!
IF( TRIM(cdname) == TRIM(cxios_context)//"_crs" ) THEN
CALL dom_grid_crs ! Save the parent grid information & Switch to coarse grid domain
!
CALL set_grid( "T", glamt_crs, gphit_crs, .FALSE., .FALSE. )
CALL set_grid( "U", glamu_crs, gphiu_crs, .FALSE., .FALSE. )
CALL set_grid( "V", glamv_crs, gphiv_crs, .FALSE., .FALSE. )
CALL set_grid( "W", glamt_crs, gphit_crs, .FALSE., .FALSE. )
CALL set_grid_znl( gphit_crs )
!
CALL dom_grid_glo ! Return to parent grid domain
!
IF( ln_cfmeta .AND. .NOT. llrst_context) THEN ! Add additional grid metadata
CALL iom_set_domain_attr("grid_T", area = real(e1e2t_crs(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_U", area = real(e1u_crs(Nis0:Nie0, Njs0:Nje0) * e2u_crs(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_V", area = real(e1v_crs(Nis0:Nie0, Njs0:Nje0) * e2v_crs(Nis0:Nie0, Njs0:Nje0), dp))
CALL iom_set_domain_attr("grid_W", area = real(e1e2t_crs(Nis0:Nie0, Njs0:Nje0), dp))
CALL set_grid_bounds( "T", glamf_crs, gphif_crs, glamt_crs, gphit_crs )
CALL set_grid_bounds( "U", glamv_crs, gphiv_crs, glamu_crs, gphiu_crs )
CALL set_grid_bounds( "V", glamu_crs, gphiu_crs, glamv_crs, gphiv_crs )
CALL set_grid_bounds( "W", glamf_crs, gphif_crs, glamt_crs, gphit_crs )
ENDIF
ENDIF
!
! vertical grid definition
IF(.NOT.llrst_context) THEN
CALL iom_set_axis_attr( "deptht", paxis = gdept_1d )
CALL iom_set_axis_attr( "depthu", paxis = gdept_1d )
CALL iom_set_axis_attr( "depthv", paxis = gdept_1d )
CALL iom_set_axis_attr( "depthw", paxis = gdepw_1d )
CALL iom_set_axis_attr( "depthf", paxis = gdept_1d )
! ABL
IF( .NOT. ALLOCATED(ght_abl) ) THEN ! force definition for xml files (xios)
ALLOCATE( ght_abl(jpka), ghw_abl(jpka), e3t_abl(jpka), e3w_abl(jpka) ) ! default allocation needed by iom
ght_abl(:) = -1._wp ; ghw_abl(:) = -1._wp
e3t_abl(:) = -1._wp ; e3w_abl(:) = -1._wp
ENDIF
CALL iom_set_axis_attr( "ght_abl", ght_abl(2:jpka) )
CALL iom_set_axis_attr( "ghw_abl", ghw_abl(2:jpka) )
! Add vertical grid bounds
zt_bnds(2,: ) = gdept_1d(:)
zt_bnds(1,2:jpk ) = gdept_1d(1:jpkm1)
zt_bnds(1,1 ) = gdept_1d(1) - e3w_1d(1)
zw_bnds(1,: ) = gdepw_1d(:)
zw_bnds(2,1:jpkm1) = gdepw_1d(2:jpk)
zw_bnds(2,jpk: ) = gdepw_1d(jpk) + e3t_1d(jpk)
CALL iom_set_axis_attr( "deptht", bounds=zw_bnds )
CALL iom_set_axis_attr( "depthu", bounds=zw_bnds )
CALL iom_set_axis_attr( "depthv", bounds=zw_bnds )
CALL iom_set_axis_attr( "depthw", bounds=zt_bnds )
CALL iom_set_axis_attr( "depthf", bounds=zw_bnds )
! ABL
za_bnds(1,:) = ghw_abl(1:jpkam1)
za_bnds(2,:) = ghw_abl(2:jpka )
CALL iom_set_axis_attr( "ght_abl", bounds=za_bnds )
za_bnds(1,:) = ght_abl(2:jpka )
za_bnds(2,:) = ght_abl(2:jpka ) + e3w_abl(2:jpka)
CALL iom_set_axis_attr( "ghw_abl", bounds=za_bnds )
CALL iom_set_axis_attr( "nfloat", (/ (REAL(ji,wp), ji=1,jpnfl) /) )
# if defined key_si3
CALL iom_set_axis_attr( "ncatice", (/ (REAL(ji,wp), ji=1,jpl) /) )
! SIMIP diagnostics (4 main arctic straits)
CALL iom_set_axis_attr( "nstrait", (/ (REAL(ji,wp), ji=1,4) /) )
# endif
#if defined key_top
IF( ALLOCATED(profsed) ) CALL iom_set_axis_attr( "profsed", paxis = profsed )
#endif
CALL iom_set_axis_attr( "icbcla", class_num )
CALL iom_set_axis_attr( "iax_20C", (/ REAL(20,wp) /) ) ! strange syntaxe and idea...
CALL iom_set_axis_attr( "iax_26C", (/ REAL(26,wp) /) ) ! strange syntaxe and idea...
CALL iom_set_axis_attr( "iax_28C", (/ REAL(28,wp) /) ) ! strange syntaxe and idea...
! for diaprt, we need to define an axis which size can be 1 (default) or 5 (if the file subbasins.nc exists)
INQUIRE( FILE = 'subbasins.nc', EXIST = ll_exist )
nbasin = 1 + 4 * COUNT( (/ll_exist/) )
CALL iom_set_axis_attr( "basin" , (/ (REAL(ji,wp), ji=1,nbasin) /) )
ENDIF
!
! automatic definitions of some of the xml attributs
IF(llrstr) THEN
IF(PRESENT(kdid)) THEN
CALL iom_set_rst_context(.TRUE.)
!set which fields will be read from restart file
CALL iom_set_vars_active(kdid)
ELSE
CALL ctl_stop( 'iom_init:', 'restart read with XIOS: missing pointer to NETCDF file' )
ENDIF
ELSE IF(llrstw) THEN
CALL iom_set_rstw_file(iom_file(kdid)%name)
ELSE
CALL set_xmlatt
ENDIF
!
! set time step length
dtime%second = rn_Dt
CALL xios_set_timestep( dtime )
!
! conditional closure of context definition
IF ( ll_closedef ) CALL iom_init_closedef
!
DEALLOCATE( zt_bnds, zw_bnds )
!
#endif
!
END SUBROUTINE iom_init
SUBROUTINE iom_init_closedef(cdname)
!!----------------------------------------------------------------------
!! *** SUBROUTINE iom_init_closedef ***
!!----------------------------------------------------------------------
!!
!! ** Purpose : Closure of context definition
!!
!!----------------------------------------------------------------------
CHARACTER(len=*), OPTIONAL, INTENT(IN) :: cdname
#if defined key_xios
LOGICAL :: llrstw
llrstw = .FALSE.
IF(PRESENT(cdname)) THEN
llrstw = (cdname == cw_ocerst_cxt)
llrstw = llrstw .OR. (cdname == cw_icerst_cxt)
llrstw = llrstw .OR. (cdname == cw_ablrst_cxt)
llrstw = llrstw .OR. (cdname == cw_toprst_cxt)
llrstw = llrstw .OR. (cdname == cw_sedrst_cxt)
ENDIF
IF( llrstw ) THEN
!set names of the fields in restart file IF using XIOS to write data
CALL iom_set_rst_context(.FALSE.)
CALL xios_close_context_definition()
ELSE
CALL xios_close_context_definition()
CALL xios_update_calendar( 0 )
ENDIF
#else
IF( .FALSE. ) WRITE(numout,*) 'iom_init_closedef: should not see this' ! useless statement to avoid compilation warnings
#endif
END SUBROUTINE iom_init_closedef
SUBROUTINE iom_set_vars_active(idnum)
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_set_vars_active ***
!!
!! ** Purpose : define filename in XIOS context for reading file,
!! enable variables present in a file for reading with XIOS
!! id of the file is assumed to be rrestart.
!!---------------------------------------------------------------------
INTEGER, INTENT(IN) :: idnum
#if defined key_xios
INTEGER :: ndims, nvars, natts, unlimitedDimId, dimlen, xtype,mdims
TYPE(xios_field) :: field_hdl
TYPE(xios_file) :: file_hdl
TYPE(xios_filegroup) :: filegroup_hdl
INTEGER :: dimids(4), jv,i, idim
CHARACTER(LEN=256) :: clinfo ! info character
INTEGER, ALLOCATABLE :: indimlens(:)
CHARACTER(LEN=nf90_max_name), ALLOCATABLE :: indimnames(:)
CHARACTER(LEN=nf90_max_name) :: dimname, varname
INTEGER :: iln
CHARACTER(LEN=lc) :: fname
LOGICAL :: lmeta
!metadata in restart file for restart read with XIOS
INTEGER, PARAMETER :: NMETA = 11
CHARACTER(LEN=lc) :: meta(NMETA)
meta(1) = "nav_lat"
meta(2) = "nav_lon"
meta(3) = "nav_lev"
meta(4) = "time_instant"
meta(5) = "time_instant_bounds"
meta(6) = "time_counter"
meta(7) = "time_counter_bounds"
meta(8) = "x"
meta(9) = "y"
meta(10) = "numcat"
meta(11) = "nav_hgt"
clinfo = ' iom_set_vars_active, file: '//TRIM(iom_file(idnum)%name)
iln = INDEX( iom_file(idnum)%name, '.nc' )
!XIOS doee not need .nc
IF(iln > 0) THEN
fname = iom_file(idnum)%name(1:iln-1)
ELSE
fname = iom_file(idnum)%name
ENDIF
!set name of the restart file and enable available fields
CALL xios_get_handle("file_definition", filegroup_hdl )
CALL xios_add_child(filegroup_hdl, file_hdl, 'rrestart')
CALL xios_set_file_attr( "rrestart", name=fname, type="one_file", &
par_access="collective", enabled=.TRUE., mode="read", &
output_freq=xios_timestep )
CALL iom_nf90_check( nf90_inquire(iom_file(idnum)%nfid, ndims, nvars, natts ), clinfo )
ALLOCATE(indimlens(ndims), indimnames(ndims))
CALL iom_nf90_check( nf90_inquire(iom_file(idnum)%nfid, unlimitedDimId = unlimitedDimId ), clinfo )
DO idim = 1, ndims
CALL iom_nf90_check( nf90_inquire_dimension(iom_file(idnum)%nfid, idim, dimname, dimlen ), clinfo )
indimlens(idim) = dimlen
indimnames(idim) = dimname
ENDDO
DO jv =1, nvars
lmeta = .FALSE.
CALL iom_nf90_check( nf90_inquire_variable(iom_file(idnum)%nfid, jv, varname, xtype, ndims, dimids, natts ), clinfo )
DO i = 1, NMETA
IF(varname == meta(i)) THEN
lmeta = .TRUE.
ENDIF
ENDDO
IF(.NOT.lmeta) THEN
CALL xios_add_child(file_hdl, field_hdl, varname)
mdims = ndims
IF(ANY(dimids(1:ndims) == unlimitedDimId)) THEN
mdims = mdims - 1
ENDIF
IF(mdims == 3) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = varname, &
domain_ref="grid_N", &
axis_ref=iom_axis(indimlens(dimids(mdims))), &
prec = 8, operation = "instant" )
ELSEIF(mdims == 2) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = varname, &
domain_ref="grid_N", prec = 8, &
operation = "instant" )
ELSEIF(mdims == 1) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = varname, &
axis_ref=iom_axis(indimlens(dimids(mdims))), &
prec = 8, operation = "instant" )
ELSEIF(mdims == 0) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = varname, &
scalar_ref = "grid_scalar", prec = 8, &
operation = "instant" )
ELSE
WRITE(ctmp1,*) 'iom_set_vars_active: variable ', TRIM(varname) ,' incorrect number of dimensions'
CALL ctl_stop( 'iom_set_vars_active:', ctmp1 )
ENDIF
ENDIF
ENDDO
DEALLOCATE(indimlens, indimnames)
#endif
END SUBROUTINE iom_set_vars_active
SUBROUTINE iom_set_rstw_file(cdrst_file)
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_set_rstw_file ***
!!
!! ** Purpose : define file name in XIOS context for writing restart
!!---------------------------------------------------------------------
CHARACTER(len=*) :: cdrst_file
#if defined key_xios
TYPE(xios_file) :: file_hdl
TYPE(xios_filegroup) :: filegroup_hdl
!set name of the restart file and enable available fields
IF(lwp) WRITE(numout,*) 'Setting restart filename (for XIOS write) to: ', TRIM(cdrst_file)
CALL xios_get_handle("file_definition", filegroup_hdl )
CALL xios_add_child(filegroup_hdl, file_hdl, 'wrestart')
IF(nxioso.eq.1) THEN
CALL xios_set_file_attr( "wrestart", type="one_file", enabled=.TRUE.,&
mode="write", output_freq=xios_timestep)
IF(lwp) write(numout,*) 'OPEN ', trim(cdrst_file), ' in one_file mode'
ELSE
CALL xios_set_file_attr( "wrestart", type="multiple_file", enabled=.TRUE.,&
mode="write", output_freq=xios_timestep)
IF(lwp) write(numout,*) 'OPEN ', trim(cdrst_file), ' in multiple_file mode'
ENDIF
CALL xios_set_file_attr( "wrestart", name=trim(cdrst_file))
#endif
END SUBROUTINE iom_set_rstw_file
SUBROUTINE iom_set_rstw_active(sdfield, rd0, rs0, rd1, rs1, rd2, rs2, rd3, rs3)
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_set_rstw_active ***
!!
!! ** Purpose : define file name in XIOS context for writing restart
!! enable variables present in restart file for writing
!!---------------------------------------------------------------------
!sets enabled = .TRUE. for each field in restart file
CHARACTER(len = *), INTENT(IN) :: sdfield
REAL(dp), OPTIONAL, INTENT(IN) :: rd0
REAL(sp), OPTIONAL, INTENT(IN) :: rs0
REAL(dp), OPTIONAL, INTENT(IN), DIMENSION(:) :: rd1
REAL(sp), OPTIONAL, INTENT(IN), DIMENSION(:) :: rs1
REAL(dp), OPTIONAL, INTENT(IN), DIMENSION(:, :) :: rd2
REAL(sp), OPTIONAL, INTENT(IN), DIMENSION(:, :) :: rs2
REAL(dp), OPTIONAL, INTENT(IN), DIMENSION(:, :, :) :: rd3
REAL(sp), OPTIONAL, INTENT(IN), DIMENSION(:, :, :) :: rs3
#if defined key_xios
TYPE(xios_field) :: field_hdl
TYPE(xios_file) :: file_hdl
CALL xios_get_handle("wrestart", file_hdl)
!define fields for restart context
CALL xios_add_child(file_hdl, field_hdl, sdfield)
IF(PRESENT(rd3)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
domain_ref = "grid_N", &
axis_ref = iom_axis(size(rd3, 3)), &
prec = 8, operation = "instant" )
ELSEIF(PRESENT(rs3)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
domain_ref = "grid_N", &
axis_ref = iom_axis(size(rd3, 3)), &
prec = 4, operation = "instant" )
ELSEIF(PRESENT(rd2)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
domain_ref = "grid_N", prec = 8, &
operation = "instant" )
ELSEIF(PRESENT(rs2)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
domain_ref = "grid_N", prec = 4, &
operation = "instant" )
ELSEIF(PRESENT(rd1)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
axis_ref = iom_axis(size(rd1, 1)), &
prec = 8, operation = "instant" )
ELSEIF(PRESENT(rs1)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
axis_ref = iom_axis(size(rd1, 1)), &
prec = 4, operation = "instant" )
ELSEIF(PRESENT(rd0)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
scalar_ref = "grid_scalar", prec = 8, &
operation = "instant" )
ELSEIF(PRESENT(rs0)) THEN
CALL xios_set_attr (field_hdl, enabled = .TRUE., name = sdfield, &
scalar_ref = "grid_scalar", prec = 4, &
operation = "instant" )
ENDIF
#endif
END SUBROUTINE iom_set_rstw_active
FUNCTION iom_axis(idlev) result(axis_ref)
!!---------------------------------------------------------------------
!! *** FUNCTION iom_axis ***
!!
!! ** Purpose : Used for grid definition when XIOS is used to read/write
!! restart. Returns axis corresponding to the number of levels
!! given as an input variable. Axes are defined in routine
!! iom_set_rst_context
!!---------------------------------------------------------------------
INTEGER, INTENT(IN) :: idlev
CHARACTER(len=lc) :: axis_ref
CHARACTER(len=12) :: str
IF(idlev == jpk) THEN
axis_ref="nav_lev"
ELSEIF(idlev == jpka) THEN
axis_ref="nav_hgt"
#if defined key_si3
ELSEIF(idlev == jpl) THEN
axis_ref="numcat"
#endif
ELSE
write(str, *) idlev
CALL ctl_stop( 'iom_axis', 'Definition for axis with '//TRIM(ADJUSTL(str))//' levels missing')
ENDIF
END FUNCTION iom_axis
FUNCTION iom_xios_setid(cdname) result(kid)
!!---------------------------------------------------------------------
!! *** FUNCTION ***
!!
!! ** Purpose : this function returns first available id to keep information about file
!! sets filename in iom_file structure and sets name
!! of XIOS context depending on cdcomp
!! corresponds to iom_nf90_open
!!---------------------------------------------------------------------
CHARACTER(len=*), INTENT(in ) :: cdname ! File name
INTEGER :: kid ! identifier of the opened file
INTEGER :: jl
kid = 0
DO jl = jpmax_files, 1, -1
IF( iom_file(jl)%nfid == 0 ) kid = jl
ENDDO
iom_file(kid)%name = TRIM(cdname)
iom_file(kid)%nfid = 1
iom_file(kid)%nvars = 0
iom_file(kid)%irec = -1
END FUNCTION iom_xios_setid
SUBROUTINE iom_set_rst_context(ld_rstr)
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_set_rst_context ***
!!
!! ** Purpose : Define domain, axis and grid for restart (read/write)
!! context
!!
!!---------------------------------------------------------------------
LOGICAL, INTENT(IN) :: ld_rstr
INTEGER :: ji
#if defined key_xios
TYPE(xios_domaingroup) :: domaingroup_hdl
TYPE(xios_domain) :: domain_hdl
TYPE(xios_axisgroup) :: axisgroup_hdl
TYPE(xios_axis) :: axis_hdl
TYPE(xios_scalar) :: scalar_hdl
TYPE(xios_scalargroup) :: scalargroup_hdl
CALL xios_get_handle("domain_definition",domaingroup_hdl)
CALL xios_add_child(domaingroup_hdl, domain_hdl, "grid_N")
CALL set_grid("N", glamt, gphit, .TRUE., ld_rstr)
CALL xios_get_handle("axis_definition",axisgroup_hdl)
CALL xios_add_child(axisgroup_hdl, axis_hdl, "nav_lev")
!AGRIF fails to compile when unit= is in call to xios_set_axis_attr
! CALL xios_set_axis_attr( "nav_lev", long_name="Vertical levels", unit="m", positive="down")
CALL xios_set_axis_attr( "nav_lev", long_name = "Vertical levels in meters", positive = "down")
CALL iom_set_axis_attr( "nav_lev", paxis = gdept_1d )
#if defined key_si3
CALL xios_add_child(axisgroup_hdl, axis_hdl, "numcat")
CALL iom_set_axis_attr( "numcat", (/ (REAL(ji,wp), ji=1,jpl) /) )
#endif
CALL xios_add_child(axisgroup_hdl, axis_hdl, "nav_hgt")
CALL iom_set_axis_attr( "nav_hgt", (/ (REAL(ji,wp), ji=1,jpka) /) )
CALL xios_get_handle("scalar_definition", scalargroup_hdl)
CALL xios_add_child(scalargroup_hdl, scalar_hdl, "grid_scalar")
#endif
END SUBROUTINE iom_set_rst_context
SUBROUTINE set_xios_context(kdid, cdcont)
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_set_rst_context ***
!!
!! ** Purpose : set correct XIOS context based on kdid
!!
!!---------------------------------------------------------------------
INTEGER, INTENT(IN) :: kdid ! Identifier of the file
CHARACTER(LEN=lc), INTENT(OUT) :: cdcont ! name of the context for XIOS read/write
cdcont = "NONE"
IF(lrxios) THEN
IF(kdid == numror) THEN
cdcont = cr_ocerst_cxt
ELSEIF(kdid == numrir) THEN
cdcont = cr_icerst_cxt
ELSEIF(kdid == numrar) THEN
cdcont = cr_ablrst_cxt
ELSEIF(kdid == numrtr) THEN
cdcont = cr_toprst_cxt
ELSEIF(kdid == numrsr) THEN
cdcont = cr_sedrst_cxt
ENDIF
ENDIF
IF(lwxios) THEN
IF(kdid == numrow) THEN
cdcont = cw_ocerst_cxt
ELSEIF(kdid == numriw) THEN
cdcont = cw_icerst_cxt
ELSEIF(kdid == numraw) THEN
cdcont = cw_ablrst_cxt
ELSEIF(kdid == numrtw) THEN
cdcont = cw_toprst_cxt
ELSEIF(kdid == numrsw) THEN
cdcont = cw_sedrst_cxt
ENDIF
ENDIF
END SUBROUTINE set_xios_context
SUBROUTINE iom_swap( cdname )
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_swap ***
!!
!! ** Purpose : swap context between different agrif grid for xmlio_server
!!---------------------------------------------------------------------
CHARACTER(len=*), INTENT(in) :: cdname
#if defined key_xios
TYPE(xios_context) :: nemo_hdl
IF( TRIM(Agrif_CFixed()) == '0' ) THEN
CALL xios_get_handle(TRIM(cdname),nemo_hdl)
ELSE
CALL xios_get_handle(TRIM(Agrif_CFixed())//"_"//TRIM(cdname),nemo_hdl)
ENDIF
!
CALL xios_set_current_context(nemo_hdl)
#endif
!
END SUBROUTINE iom_swap
SUBROUTINE iom_open( cdname, kiomid, ldwrt, ldstop, ldiof, kdlev, cdcomp )
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_open ***
!!
!! ** Purpose : open an input file (return 0 if not found)
!!---------------------------------------------------------------------
CHARACTER(len=*), INTENT(in ) :: cdname ! File name
INTEGER , INTENT( out) :: kiomid ! iom identifier of the opened file
LOGICAL , INTENT(in ), OPTIONAL :: ldwrt ! open in write modeb (default = .FALSE.)
LOGICAL , INTENT(in ), OPTIONAL :: ldstop ! stop if open to read a non-existing file (default = .TRUE.)
LOGICAL , INTENT(in ), OPTIONAL :: ldiof ! Interp On the Fly, needed for AGRIF (default = .FALSE.)
INTEGER , INTENT(in ), OPTIONAL :: kdlev ! number of vertical levels
CHARACTER(len=3), INTENT(in ), OPTIONAL :: cdcomp ! name of component calling iom_nf90_open
!
CHARACTER(LEN=256) :: clname ! the name of the file based on cdname [[+clcpu]+clcpu]
CHARACTER(LEN=256) :: cltmpn ! tempory name to store clname (in writting mode)
CHARACTER(LEN=10) :: clsuffix ! ".nc"
CHARACTER(LEN=15) :: clcpu ! the cpu number (max jpmax_digits digits)
CHARACTER(LEN=256) :: clinfo ! info character
LOGICAL :: llok ! check the existence
LOGICAL :: llwrt ! local definition of ldwrt
LOGICAL :: llstop ! local definition of ldstop
LOGICAL :: lliof ! local definition of ldiof
INTEGER :: icnt ! counter for digits in clcpu (max = jpmax_digits)
INTEGER :: iln, ils ! lengths of character
INTEGER :: istop !
! local number of points for x,y dimensions
! position of first local point for x,y dimensions
! position of last local point for x,y dimensions
! start halo size for x,y dimensions
! end halo size for x,y dimensions
!---------------------------------------------------------------------
! Initializations and control
! =============
kiomid = -1
clinfo = ' iom_open ~~~ '
istop = nstop
! if iom_open is called for the first time: initialize iom_file(:)%nfid to 0
! (could be done when defining iom_file in f95 but not in f90)
IF( Agrif_Root() ) THEN
IF( iom_open_init == 0 ) THEN
iom_file(:)%nfid = 0
iom_open_init = 1
ENDIF
ENDIF
! do we read or write the file?
IF( PRESENT(ldwrt) ) THEN ; llwrt = ldwrt
ELSE ; llwrt = .FALSE.
ENDIF
! do we call ctl_stop if we try to open a non-existing file in read mode?
IF( PRESENT(ldstop) ) THEN ; llstop = ldstop
ELSE ; llstop = .TRUE.
ENDIF
! are we using interpolation on the fly?
IF( PRESENT(ldiof) ) THEN ; lliof = ldiof
ELSE ; lliof = .FALSE.
ENDIF
! create the file name by added, if needed, TRIM(Agrif_CFixed()) and TRIM(clsuffix)
! =============
clname = trim(cdname)
IF ( .NOT. Agrif_Root() .AND. .NOT. lliof ) THEN
iln = INDEX(clname,'/', BACK=.TRUE.)
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cltmpn = clname(1:iln)
clname = clname(iln+1:LEN_TRIM(clname))
clname=TRIM(cltmpn)//TRIM(Agrif_CFixed())//'_'//TRIM(clname)
ENDIF
! which suffix should we use?
clsuffix = '.nc'
! Add the suffix if needed
iln = LEN_TRIM(clname)
ils = LEN_TRIM(clsuffix)
IF( iln <= ils .OR. INDEX( TRIM(clname), TRIM(clsuffix), back = .TRUE. ) /= iln - ils + 1 ) &
& clname = TRIM(clname)//TRIM(clsuffix)
cltmpn = clname ! store this name
! try to find if the file to be opened already exist
! =============
INQUIRE( FILE = clname, EXIST = llok )
IF( .NOT.llok ) THEN
! we try to add the cpu number to the name
WRITE(clcpu,*) narea-1
clcpu = TRIM(ADJUSTL(clcpu))
iln = INDEX(clname,TRIM(clsuffix), back = .TRUE.)
clname = clname(1:iln-1)//'_'//TRIM(clcpu)//TRIM(clsuffix)
icnt = 0
INQUIRE( FILE = clname, EXIST = llok )
! we try different formats for the cpu number by adding 0
DO WHILE( .NOT.llok .AND. icnt < jpmax_digits )
clcpu = "0"//trim(clcpu)
clname = clname(1:iln-1)//'_'//TRIM(clcpu)//TRIM(clsuffix)
INQUIRE( FILE = clname, EXIST = llok )
icnt = icnt + 1
END DO
ELSE
lxios_sini = .TRUE.
ENDIF
! Open the NetCDF file
! =============
! do we have some free file identifier?
IF( MINVAL(iom_file(:)%nfid) /= 0 ) &
& CALL ctl_stop( TRIM(clinfo), 'No more free file identifier', 'increase jpmax_files in iom_def' )
! if no file was found...
IF( .NOT. llok ) THEN
IF( .NOT. llwrt ) THEN ! we are in read mode
IF( llstop ) THEN ; CALL ctl_stop( TRIM(clinfo), 'File '//TRIM(cltmpn)//'* not found' )
ELSE ; istop = nstop + 1 ! make sure that istop /= nstop so we don't open the file
ENDIF
ELSE ! we are in write mode so we
clname = cltmpn ! get back the file name without the cpu number
ENDIF
ELSE
IF( llwrt .AND. .NOT. ln_clobber ) THEN ! we stop as we want to write in a new file
CALL ctl_stop( TRIM(clinfo), 'We want to write in a new file but '//TRIM(clname)//' already exists...' )
istop = nstop + 1 ! make sure that istop /= nstop so we don't open the file
ELSEIF( llwrt ) THEN ! the file exists and we are in write mode with permission to
clname = cltmpn ! overwrite so get back the file name without the cpu number
ENDIF
ENDIF
IF( istop == nstop ) THEN ! no error within this routine
CALL iom_nf90_open( clname, kiomid, llwrt, llok, kdlev = kdlev, cdcomp = cdcomp )
ENDIF
!
END SUBROUTINE iom_open
SUBROUTINE iom_close( kiomid )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_close ***
!!
!! ** Purpose : close an input file, or all files opened by iom
!!--------------------------------------------------------------------
INTEGER, INTENT(inout), OPTIONAL :: kiomid ! iom identifier of the file to be closed
! ! return 0 when file is properly closed
! ! No argument: all files opened by iom are closed
INTEGER :: jf ! dummy loop indices
INTEGER :: i_s, i_e ! temporary integer
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
!
IF( iom_open_init == 0 ) RETURN ! avoid to use iom_file(jf)%nfid that us not yet initialized
!
clinfo = ' iom_close ~~~ '
IF( PRESENT(kiomid) ) THEN
i_s = kiomid
i_e = kiomid
ELSE
i_s = 1
i_e = jpmax_files
ENDIF
IF( i_s > 0 ) THEN
DO jf = i_s, i_e
IF( iom_file(jf)%nfid > 0 ) THEN
CALL iom_nf90_close( jf )
iom_file(jf)%nfid = 0 ! free the id
IF( PRESENT(kiomid) ) kiomid = 0 ! return 0 as id to specify that the file was closed
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' close file: '//TRIM(iom_file(jf)%name)//' ok'
ELSEIF( PRESENT(kiomid) ) THEN
WRITE(ctmp1,*) '--->', kiomid
CALL ctl_stop( TRIM(clinfo)//' Invalid file identifier', ctmp1 )
ENDIF
END DO
ENDIF
!
END SUBROUTINE iom_close
FUNCTION iom_varid ( kiomid, cdvar, kdimsz, kndims, lduld, ldstop )
!!-----------------------------------------------------------------------
!! *** FUNCTION iom_varid ***
!!
!! ** Purpose : get the id of a variable in a file (return 0 if not found)
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! file Identifier
CHARACTER(len=*) , INTENT(in ) :: cdvar ! name of the variable
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)
LOGICAL , INTENT(in ), OPTIONAL :: ldstop ! stop if looking for non-existing variable (default = .TRUE.)
!
INTEGER :: iom_varid, iiv, i_nvd
LOGICAL :: ll_fnd
CHARACTER(LEN=100) :: clinfo ! info character
LOGICAL :: llstop ! local definition of ldstop
!!-----------------------------------------------------------------------
iom_varid = 0 ! default definition
! do we call ctl_stop if we look for non-existing variable?
IF( PRESENT(ldstop) ) THEN ; llstop = ldstop
ELSE ; llstop = .TRUE.
ENDIF
!
IF( kiomid > 0 ) THEN
clinfo = 'iom_varid, file: '//trim(iom_file(kiomid)%name)//', var: '//trim(cdvar)
IF( iom_file(kiomid)%nfid == 0 ) THEN
CALL ctl_stop( trim(clinfo), 'the file is not open' )
ELSE
ll_fnd = .FALSE.
iiv = 0
!
DO WHILE ( .NOT.ll_fnd .AND. iiv < iom_file(kiomid)%nvars )
iiv = iiv + 1
ll_fnd = ( TRIM(cdvar) == TRIM(iom_file(kiomid)%cn_var(iiv)) )
END DO
!
IF( .NOT.ll_fnd ) THEN
iiv = iiv + 1
IF( iiv <= jpmax_vars ) THEN
iom_varid = iom_nf90_varid( kiomid, cdvar, iiv, kdimsz, kndims, lduld )
ELSE
CALL ctl_stop( trim(clinfo), 'Too many variables in the file '//iom_file(kiomid)%name, &
& 'increase the parameter jpmax_vars')
ENDIF
IF( llstop .AND. iom_varid == -1 ) CALL ctl_stop( TRIM(clinfo)//' not found' )
ELSE
iom_varid = iiv
IF( PRESENT(kdimsz) ) THEN
i_nvd = iom_file(kiomid)%ndims(iiv)
IF( i_nvd <= size(kdimsz) ) THEN
kdimsz(1:i_nvd) = iom_file(kiomid)%dimsz(1:i_nvd,iiv)
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(iiv)
IF( PRESENT( lduld) ) lduld = iom_file(kiomid)%luld( iiv)
ENDIF
ENDIF
ENDIF
!
END FUNCTION iom_varid
!!----------------------------------------------------------------------
!! INTERFACE iom_get
!!----------------------------------------------------------------------
SUBROUTINE iom_g0d_sp( kiomid, cdvar, pvar, ktime )
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*), INTENT(in ) :: cdvar ! Name of the variable
REAL(sp) , INTENT( out) :: pvar ! read field
REAL(dp) :: ztmp_pvar ! tmp var to read field
INTEGER , INTENT(in ), OPTIONAL :: ktime ! record number
!
INTEGER :: idvar ! variable id
INTEGER :: idmspc ! number of spatial dimensions
INTEGER , DIMENSION(1) :: itime ! record number
CHARACTER(LEN=100) :: clinfo ! info character
CHARACTER(LEN=100) :: clname ! file name
CHARACTER(LEN=1) :: cldmspc !
CHARACTER(LEN=lc) :: context
!
CALL set_xios_context(kiomid, context)
IF(context == "NONE") THEN ! read data using default library
itime = 1
IF( PRESENT(ktime) ) itime = ktime
!
clname = iom_file(kiomid)%name
clinfo = ' iom_g0d, file: '//trim(clname)//', var: '//trim(cdvar)
!
IF( kiomid > 0 ) THEN
idvar = iom_varid( kiomid, cdvar )
IF( iom_file(kiomid)%nfid > 0 .AND. idvar > 0 ) THEN
idmspc = iom_file ( kiomid )%ndims( idvar )
IF( iom_file(kiomid)%luld(idvar) ) idmspc = idmspc - 1
WRITE(cldmspc , fmt='(i1)') idmspc
IF( idmspc > 0 ) CALL ctl_stop( TRIM(clinfo), 'When reading to a 0D array, we do not accept data', &
& 'with 1 or more spatial dimensions: '//cldmspc//' were found.' , &
& 'Use ncwa -a to suppress the unnecessary dimensions' )
CALL iom_nf90_get( kiomid, idvar, ztmp_pvar, itime )
pvar = ztmp_pvar
ENDIF
ENDIF
ELSE
#if defined key_xios
IF(lwp) WRITE(numout,*) 'XIOS RST READ (0D): ', trim(cdvar)
CALL iom_swap(context)
CALL xios_recv_field( trim(cdvar), pvar)
CALL iom_swap(cxios_context)
#else
WRITE(ctmp1,*) 'Can not use XIOS in iom_g0d, file: '//trim(clname)//', var:'//trim(cdvar)
CALL ctl_stop( 'iom_g0d', ctmp1 )
#endif
ENDIF
END SUBROUTINE iom_g0d_sp
SUBROUTINE iom_g0d_dp( kiomid, cdvar, pvar, ktime )
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*), INTENT(in ) :: cdvar ! Name of the variable
REAL(dp) , INTENT( out) :: pvar ! read field
INTEGER , INTENT(in ), OPTIONAL :: ktime ! record number
!
INTEGER :: idvar ! variable id
INTEGER :: idmspc ! number of spatial dimensions
INTEGER , DIMENSION(1) :: itime ! record number
CHARACTER(LEN=100) :: clinfo ! info character
CHARACTER(LEN=100) :: clname ! file name
CHARACTER(LEN=1) :: cldmspc !
CHARACTER(LEN=lc) :: context
!
CALL set_xios_context(kiomid, context)
IF(context == "NONE") THEN ! read data using default library
itime = 1
IF( PRESENT(ktime) ) itime = ktime
!