Commit e8e2f62f authored by Marc Howison's avatar Marc Howison

added coordinate attribute to H5Block

parent 23045a3f
......@@ -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
......
......@@ -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
......
......@@ -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
......@@ -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,
......
......@@ -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;
}
......@@ -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;
......
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
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