added coordinate attribute to H5Block

.gitattributes

@@ -77,6 +77,7 @@ test/H5test.cc -text
 test/H5testF.f -text
 test/H5testFpar.F90 -text
 test/Makefile.am -text
+test/coords.F90 -text
 test/params.h -text
 test/read.c -text
 test/test.c -text

src/H5Block.c

@@ -2009,6 +2009,250 @@ H5Block3dSetFieldSpacing (
 		3 );
 }
 
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of X coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the X
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldXCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: X coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldXCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->i_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->i_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_XCOORD_NAME,
+		coords );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of X coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the X
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldXCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: X coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldXCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->i_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->i_max + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_XCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of Y coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Y
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldYCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: Y coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldYCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->j_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Y dimension (%lld)",
+		    (long long)coords_len, (long long)b->j_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_YCOORD_NAME,
+		coords );
+}
+
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of Y coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Y
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldYCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: Y coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldYCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->j_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->j_max + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_YCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Get the explicit list of Z coordinates for field \c field_name in the current
+  time step. The coordinates are read into the 1D array \c coords which has
+  length \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Z
+  dimension of the field, and a warning will be printed if they differ.
+
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dGetFieldZCoords(
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	h5part_float64_t *coords,		/*!< OUT: Z coordinates */
+	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockGetFieldZCoords" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->k_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Z dimension (%lld)",
+		    (long long)coords_len, (long long)b->k_max + 1);
+
+	return _read_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_ZCOORD_NAME,
+		coords );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Set an explicit list of Z coordinates for field \c field_name in the current
+  time step. The coordinates are a 1D array of floating point values with
+  dimension \c coords_len.
+
+  By convention, the \c coords array should have the same length as the Z
+  dimension of the field, and a warning will be printed if not.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dSetFieldZCoords (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const h5part_float64_t *coords,		/*!< IN: Z coordinates */
+	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
+	) {
+
+	SET_FNAME ( "H5BlockSetFieldZCoords" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+	CHECK_LAYOUT( f );
+
+	struct H5BlockStruct *b = f->block;
+
+	if (coords_len != b->k_max + 1)
+	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
+		    (long long)coords_len, (long long)b->k_max  + 1);
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		H5BLOCK_FIELD_ZCOORD_NAME,
+		(const hid_t)H5PART_FLOAT64, 
+		coords,
+		coords_len
+		 );
+}
+
 /*!
   \ingroup h5block_model
 

src/H5Block.f90

@@ -232,4 +232,69 @@ INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z )
     REAL*8, INTENT(IN) :: z
 END FUNCTION
   
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldXCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_xcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
   
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldXCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_xcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldYCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_ycoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldYCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_ycoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldZCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_zcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldZCoords
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_zcoords ( filehandle, name, coords )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: coords(*)
+    INTEGER*8, INTENT(IN) :: coords_len
+END FUNCTION
+

src/H5Block.h

@@ -13,6 +13,9 @@ extern "C" {
 
 #define H5BLOCK_FIELD_ORIGIN_NAME	"__Origin__"
 #define H5BLOCK_FIELD_SPACING_NAME	"__Spacing__"
+#define H5BLOCK_FIELD_XCOORD_NAME	"__X_Coordinates__"
+#define H5BLOCK_FIELD_YCOORD_NAME	"__Y_Coordinates__"
+#define H5BLOCK_FIELD_ZCOORD_NAME	"__Z_Coordinates__"
 
 /*! 
   Interface for block structured field data.
@@ -138,6 +141,54 @@ H5Block3dSetFieldSpacing (
 	const h5part_float64_t z_spacing
 	);
 
+h5part_int64_t
+H5Block3dGetFieldXCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetFieldXCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dGetFieldYCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetFieldYCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dGetFieldZCoords (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
+h5part_int64_t
+H5Block3dSetZCoords (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t coords_len
+	);
+
 h5part_int64_t
 H5BlockWriteFieldAttrib (
 	H5PartFile *f,

src/H5BlockF.c

@@ -68,6 +68,24 @@
 #define h5bl_3d_get_field_origin F77NAME (				\
 					h5bl_3d_get_field_origin_,	\
 					H5BL_3D_GET_FIELD_origin )
+#define h5bl_3d_get_field_xcoords F77NAME (				\
+					h5bl_3d_get_field_xcoords_,	\
+					H5BL_3D_GET_FIELD_XCOORDS )
+#define h5bl_3d_set_field_xcoords F77NAME (				\
+					h5bl_3d_set_field_xcoords_,	\
+					H5BL_3D_SET_FIELD_XCOORDS )
+#define h5bl_3d_get_field_ycoords F77NAME (				\
+					h5bl_3d_get_field_ycoords_,	\
+					H5BL_3D_GET_FIELD_YCOORDS )
+#define h5bl_3d_set_field_ycoords F77NAME (				\
+					h5bl_3d_set_field_ycoords_,	\
+					H5BL_3D_SET_FIELD_YCOORDS )
+#define h5bl_3d_get_field_zcoords F77NAME (				\
+					h5bl_3d_get_field_zcoords_,	\
+					H5BL_3D_GET_FIELD_ZCOORDS )
+#define h5bl_3d_set_field_zcoords F77NAME (				\
+					h5bl_3d_set_field_zcoords_,	\
+					H5BL_3D_SET_FIELD_ZCOORDS )
 #endif
 
 h5part_int64_t
@@ -447,3 +465,123 @@ h5bl_3d_set_field_origin (
 	free ( field_name2 );
 	return herr;
 }
+
+h5part_int64_t
+h5bl_3d_set_field_xcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldXCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_xcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldXCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_ycoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldYCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_ycoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldYCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_zcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldZCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_zcoords (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *coords,
+	const h5part_int64_t *coords_len,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldZCoords (
+		filehandle, field_name2, coords, *coords_len );
+
+	free ( field_name2 );
+	return herr;
+}

src/H5Part.c

@@ -1347,7 +1347,6 @@ _H5Part_read_attrib (
 
 	herr_t herr;
 	hid_t attrib_id;
-	hid_t space_id;
 	hid_t type_id;
 
 #ifdef H5PART_HAVE_HDF5_18
@@ -1363,15 +1362,9 @@ _H5Part_read_attrib (
 	type_id = H5Aget_type ( attrib_id );
 	if ( type_id < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
 
-	space_id = H5Aget_space ( attrib_id );
-	if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;
-
 	herr = H5Aread ( attrib_id, type_id, attrib_value );
 	if ( herr < 0 ) return HANDLE_H5A_READ_ERR;
 
-	herr = H5Sclose ( space_id );
-	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
-
 	herr = H5Tclose ( type_id );
 	if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
 

test/coords.F90

@@ -0,0 +1,97 @@
+program H5BlockCoordsTest
+  implicit none
+
+#ifdef PARALLEL_IO
+  include 'mpif.h'
+#endif
+  include 'H5PartF.h'
+
+#ifdef PARALLEL_IO
+  integer :: ierr, comm
+#endif
+  integer*8 :: file_id, status, i
+  real*8, allocatable :: r8buf(:,:,:), r8buf3(:,:,:,:), coords(:)
+  real*8 :: x, y, z
+
+#ifdef PARALLEL_IO
+  call MPI_INIT(ierr)
+  comm = MPI_COMM_WORLD
+#endif
+
+  ! this enables level 4 ("debug") messages to be
+  ! printed by the H5Part library
+  ! (4_8 is the literal for an integer*8 with value 4)
+  status = h5pt_set_verbosity_level (4_8)
+
+  ! open the a file called 'test.h5' in parallel for writing
+#ifdef PARALLEL_IO
+  file_id = h5pt_openw_par_align ('test.h5', comm, 1048576_8, "vfd_mpiposix")
+#else
+  file_id = h5pt_openw_align ('test.h5', 1048576_8, "vfd_mpiposix")
+#endif
+
+  status = h5bl_define3dlayout(file_id, 1_8, 30_8, 1_8, 30_8, 1_8, 30_8)
+
+  ! in the Fortran API, steps start at 1
+  status = h5pt_setstep (file_id, 1_8)
+
+  ! create fake data
+  allocate(r8buf(30,30,30))
+  allocate(r8buf3(30,30,30,3))
+  allocate(coords(30))
+  x = 1.0
+  y = 2.0
+  z = 3.0
+
+  ! write the data
+  status = h5bl_3d_write_scalar_field_r8(file_id, "x", r8buf(1,1,1))
+  status = h5bl_3d_set_field_origin(file_id, "x", x, y, z)
+  status = h5bl_3d_set_field_spacing(file_id, "x", x, y, z)
+
+  status = h5bl_3d_write_3dvector_field_r8(file_id, "v", r8buf3(1,1,1,1), r8buf3(1,1,1,2), r8buf3(1,1,1,3))
+  status = h5bl_3d_set_field_origin(file_id, "v", x, y, z)
+  status = h5bl_3d_set_field_spacing(file_id, "v", x, y, z)
+
+  ! create fake coordinates
+  do i = 1, 30
+    coords(i) = 3*i
+  enddo
+  status = h5bl_3d_set_field_xcoords(file_id, "v", coords, 30_8)
+  do i = 1, 30
+    coords(i) = 3*i + 1
+  enddo
+  status = h5bl_3d_set_field_ycoords(file_id, "v", coords, 30_8)
+  do i = 1, 30
+    coords(i) = 3*i + 2
+  enddo
+  status = h5bl_3d_set_field_zcoords(file_id, "v", coords, 30_8)
+
+  ! read fake coordinates
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_xcoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_ycoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+  do i = 1, 30
+    coords(i) = -1
+  enddo
+  status = h5bl_3d_get_field_zcoords(file_id, "v", coords, 30_8)
+  write(*, *) coords
+  !write(*, "I3") ( coords(i), i=1, 30 )
+
+  ! close the file
+  status = h5pt_close (file_id)
+
+#ifdef PARALLEL_IO
+  call MPI_FINALIZE(ierr)
+#endif
+
+end program H5BlockCoordsTest
+