! $Id: hdf_mod.f,v 1.1 2010/02/02 16:57:46 bmy Exp $ !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !MODULE: hdf_mod ! ! !DESCRIPTION: Module HDF\_MOD contains routines to write data to ! HDF5 files. !\\ !\\ ! !INTERFACE: ! MODULE HDF_MOD ! ! !USES: ! IMPLICIT NONE # include "define.h" PRIVATE ! ! !PUBLIC MEMBER FUNCTIONS: ! PUBLIC :: CLEANUP_HDF PUBLIC :: CLOSE_HDF PUBLIC :: INIT_HDF PUBLIC :: OPEN_HDF PUBLIC :: WRITE_HDF ! ! !PUBLIC DATA MEMBERS: ! PUBLIC :: HDFCATEGORY PUBLIC :: HDFDESCRIPT PUBLIC :: HDFNAME PUBLIC :: HDFFNAME PUBLIC :: HDFMOLC PUBLIC :: HDFMWT PUBLIC :: HDFSCALE PUBLIC :: HDFUNIT CHARACTER(LEN=40), ALLOCATABLE :: HDFCATEGORY(:) CHARACTER(LEN=40), ALLOCATABLE :: HDFDESCRIPT(:) INTEGER :: MAXDIAG INTEGER :: MAXTRACER INTEGER :: MAXCAT INTEGER, ALLOCATABLE :: HDFMOLC(:,:) REAL*4, ALLOCATABLE :: HDFMWT(:,:) REAL*4, ALLOCATABLE :: HDFSCALE(:,:) CHARACTER(LEN=40), ALLOCATABLE :: HDFNAME(:,:) CHARACTER(LEN=40), ALLOCATABLE :: HDFFNAME(:,:) CHARACTER(LEN=40), ALLOCATABLE :: HDFUNIT(:,:) ! ! !REMARKS: ! If you have the HDF5 library installed on your system, then you can ! compile GEOS-Chem with the option: ! . ! make HDF5=yes ! . ! which will activate the HDF5-specific code in this module to enable file ! I/O to HDF5 format. You must also specify the HDF5 include and library ! paths in the Makefile_header.mk. ! . ! The default is not to activate the HDF5-specific code. ! ! !REVISION HISTORY: ! 19 Nov 2009 - A. van Donkelaar - Initial Version ! 21 Dec 2009 - R. Yantosca - Modified to block out HDF5-specific code ! so that users w/o HDF5 library can still ! compile & run GEOS-Chem ! 21 Dec 2009 - R. Yantosca - Updated comments !EOP !------------------------------------------------------------------------------ !BOC CONTAINS !EOC !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !IROUTINE: open_hdf ! ! !DESCRIPTION: Subroutine OPEN\_HDF creates and opens an hdf file for output. !\\ !\\ ! !INTERFACE: ! #if defined( USE_HDF5 ) !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: Subroutine is used only when USE_HDF5 is defined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SUBROUTINE OPEN_HDF( IU_HDF, FILENAME, IMAX, IMIN, & JMAX, JMIN, NI, NJ ) ! ! !USES: ! USE HDF5 USE GRID_MOD, ONLY : GET_XMID USE GRID_MOD, ONLY : GET_YMID USE CMN_SIZE_MOD ! Size parameters ! ! !INPUT PARAMETERS: ! CHARACTER(LEN=*), INTENT(IN) :: FILENAME ! File name to open INTEGER, INTENT(IN) :: IMIN ! Min longitude index INTEGER, INTENT(IN) :: IMAX ! Max longitude index INTEGER, INTENT(IN) :: JMIN ! Min latitude index INTEGER, INTENT(IN) :: JMAX ! Max latitude index INTEGER, INTENT(IN) :: NI ! # of longitudes INTEGER, INTENT(IN) :: NJ ! # of latitudes ! ! !INPUT/OUTPUT PARAMETERS: ! INTEGER(HID_T), INTENT(INOUT) :: IU_HDF ! HDF5 file identifier ! ! !REVISION HISTORY: ! Nov 20 2009 - A. van Donkelaar - Initial Version ! 21 Dec 2009 - R. Yantosca - Modified to block out HDF5-specific code ! so that users w/o HDF5 library can still ! compile & run GEOS-Chem ! 21 Dec 2009 - R. Yantosca - Updated comments !EOP !------------------------------------------------------------------------------ !BOC ! ! !LOCAL VARIABLES: ! INTEGER(HID_T) :: dset_id ! Dataset identifier INTEGER(HID_T) :: dspace_id ! Dataspace identifier INTEGER(HSIZE_T), DIMENSION(1) :: dims ! Dataset dimensions INTEGER :: rank = 1 ! Dataset rank CHARACTER(LEN=60) :: dsetname ! Dataset name INTEGER :: error ! Error flag REAL*4 :: LAT(NJ) REAL*4 :: LON(NI) INTEGER :: I, J ! Initialize FORTRAN interface. CALL h5open_f( error ) ! Create a new file using default properties. CALL h5fcreate_f( TRIM(FILENAME), H5F_ACC_TRUNC_F, IU_HDF, error ) ! Write LAT/LON to new file ! Does not wrap around date line DO I = 0, NI-1 LON(I+1) = GET_XMID(I+IMIN) ENDDO DO J = 0, NJ-1 LAT(J+1) = GET_YMID(J+JMIN) ENDDO DO I = 1,2 IF (I .eq. 1) THEN dims = NI dsetname = 'LON' ELSEIF (I .eq. 2) THEN dims = NJ dsetname = 'LAT' ENDIF ! Create the dataspace. CALL h5screate_simple_f(rank, dims, dspace_id, error) ! Create the dataset with default properties. CALL h5dcreate_f(IU_HDF, dsetname, H5T_NATIVE_REAL, & dspace_id, dset_id, error) ! Write the dataset. IF ( I .eq. 1 ) THEN CALL h5dwrite_f(dset_id, H5T_NATIVE_REAL, LON, dims, error) ELSEIF ( I .eq. 2 ) THEN CALL h5dwrite_f(dset_id, H5T_NATIVE_REAL, LAT, dims, error) ENDIF ! End access to the dataset and release resources used by it. CALL h5dclose_f(dset_id, error) ! Terminate access to the data space. CALL h5sclose_f(dspace_id, error) ENDDO END SUBROUTINE OPEN_HDF #else SUBROUTINE OPEN_HDF !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: OPEN_HDF will be a stub if USE_HDF5 is undefined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END SUBROUTINE OPEN_HDF #endif !EOC !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !IROUTINE: close_hdf ! ! !DESCRIPTION: Subroutine CLOSE\_HDF closes an HDF5 file that is already open. !\\ !\\ ! !INTERFACE: ! #if defined( USE_HDF5 ) !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: Subroutine is used only when USE_HDF5 is defined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SUBROUTINE CLOSE_HDF( IU_HDF ) ! ! !USES: ! USE HDF5 ! ! !INPUT/OUTPUT PARAMETERS: ! INTEGER(HID_T), INTENT(INOUT) :: IU_HDF ! HDF5 File identifier ! ! !REVISION HISTORY: ! 20 Nov 2009 - A. van Donkelaar - Initial Version ! 21 Dec 2009 - R. Yantosca - Modified to block out HDF5-specific code ! so that users w/o HDF5 library can still ! compile & run GEOS-Chem ! 21 Dec 2009 - R. Yantosca - Updated comments !EOP !------------------------------------------------------------------------------ !BOC ! ! !LOCAL VARIABLES: ! INTEGER :: error ! Error flag ! Initialize FORTRAN interface. CALL h5open_f ( error ) ! Terminate access to the file. CALL h5fclose_f( IU_HDF, error ) END SUBROUTINE CLOSE_HDF #else SUBROUTINE CLOSE_HDF !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: CLOSE_HDF will be a stub if USE_HDF5 is undefined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END SUBROUTINE CLOSE_HDF #endif !EOC !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !IROUTINE: write_hdf ! ! !DESCRIPTION: Subroutine WRITE\_HDF writes data to an open HDF5 file. !\\ !\\ ! !INTERFACE: ! #if defined( USE_HDF5 ) !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: Subroutine is used only when USE_HDF5 is defined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SUBROUTINE WRITE_HDF( IU_HDF, N, NDCATEGORY, NDTRACER, & NDUNIT, TAU0, TAU1, RESERVED, & NI, NJ, NL, IFIRST, & JFIRST, LFIRST, ARRAY ) ! ! !USES: ! USE HDF5 ! ! !INPUT PARAMETERS: ! INTEGER, INTENT(IN) :: IU_HDF ! HDF file unit # INTEGER, INTENT(IN) :: N ! Actual tracer # CHARACTER(LEN=40), INTENT(IN) :: NDCATEGORY ! Diagnostic category INTEGER, INTENT(IN) :: NDTRACER ! Tracer # for file CHARACTER(LEN=40), INTENT(IN) :: NDUNIT ! Units of data REAL*8, INTENT(IN) :: TAU0 ! TAU at start & end REAL*8, INTENT(IN) :: TAU1 ! of diag interval CHARACTER(LEN=40), INTENT(IN) :: RESERVED ! Descriptive string INTEGER, INTENT(IN) :: NI ! # of longitudes INTEGER, INTENT(IN) :: NJ ! # of latitudes INTEGER, INTENT(IN) :: NL ! # of levels INTEGER, INTENT(IN) :: IFIRST ! Index of 1st lon INTEGER, INTENT(IN) :: JFIRST ! Index of 1st lat INTEGER, INTENT(IN) :: LFIRST ! Index of 1st lev REAL*4, INTENT(IN) :: ARRAY(NI,NJ,NL) ! Data array ! ! !REVISION HISTORY: ! 20 Nov 2009 - A. van Donkelaar - Initial Version ! 21 Dec 2009 - R. Yantosca - Modified to block out HDF5-specific code ! so that users w/o HDF5 library can still ! compile & run GEOS-Chem ! 21 Dec 2009 - R. Yantosca - Updated comments !EOP !------------------------------------------------------------------------------ !BOC ! ! !LOCAL VARIABLES: ! INTEGER :: error ! Error flag INTEGER(HID_T) :: dset_id ! Dataset identifier INTEGER(HID_T) :: dspace_id ! Dataspace identifier INTEGER(HSIZE_T) :: dims(3) ! Dataset dimensions INTEGER :: rank = 3 ! Dataset rank CHARACTER(LEN=60) :: dsetname ! Dataset name INTEGER(HID_T) :: attr_id ! Attribute identifier INTEGER(HID_T) :: aspace_id ! Attribute Dataspace identifier INTEGER(HID_T) :: atype_id ! Attribute Dataspace identifier INTEGER(HSIZE_T) :: adims(1) = (/1/) ! Attribute dimension INTEGER :: arank = 1 ! Attribute rank INTEGER(SIZE_T) :: attrlen ! Length of the attribute string CHARACTER(LEN=20) :: aname ! Attibute Name CHARACTER(LEN=40) :: attr_data ! Attribute Data REAL*8 :: attr_data_num ! Attribute Data INTEGER :: I, GAMAPI, GAMAPI2 ! Initialize FORTRAN interface. CALL h5open_f (error) dims(1) = NI dims(2) = NJ dims(3) = NL ! Create the dataspace. CALL h5screate_simple_f(rank, dims, dspace_id, error) GAMAPI = 0 DO I = 1, MAXDIAG IF ( HDFCATEGORY(I) .EQ. NDCATEGORY ) THEN GAMAPI = I ENDIF ENDDO IF ( GAMAPI .eq. 0 ) THEN PRINT*, 'BAD HDF CATEGORY:', NDCATEGORY CALL FLUSH(6) ENDIF IF ( NDCATEGORY .eq. 'IJ-AVG-$' ) THEN GAMAPI2 = 45 ELSEIF ( NDCATEGORY .eq. 'BXHGHT-$' ) THEN GAMAPI2 = 68 ELSEIF ( NDCATEGORY .eq. 'DAO-3D-$' ) THEN GAMAPI2 = 66 ELSEIF ( NDCATEGORY .eq. 'OD-MAP-$' ) THEN GAMAPI2 = 21 ELSEIF ( NDCATEGORY .eq. 'PEDGE-$' ) THEN GAMAPI2 = 31 HDFNAME(NDTRACER,GAMAPI2) = 'PEDGE' HDFFNAME(NDTRACER,GAMAPI2) = 'Box Edge Pressure' HDFUNIT(NDTRACER,GAMAPI2) = 'hPa' HDFMOLC(NDTRACER,GAMAPI2) = 1 HDFMWT(NDTRACER,GAMAPI2) = 0 HDFSCALE(NDTRACER,GAMAPI2) = 1 ELSEIF ( NDCATEGORY .eq. 'TIME-SER' ) THEN GAMAPI2 = 48 ELSE GAMAPI2 = 0 ENDIF IF (GAMAPI2 .eq. 0) THEN PRINT*, 'BAD HDF CATEGORY 2' CALL FLUSH(6) ENDIF WRITE(dsetname,*) TRIM(NDCATEGORY), '::', & TRIM(HDFNAME(NDTRACER,GAMAPI2)) ! remove space at beginning of dataset name ! don't understand why this is needed (amv) dsetname=dsetname(2:60) ! Create the dataset with default properties. CALL h5dcreate_f(IU_HDF, dsetname, H5T_NATIVE_REAL, dspace_id, & dset_id, error) ! Write the dataset. CALL h5dwrite_f(dset_id, H5T_NATIVE_REAL, ARRAY(:,:,:) * & HDFSCALE(NDTRACER,GAMAPI2), dims, error) DO I = 1,7 !1,7 IF ( I .eq. 1 ) THEN attrlen = 40 adims = 1 aname = 'CATEGORY DESCRIPTION' attr_data = HDFDESCRIPT(GAMAPI) ELSEIF ( I .eq. 2 ) THEN attrlen = 40 adims = 1 aname = 'TRACER DESCRIPTION' attr_data = HDFFNAME(NDTRACER,GAMAPI2) ELSEIF ( I .eq. 3 ) THEN attrlen = 40 adims = 1 aname = 'UNITS' attr_data = HDFUNIT(NDTRACER,GAMAPI2) ELSEIF ( I .eq. 4 ) THEN attrlen = 8 adims = 1 aname = 'SCALE' attr_data_num = HDFSCALE(NDTRACER,GAMAPI2) ELSEIF ( I .eq. 5 ) THEN attrlen = 8 adims = 1 aname = 'MWT' attr_data_num = HDFMWT(NDTRACER,GAMAPI2) ELSEIF ( I .eq. 6 ) THEN attrlen = 8 adims = 1 aname = 'MOLC' attr_data_num = HDFMOLC(NDTRACER,GAMAPI2) ELSEIF ( I .eq. 7 ) THEN attrlen = 8 adims = 1 aname = 'GMTRACER' attr_data_num = NDTRACER ENDIF ! Create scalar data space for the attribute. CALL h5screate_simple_f(arank, adims, aspace_id, error) ! Create datatype for the attribute. IF (I < 4) THEN CALL h5tcopy_f(H5T_NATIVE_CHARACTER, atype_id, error) ELSE CALL h5tcopy_f(H5T_NATIVE_DOUBLE, atype_id, error) ENDIF CALL h5tset_size_f(atype_id, attrlen, error) ! Create dataset attribute. CALL h5acreate_f(dset_id, aname, atype_id, aspace_id, & attr_id, error) ! Write the attribute data. IF (I < 4) THEN CALL h5awrite_f(attr_id, atype_id, attr_data, & adims, error) ELSE CALL h5awrite_f(attr_id, atype_id, attr_data_num, & adims, error) ENDIF ! Close the attribute. CALL h5aclose_f(attr_id, error) ENDDO ! End access to the dataset and release resources used by it. CALL h5dclose_f(dset_id, error) ! Terminate access to the data space. CALL h5sclose_f(dspace_id, error) END SUBROUTINE WRITE_HDF #else SUBROUTINE WRITE_HDF !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% !%%% NOTE: WRITE_HDF will be a stub if USE_HDF5 is undefined! %%% !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% END SUBROUTINE WRITE_HDF #endif !EOC !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !IROUTINE: init_hdf ! ! !DESCRIPTION: Subroutine INIT\_HDF allocates all module variables. !\\ !\\ ! !INTERFACE: ! SUBROUTINE INIT_HDF( GMMAXCAT, GMMAXTRACER, GMMAXDIAG ) ! ! !USES: ! USE ERROR_MOD, ONLY : ALLOC_ERR ! ! !INPUT PARAMETERS: ! INTEGER, INTENT(IN) :: GMMAXCAT INTEGER, INTENT(IN) :: GMMAXTRACER INTEGER, INTENT(IN) :: GMMAXDIAG ! ! !REVISION HISTORY: ! 23 Nov 2009 - A. van Donkelaar - Initial Version ! 21 Dec 2009 - R. Yantosca - Modified to block out HDF5-specific code ! so that users w/o HDF5 library can still ! compile & run GEOS-Chem ! 21 Dec 2009 - R. Yantosca - Updated comments !EOP !------------------------------------------------------------------------------ !BOC ! ! !LOCAL VARIABLES: ! INTEGER :: AS MAXCAT = GMMAXCAT MAXTRACER = GMMAXTRACER MAXDIAG = GMMAXDIAG ALLOCATE( HDFCATEGORY( MAXCAT ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFCATEGORY' ) HDFCATEGORY = '' ALLOCATE( HDFDESCRIPT( MAXCAT ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFDESCRIPT' ) HDFDESCRIPT = '' ALLOCATE( HDFNAME( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFNAME' ) HDFNAME = '' ALLOCATE( HDFFNAME( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFFNAME' ) HDFFNAME = '' ALLOCATE( HDFUNIT( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFUNIT' ) HDFUNIT = '' ALLOCATE( HDFMOLC( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFMOLC' ) HDFMOLC = 0 ALLOCATE( HDFMWT( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFMWT' ) HDFMWT = 0.0 ALLOCATE( HDFSCALE( MAXTRACER, MAXDIAG ), STAT=AS ) IF ( AS /= 0 ) CALL ALLOC_ERR( 'HDFSCALE' ) HDFSCALE = 0.0 END SUBROUTINE INIT_HDF !EOC !------------------------------------------------------------------------------ ! Dalhousie University Atmospheric Composition Analysis Group ! !------------------------------------------------------------------------------ !BOP ! ! !IROUTINE: cleanup_hdf ! ! !DESCRIPTION: Subroutine CLEANUP\_HDF deallocates all module variables. !\\ !\\ ! !INTERFACE: ! SUBROUTINE CLEANUP_HDF ! ! !REVISION HISTORY: ! 21 Dec 2009 - R. Yantosca - Initial version !EOP !------------------------------------------------------------------------------ !BOC IF ( ALLOCATED( HDFCATEGORY ) ) DEALLOCATE( HDFCATEGORY ) IF ( ALLOCATED( HDFDESCRIPT ) ) DEALLOCATE( HDFDESCRIPT ) IF ( ALLOCATED( HDFNAME ) ) DEALLOCATE( HDFNAME ) IF ( ALLOCATED( HDFFNAME ) ) DEALLOCATE( HDFFNAME ) IF ( ALLOCATED( HDFUNIT ) ) DEALLOCATE( HDFUNIT ) IF ( ALLOCATED( HDFMOLC ) ) DEALLOCATE( HDFMOLC ) IF ( ALLOCATED( HDFMWT ) ) DEALLOCATE( HDFMWT ) IF ( ALLOCATED( HDFSCALE ) ) DEALLOCATE( HDFSCALE ) END SUBROUTINE CLEANUP_HDF !EOC END MODULE HDF_MOD