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- update/review documentation
- re-introduce old API functions
This commit is contained in:
gsell
2016-03-17 17:50:42 +01:00
parent 538c9cdd76
commit 91316f314d
11 changed files with 233 additions and 346 deletions
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doc/Doxyfile
+4 -3
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@@ -1958,7 +1958,7 @@ PERLMOD_MAKEVAR_PREFIX =
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = NO
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
# in the source code. If set to NO, only conditional compilation will be
@@ -1967,7 +1967,7 @@ ENABLE_PREPROCESSING = NO
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = NO
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
@@ -2007,7 +2007,8 @@ INCLUDE_FILE_PATTERNS =
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED = PARALLEL_IO
PREDEFINED = PARALLEL_IO \
H5HUT_API_VERSION=2
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
doc/H5.dox
+5 -5
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@@ -45,12 +45,12 @@ For more information, please contact the
\defgroup h5hut_error error handling
@}
\defgroup h5hut_c_api H5
\defgroup h5_c_api H5
@{
\defgroup h5hut_file file handling
\defgroup h5hut_model setting up the data model
\defgroup h5hut_file_attribs reading and writing file attributes
\defgroup h5hut_step_attribs reading and writing step attributes
\defgroup h5_file file handling
\defgroup h5_model setting up the data model
\defgroup h5_file_attribs reading and writing file attributes
\defgroup h5_step_attribs reading and writing step attributes
@}
\defgroup h5part_c_api H5Part
@{
src/include/H5.h
+146 -44
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@@ -15,15 +15,23 @@
#include "H5_model.h"
#include "H5_attribs.h"
/**
\ingroup h5_c_api
\addtogroup h5_file
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5hut_c_api
\addtogroup h5hut_file
@{
*/
#if H5HUT_API_VERSION == 2
#define H5OpenFile2 H5OpenFile
#define H5SetVerbosityLevel2 H5SetVerbosityLevel
#elif H5HUT_API_VERSION == 1
#define H5OpenFile1 H5OpenFile
#define H5SetVerbosityLevel1 H5SetVerbosityLevel
#endif
/**
Create a new, empty file property list.
@@ -43,6 +51,11 @@ extern "C" {
\see H5SetPropFileCoreVFD()
\see H5SetPropFileAlign()
\see H5SetPropFileThrottle()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_prop_t
H5CreateFileProp (
@@ -56,36 +69,17 @@ H5CreateFileProp (
Stores MPI IO communicator information to given file property list. If used in
\ref H5OpenFile(), MPI collective IO will be used.
\note H5SetPropFileMPIO() is deprecated. Use H5SetPropFileMPIOCollective() instead.
\return \c H5_SUCCESS on success
\return \c H5_FAILURE on error
\see H5SetPropFileMPIOIndependent()
\see H5SetPropFileMPIOPosix() (HDF5 <= 1.8.12 only)
\see H5SetPropFileCoreVFD()
*/
static inline h5_err_t
H5SetPropFileMPIO (
h5_prop_t prop, ///< [in,out] identifier for file property list
MPI_Comm* comm ///< [in] MPI communicator
) {
H5_API_ENTER (h5_err_t, "prop=%p, comm=%p", (void*)prop, comm);
H5_API_RETURN (h5_set_prop_file_mpio_collective (prop, comm));
}
/**
Stores MPI IO communicator information to given file property list. If used in
\ref H5OpenFile(), MPI collective IO will be used.
\return \c H5_SUCCESS on success
\return \c H5_FAILURE on error
\note This function deprecates H5SetPropFileMPIO().
\see H5SetPropFileMPIOIndependent()
\see H5SetPropFileMPIOPosix() (HDF5 <= 1.8.12 only)
\see H5SetPropFileCoreVFD()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileMPIOCollective (
@@ -106,6 +100,11 @@ H5SetPropFileMPIOCollective (
\see H5SetPropFileMPIOCollective()
\see H5SetPropFileMPIOPosix() (HDF5 <= 1.8.12 only)
\see H5SetPropFileCoreVFD()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileMPIOIndependent (
@@ -125,12 +124,17 @@ H5SetPropFileMPIOIndependent (
\return \c H5_SUCCESS on success
\return \c H5_FAILURE on error
\note This function is available only, if H5hut has been compiled with
HDF5 1.8.12 or older.
\see H5SetPropFileMPIOCollective()
\see H5SetPropFileMPIOIndependent()
\see H5SetPropFileCoreVFD()
\note This function is available only, if H5hut has been compiled with
HDF5 1.8.12 or older.
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileMPIOPosix (
@@ -152,6 +156,11 @@ H5SetPropFileMPIOPosix (
\return \c H5_SUCCESS on success
\return \c H5_FAILURE on error
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileCoreVFD (
@@ -181,13 +190,19 @@ H5SetPropFileCoreVFD (
\return \c H5_FAILURE on error
\see H5SetPropFileCoreVFD()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileAlign (
h5_prop_t prop, ///< [in,out] identifier for file property list
h5_int64_t align ///< [in] alignment
) {
H5_API_ENTER (h5_err_t, "prop=%p, align=%lld", (void*)prop, (long long int)align);
H5_API_ENTER (h5_err_t, "prop=%p, align=%lld",
(void*)prop, (long long int)align);
H5_API_RETURN (h5_set_prop_file_align (prop, align));
}
@@ -205,18 +220,29 @@ H5SetPropFileAlign (
\return \c H5_SUCCESS on success
\return \c H5_FAILURE on error
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetPropFileThrottle (
h5_prop_t prop, ///< [in,out] identifier for file property list
h5_int64_t throttle ///< [in] throttle factor
) {
H5_API_ENTER (h5_err_t, "prop=%p, throttle=%lld", (void*)prop, (long long int)throttle);
H5_API_ENTER (h5_err_t, "prop=%p, throttle=%lld",
(void*)prop, (long long int)throttle);
H5_API_RETURN (h5_set_prop_file_throttle (prop, throttle));
}
/**
Close file property list.
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5CloseProp (
@@ -234,9 +260,9 @@ H5CloseProp (
- \c H5_O_WRONLY: create new file, dataset must not exist
- \c H5_O_APPENDONLY: allows to append new data to an existing file
- \c H5_O_RDWR: dataset may exist
- \c H5_FS_LUSTRE - enable optimizations for the Lustre file system
- \c H5_VFD_MPIO_POSIX - use the HDF5 MPI-POSIX virtual file driver
- \c H5_VFD_MPIO_INDEPENDENT - use MPI-IO in indepedent mode
- \c H5_FS_LUSTRE: enable optimizations for the Lustre file system
- \c H5_VFD_MPIO_POSIX: use the HDF5 MPI-POSIX virtual file driver
- \c H5_VFD_MPIO_INDEPENDENT: use MPI-IO in indepedent mode
The file is opened with the properties set in the file property list
\c prop. This argument can also be set to \c H5_PROP_DEFAULT to use
@@ -249,9 +275,13 @@ H5CloseProp (
\return \c H5_FAILURE on error
\see H5CreateFileProp()
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | API changed, old implementation is available as \c H5OpenFile1() |
*/
static inline h5_file_t
H5OpenFile (
H5OpenFile2 (
const char* filename, ///< [in] name of file
h5_int64_t mode, ///< [in] file mode
h5_prop_t props ///< [in] identifier for file property list
@@ -262,6 +292,41 @@ H5OpenFile (
H5_API_RETURN (h5_open_file2 (filename, mode, props));
}
/**
Open file with name \c filename.
File mode flags are:
- \c H5_O_RDONLY: Only reading allowed
- \c H5_O_WRONLY: create new file, dataset must not exist
- \c H5_O_APPENDONLY: allows to append new data to an existing file
- \c H5_O_RDWR: dataset may exist
- \c H5_FS_LUSTRE - enable optimizations for the Lustre file system
- \c H5_VFD_MPIO_POSIX - use the HDF5 MPI-POSIX virtual file driver
(hdf5 <= 1.8.12 only)
- \c H5_VFD_MPIO_INDEPENDENT - use MPI-IO in indepedent mode
In the serial version of H5hut, \c comm can be set to any value.
\return File handle.
\return (h5_file_p*)H5_FAILURE
\note This function is deprecated!
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Old implementation of \c H5OpenFile() |
*/
static inline h5_file_p
H5OpenFile1 (
const char* filename, ///< [in] file name
h5_int32_t flags, ///< [in] file open flags
MPI_Comm comm ///< [in] MPI communicator
) {
H5_API_ENTER (h5_file_p, "filename='%s', flags=%d, ...",filename,flags);
H5_API_RETURN (h5_open_file (filename, flags, comm, 0));
}
/**
Close file and free all memory associated with the file handle.
@@ -348,7 +413,7 @@ H5Finalize (
\addtogroup h5hut_verbosity
@{
*/
/**
Set verbosity level to \c level.
@@ -358,17 +423,44 @@ H5Finalize (
- \c H5_VERBOSE_WARN: output error messages and warning
- \c H5_VERBOSE_INFO: output error messages, warnings and informational messages
The default verbosity level ist \c H5_VERBOSE_ERROR.
The default verbosity level is \c H5_VERBOSE_ERROR.
\return \c H5_SUCCESS
\see H5GetVerbosityLevel()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function cannot be used to set the debug level. |
*/
static inline h5_err_t
H5SetVerbosityLevel2 (
const h5_id_t level ///< [in] verbosity level.
) {
return h5_set_debuglevel (level & 0x03);
}
/**
Set verbosity and debug level to \p level.
Verbosity levels are:
- \c H5_VERBOSE_NONE: be quiet
- \c H5_VERBOSE_ERROR: output error messages
- \c H5_VERBOSE_WARN: output error messages and warning
- \c H5_VERBOSE_INFO: output error messages, warnings and informational messages
The default verbosity level is \c H5_VERBOSE_ERROR.
\return \c H5_SUCCESS
\see H5GetVerbosityLevel()
*/
static inline h5_err_t
H5SetVerbosityLevel (
H5SetVerbosityLevel1 (
const h5_id_t level ///< [in] verbosity level.
) {
return h5_set_debuglevel (level & 0x03);
return h5_set_debuglevel (level);
}
/**
@@ -396,7 +488,7 @@ H5GetVerbosityLevel (
Set debug mask. The debug mask is an or'ed value of
- \c H5_DEBUG_API: C-API calls
- \c H5_DEBUG_CORE_API: core API calls. The core API is used by the C- and Fortran API.
- \c H5_DEBUG_CORE_API: core API calls.
- \c H5_DEBUG_PRIV_API: private API calls
- \c H5_DEBUG_PRIV_FUNC: static functions
- \c H5_DEBUG_HDF5: HDF5 wrapper calls
@@ -407,6 +499,11 @@ H5GetVerbosityLevel (
\return \c H5_SUCCESS
\see H5GetDebugMask()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_err_t
H5SetDebugMask (
@@ -421,6 +518,11 @@ H5SetDebugMask (
\return debug mask
\see H5SetDebugMask()
\note
| Release | Change |
| :------ | :----- |
| \c 1.99.15 | Function introduced in this release. |
*/
static inline h5_id_t
H5GetDebugMask (
@@ -560,10 +662,10 @@ H5GetErrno (
return h5_get_errno ();
}
///< @}
#ifdef __cplusplus
}
#endif
///< @}
#endif
src/include/H5Block_attribs.h
+9 -66
View File
@@ -16,14 +16,18 @@
#include "h5core/h5.h"
#include "h5core/h5_debug.h"
#include "h5core/h5b_attribs.h"
/**
\ingroup h5block_c_api
\addtogroup h5block_attrib
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5block_attrib
\anchor H5BlockGetNumFieldAttribs
Query the number of attributes of field \c field_name.
\return number of attributes
@@ -41,9 +45,6 @@ H5BlockGetNumFieldAttribs (
}
/**
\ingroup h5block_attrib
\anchor H5BlockGetFieldAttribInfo
Gets the name, type and number of elements of the field attribute
specified by its index.
@@ -91,9 +92,6 @@ H5BlockGetFieldAttribInfo (
/********************** reading and writing attribute ************************/
/**
\ingroup h5block_attrib
\anchor H5BlockWriteFieldAttribString
Write the string in \c buffer as attribute \c attrib_name of field
\c field_name.
@@ -127,9 +125,6 @@ H5BlockWriteFieldAttribString (
}
/**
\ingroup h5block_attrib
\anchor H5BlockReadFieldAttribString (
Read the string value from attribute \c attrib_name of field
\c field_name into \c buffer.
@@ -163,9 +158,6 @@ H5BlockReadFieldAttribString (
/**
\ingroup h5block_attrib
\anchor H5BlockWriteFieldAttribFloat64
Write float64 \c values as attribute \c attrib_name of field
\c field_name.
@@ -195,9 +187,6 @@ H5BlockWriteFieldAttribFloat64 (
}
/**
\ingroup h5block_attrib
\anchor H5BlockReadFieldAttribFloat64
Read float64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
@@ -225,9 +214,6 @@ H5BlockReadFieldAttribFloat64 (
/**
\ingroup h5block_attrib
\anchor H5BlockWriteFieldAttribFloat32
Write float32 \c values as attribute \c attrib_name of field
\c field_name.
@@ -257,9 +243,6 @@ H5BlockWriteFieldAttribFloat32 (
}
/**
\ingroup h5block_attrib
\anchor H5BlockReadFieldAttribFloat32
Read float32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
@@ -286,9 +269,6 @@ H5BlockReadFieldAttribFloat32 (
}
/**
\ingroup h5block_attrib
\anchor H5BlockWriteFieldAttribInt64
Write int64 \c values as attribute \c attrib_name of field
\c field_name.
@@ -317,9 +297,6 @@ H5BlockWriteFieldAttribInt64 (
}
/**
\ingroup h5block_attrib
\anchor H5BlockReadFieldAttribInt64
Read int64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
@@ -347,9 +324,6 @@ H5BlockReadFieldAttribInt64 (
/**
\ingroup h5block_attrib
\anchor H5BlockWriteFieldAttribInt32
Write int32 \c values as attribute \c attrib_name of field
\c field_name.
@@ -379,9 +353,6 @@ H5BlockWriteFieldAttribInt32 (
}
/**
\ingroup h5block_attrib
\anchor H5BlockReadFieldAttribInt32
Read int32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
@@ -407,9 +378,6 @@ H5BlockReadFieldAttribInt32 (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dGetFieldOrigin
Get field origin.
\return \c H5_SUCCESS on success
@@ -443,9 +411,6 @@ H5Block3dGetFieldOrigin (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dSetFieldOrigin
Set field origin.
\return \c H5_SUCCESS on success
@@ -473,9 +438,6 @@ H5Block3dSetFieldOrigin (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dGetFieldSpacing
Get field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS on success
@@ -507,9 +469,6 @@ H5Block3dGetFieldSpacing (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dSetFieldSpacing
Set field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS on success
@@ -537,9 +496,6 @@ H5Block3dSetFieldSpacing (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dSetFieldXCoords
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 n_coords.
@@ -571,9 +527,6 @@ H5Block3dSetFieldXCoords (
/**
\ingroup h5block_attrib
\anchor H5Block3dGetFieldXCoords
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 n_coords.
@@ -604,9 +557,6 @@ H5Block3dGetFieldXCoords (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dSetFieldYCoords
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 n_coords.
@@ -638,9 +588,6 @@ H5Block3dSetFieldYCoords (
/**
\ingroup h5block_attrib
\anchor H5Block3dGetFieldYCoords
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 n_coords.
@@ -671,9 +618,6 @@ H5Block3dGetFieldYCoords (
}
/**
\ingroup h5block_attrib
\anchor H5Block3dSetFieldZCoords
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 n_coords.
@@ -705,9 +649,6 @@ H5Block3dSetFieldZCoords (
/**
\ingroup h5block_attrib
\anchor H5Block3dGetFieldZCoords
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 n_coords.
@@ -741,4 +682,6 @@ H5Block3dGetFieldZCoords (
}
#endif
///< @}
#endif
src/include/H5Block_io.h
+8 -48
View File
@@ -15,13 +15,17 @@
#include "h5core/h5_debug.h"
#include "h5core/h5b_io.h"
/**
\ingroup h5block_c_api
\addtogroup h5block_io
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5block_io
Attempts to write the 3-dimensional field \p name from the
buffer pointed to by \p buffer to the current step using the
previously defined field view.
@@ -48,9 +52,6 @@ H5Block3dWriteScalarFieldFloat64 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadScalarFieldFloat64
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (64-bit).
@@ -74,9 +75,6 @@ H5Block3dReadScalarFieldFloat64 (
}
/**
\ingroup h5block_io
\anchor H5Block3dWriteVector3dFieldFloat64
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -104,9 +102,6 @@ H5Block3dWriteVector3dFieldFloat64 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadVector3dFieldFloat64
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -135,9 +130,6 @@ H5Block3dReadVector3dFieldFloat64 (
/**
\ingroup h5block_io
\anchor H5Block3dWriteScalarFieldFloat32
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
floating points (32-bit).
@@ -161,9 +153,6 @@ H5Block3dWriteScalarFieldFloat32 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadScalarFieldFloat32
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (32-bit).
@@ -187,9 +176,6 @@ H5Block3dReadScalarFieldFloat32 (
}
/**
\ingroup h5block_io
\anchor H5Block3dWriteVector3dFieldFloat32
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -217,9 +203,6 @@ H5Block3dWriteVector3dFieldFloat32 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadVector3dFieldFloat32
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -248,9 +231,6 @@ H5Block3dReadVector3dFieldFloat32 (
/**
\ingroup h5block_io
\anchor H5Block3dWriteScalarFieldInt64
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (64-bit).
@@ -274,9 +254,6 @@ H5Block3dWriteScalarFieldInt64 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadScalarFieldInt64
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (64-bit).
@@ -301,9 +278,6 @@ H5Block3dReadScalarFieldInt64 (
/**
\ingroup h5block_io
\anchor H5Block3dWriteVector3dFieldInt64
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -331,9 +305,6 @@ H5Block3dWriteVector3dFieldInt64 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadVector3dFieldInt64
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -362,9 +333,6 @@ H5Block3dReadVector3dFieldInt64 (
/**
\ingroup h5block_io
\anchor H5Block3dWriteScalarFieldInt32
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (32-bit).
@@ -388,9 +356,6 @@ H5Block3dWriteScalarFieldInt32 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadScalarFieldInt32
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (32-bit).
@@ -415,9 +380,6 @@ H5Block3dReadScalarFieldInt32 (
/**
\ingroup h5block_io
\anchor H5Block3dWriteVector3dFieldInt32
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -445,9 +407,6 @@ H5Block3dWriteVector3dFieldInt32 (
}
/**
\ingroup h5block_io
\anchor H5Block3dReadVector3dFieldInt32
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
@@ -474,9 +433,10 @@ H5Block3dReadVector3dFieldInt32 (
x_buf, y_buf, z_buf, H5T_NATIVE_INT32));
}
#ifdef __cplusplus
}
#endif
///< @}
#endif
src/include/H5Block_model.h
+14 -47
View File
@@ -15,6 +15,12 @@
#include "h5core/h5_debug.h"
#include "h5core/h5b_model.h"
/**
\ingroup h5block_c_api
\addtogroup h5block_model
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
@@ -22,14 +28,11 @@ extern "C" {
/********************** defining the layout **********************************/
/**
\ingroup h5block_model
\anchor H5BlockHasFieldData
Checks whether the current time-step has field data or not.
\return \c H5_OK if field data is available
\return \c H5_NOK if no field data is available
\return \c H5_FAILURE on error
\return true (value \c >0) if step exists
\return false (\c 0) if step does not exist
\return \c H5_FAILURE on error
*/
static inline h5_err_t
H5BlockHasFieldData (
@@ -42,15 +45,12 @@ H5BlockHasFieldData (
}
/**
\ingroup h5block_model
\anchor H5Block3dHasView
Tests whether a view has been set, either directly with
\ref H5Block3dSetView or indirectly with \ref H5Block3dSetGrid.
\return \c H5_OK if field data is available
\return \c H5_NOK if no field data is available
\return \c H5_FAILURE on error
\return true (value \c >0) if step exists
\return false (\c 0) if step does not exist
\return \c H5_FAILURE on error
*/
static inline h5_int64_t
H5Block3dHasView (
@@ -63,9 +63,6 @@ H5Block3dHasView (
}
/**
\ingroup h5block_model
\anchor H5Block3dSetView
Defines the partition of the field that this processor owns, using
Fortran ordering: the fastest moving index is \c i.
@@ -103,8 +100,6 @@ H5Block3dSetView (
}
/**
\ingroup h5block_model
\anchor H5Block3dGetView
Return the view of this processor.
\return \c H5_SUCCESS on success
@@ -133,9 +128,6 @@ H5Block3dGetView (
}
/**
\ingroup h5block_model
\anchor H5Block3dGetReducedView
Return the reduced (ghost-zone free) view of this processor.
\return \c H5_SUCCESS on success
@@ -164,9 +156,6 @@ H5Block3dGetReducedView (
}
/**
\ingroup h5block_model
\anchor H5Block3dSetChunkSize
Define the chunk dimensions and enable chunking in the underlying
HDF5 dataset.
@@ -190,9 +179,6 @@ H5Block3dSetChunkSize (
}
/**
\ingroup h5block_model
\anchor H5Block3dGetChunkSize
Lookup the chunk dimensions of the underlying HDF5 dataset.
\return \c H5_SUCCESS on success
@@ -214,9 +200,6 @@ H5Block3dGetChunkSize (
#ifdef PARALLEL_IO
/**
\ingroup h5block_model
\anchor H5Block3dSetGrid
Define an underlying 3D Cartesian grid on the processors with dimensions
(\c i,\c j,\c k). You can look up a processor's index into the grid
using \ref H5Block3dGetGridCoords.
@@ -246,9 +229,6 @@ H5Block3dSetGrid (
}
/**
\ingroup h5block_model
\anchor H5Block3dGetGridCoords
Look up the index (\c i, \c j, \c k) in the grid belonging to MPI processor
\c proc.
@@ -270,9 +250,6 @@ H5Block3dGetGridCoords (
}
/**
\ingroup h5block_model
\anchor H5Block3dSetDims
Set the dimensions of each processor's block when the field is a regular
grid.
@@ -300,9 +277,6 @@ H5Block3dSetDims (
#endif
/**
\ingroup h5block_model
\anchor H5Block3dSetHalo
Sets the additional cells (\c i, \c j, \c k) in each direction to use as
the `halo` region (or `ghost zone`) that overlaps between neighboring
processors on the grid.
@@ -330,9 +304,6 @@ H5Block3dSetHalo (
}
/**
\ingroup h5block_model
\anchor H5BlockGetNumFields
Query number of fields in current time step.
\return \c number of fields
@@ -350,9 +321,6 @@ H5BlockGetNumFields (
/**
\ingroup h5block_model
\anchor H5BlockGetFieldInfo
Get the name, rank and dimensions of the field specified by the
index \c idx.
@@ -399,9 +367,6 @@ H5BlockGetFieldInfo (
}
/**
\ingroup h5block_model
\anchor H5BlockGetFieldInfoByName
Get the rank and dimensions of the field specified by its name.
\return \c H5_SUCCESS on success
@@ -432,6 +397,8 @@ H5BlockGetFieldInfoByName (
type));
}
///< @}
#ifdef __cplusplus
}
#endif
src/include/H5Part_io.h
+8 -16
View File
@@ -15,13 +15,17 @@
#include "h5core/h5_debug.h"
#include "h5core/h5u_io.h"
/**
\ingroup h5part_c_api
\addtogroup h5part_io
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5part_io
Write array of 64 bit floating point data to file.
After setting the number of elements with \c H5PartSetNumParticles() and
@@ -59,8 +63,6 @@ H5PartWriteDataFloat64 (
}
/**
\ingroup h5part_io
Write array of 32 bit floating point data to file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -81,8 +83,6 @@ H5PartWriteDataFloat32 (
}
/**
\ingroup h5part_io
Write array of 64 bit integer data to file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -103,8 +103,6 @@ H5PartWriteDataInt64 (
}
/**
\ingroup h5part_io
Write array of 32 bit integer data to file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -125,8 +123,6 @@ H5PartWriteDataInt32 (
}
/**
\ingroup h5part_io
Read array of 64 bit floating point data from file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -147,8 +143,6 @@ H5PartReadDataFloat64 (
}
/**
\ingroup h5part_io
Read array of 32 bit floating point data from file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -169,8 +163,6 @@ H5PartReadDataFloat32 (
}
/**
\ingroup h5part_io
Read array of 64 bit integer data from file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -191,8 +183,6 @@ H5PartReadDataInt64 (
}
/**
\ingroup h5part_io
Read array of 32 bit integer data from file.
See \ref H5PartWriteDataFloat64() for more details.
@@ -216,4 +206,6 @@ H5PartReadDataInt32 (
}
#endif
///< @}
#endif
src/include/H5Part_model.h
+11 -33
View File
@@ -15,13 +15,17 @@
#include "h5core/h5_debug.h"
#include "h5core/h5u_model.h"
/**
\ingroup h5part_c_api
\addtogroup h5part_model
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5part_model
Set the number of points/particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
@@ -60,8 +64,6 @@ H5PartSetNumPoints (
}
/**
\ingroup h5part_model
\see H5PartSetNumPoints()
*/
static inline h5_err_t
@@ -77,8 +79,6 @@ H5PartSetNumParticles (
}
/**
\ingroup h5part_model
Set the number of particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
@@ -119,8 +119,6 @@ H5PartSetNumParticlesStrided (
}
/**
\ingroup h5part_model
Define the chunk \c size and enables chunking in the underlying
HDF5 layer.
@@ -148,8 +146,6 @@ H5PartSetChunkSize (
}
/**
\ingroup h5part_model
Get the number of datasets that are stored at the current time-step.
\return number of datasets in current timestep
@@ -166,8 +162,6 @@ H5PartGetNumDatasets (
}
/**
\ingroup h5part_model
This reads the name of a dataset specified by it's index in the current
time-step.
@@ -194,8 +188,6 @@ H5PartGetDatasetName (
}
/**
\ingroup h5part_model
Gets the name, type and number of elements of a dataset based on its
index in the current timestep.
@@ -232,8 +224,6 @@ H5PartGetDatasetInfo (
}
/**
\ingroup h5part_model
This function returns the number of particles in this processor's view,
if a view has been set.
@@ -263,8 +253,6 @@ H5PartGetNumPoints (
}
/**
\ingroup h5part_model
\see H5PartGetNumPoints()
*/
static inline h5_ssize_t
@@ -278,8 +266,6 @@ H5PartGetNumParticles (
}
/**
\ingroup h5part_model
Reset the view.
\return \c H5_SUCCESS on success
@@ -296,15 +282,13 @@ H5PartResetView (
}
/**
\ingroup h5part_model
Check whether a view has been set, either automatically with
\ref H5PartSetNumParticles() or manually with \ref H5PartSetView
or \ref H5PartSetViewIndices.
\return \c H5_OK if view has been set.
\return \c H5_NOK if no view has been set.
\return \c H5_FAILURE on error.
\return true (value \c >0) if step exists
\return false (\c 0) if step does not exist
\return \c H5_FAILURE on error
*/
static inline h5_err_t
H5PartHasView (
@@ -317,8 +301,6 @@ H5PartHasView (
}
/**
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
particle dataset to operate on.
@@ -351,8 +333,6 @@ H5PartSetView (
}
/**
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
dataset to operate on by specifying a list of indices.
@@ -387,8 +367,6 @@ H5PartSetViewIndices (
}
/**
\ingroup h5part_model
Allows you to query the current view. Start and End
will be \c -1 if there is no current view established.
Use \c H5PartHasView() to see if the view is smaller than the
@@ -410,8 +388,6 @@ H5PartGetView (
}
/**
\ingroup h5part_model
If it is too tedious to manually set the start and end coordinates
for a view, \c H5SetCanonicalView() will automatically select an
appropriate domain decomposition of the data arrays for the degree
@@ -434,4 +410,6 @@ H5PartSetCanonicalView (
}
#endif
///< @}
#endif
src/include/H5_attribs.h
+14 -52
View File
@@ -17,6 +17,12 @@
#include "h5core/h5_debug.h"
#include "h5core/h5_attribs.h"
/**
\ingroup h5_c_api
\addtogroup h5_file_attribs
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
@@ -36,8 +42,6 @@ extern "C" {
*/
/**
\ingroup h5hut_file_attribs
Gets the number of attributes in the file's root ("/").
\return Number of attributes
@@ -54,8 +58,6 @@ H5GetNumFileAttribs (
}
/**
\ingroup h5hut_file_attribs
Gets the name, type and number of elements of the file attribute
specified by its index.
@@ -95,8 +97,6 @@ H5GetFileAttribInfo (
}
/**
\ingroup h5hut_file_attribs
Get the type and number of elements of the file attribute
specified by its name.
@@ -138,8 +138,6 @@ H5GetFileAttribInfoByName (
*/
/**
\ingroup h5hut_file_attribs
Write an attribute \c name with the string \c value to
the file root ("/").
@@ -164,8 +162,6 @@ H5WriteFileAttribString (
}
/**
\ingroup h5hut_file_attribs
Read a string into a \c buffer from an attribute \c name
in the file root ("/").
@@ -189,8 +185,6 @@ H5ReadFileAttribString (
}
/**
\ingroup h5hut_file_attribs
Write an attribute \c name with float64 \c values to
the file root ("/").
@@ -216,8 +210,6 @@ H5WriteFileAttribFloat64 (
}
/**
\ingroup h5hut_file_attribs
Read float64 values into a \c buffer from an attribute \c name
in the file root ("/").
@@ -242,8 +234,6 @@ H5ReadFileAttribFloat64 (
/**
\ingroup h5hut_file_attribs
Write an attribute \c name with float32 \c values to
the file root ("/").
@@ -269,8 +259,6 @@ H5WriteFileAttribFloat32 (
}
/**
\ingroup h5hut_file_attribs
Read float32 values into a \c buffer from an attribute \c name
in the file root ("/").
@@ -294,8 +282,6 @@ H5ReadFileAttribFloat32 (
}
/**
\ingroup h5hut_file_attribs
Write an attribute \c name with int64 \c values to
the file root ("/").
@@ -321,8 +307,6 @@ H5WriteFileAttribInt64 (
}
/**
\ingroup h5hut_file_attribs
Read int64 values into a \c buffer from an attribute \c name
in the file root ("/").
@@ -346,8 +330,6 @@ H5ReadFileAttribInt64 (
}
/**
\ingroup h5hut_file_attribs
Write an attribute \c name with int32 \c values to
the file root ("/").
@@ -373,8 +355,6 @@ H5WriteFileAttribInt32 (
}
/**
\ingroup h5hut_file_attribs
Read int32 values into a \c buffer from an attribute \c name
in the file root ("/").
@@ -396,6 +376,13 @@ H5ReadFileAttribInt32 (
H5_INT32_T,
(void*)buffer));
}
///< @}
/**
\ingroup h5_c_api
\addtogroup h5_step_attribs
@{
*/
/*
_ _ _ _ _ _
@@ -413,8 +400,6 @@ H5ReadFileAttribInt32 (
*/
/**
\ingroup h5hut_step_attribs
Gets the number of attributes bound to the current step.
\return Number of attributes
@@ -431,8 +416,6 @@ H5GetNumStepAttribs (
}
/**
\ingroup h5hut_step_attribs
Gets the name, type and number of elements of the step attribute
specified by its index.
@@ -473,8 +456,6 @@ H5GetStepAttribInfo (
}
/**
\ingroup h5hut_step_attribs
Gets the type and number of elements of the step attribute
specified by its name.
@@ -517,8 +498,6 @@ H5GetStepAttribInfoByName (
*/
/**
\ingroup h5hut_step_attribs
Write an attribute \c name with the string \c value to
the current timestep.
@@ -543,8 +522,6 @@ H5WriteStepAttribString (
}
/**
\ingroup h5hut_step_attribs
Read a string into a \c buffer from an attribute \c name
in the current timestep.
@@ -568,8 +545,6 @@ H5ReadStepAttribString (
}
/**
\ingroup h5hut_step_attribs
Write an attribute \c name with float64 \c values to
the current time step.
@@ -595,8 +570,6 @@ H5WriteStepAttribFloat64 (
}
/**
\ingroup h5hut_step_attribs
Read float64 values into a \c buffer from an attribute \c name
in the current time step.
@@ -620,8 +593,6 @@ H5ReadStepAttribFloat64 (
}
/**
\ingroup h5hut_step_attribs
Write an attribute \c name with float32 \c values to
the current time step.
@@ -647,8 +618,6 @@ H5WriteStepAttribFloat32 (
}
/**
\ingroup h5hut_step_attribs
Read float32 values into a \c buffer from an attribute \c name
in the current time step.
@@ -672,8 +641,6 @@ H5ReadStepAttribFloat32 (
}
/**
\ingroup h5hut_step_attribs
Write an attribute \c name with int64 \c values to
the current time step.
@@ -699,8 +666,6 @@ H5WriteStepAttribInt64 (
}
/**
\ingroup h5hut_step_attribs
Read int64 values into a \c buffer from an attribute \c name
in the current time step.
@@ -725,8 +690,6 @@ H5ReadStepAttribInt64 (
}
/**
\ingroup h5hut_step_attribs
Write an attribute \c name with int32 \c values to
the current time step.
@@ -752,8 +715,6 @@ H5WriteStepAttribInt32 (
}
/**
\ingroup h5hut_step_attribs
Read int32 values into a \c buffer from an attribute \c name
in the current time step.
@@ -776,6 +737,7 @@ H5ReadStepAttribInt32 (
(void*)buffer));
}
///< @}
#ifdef __cplusplus
}
src/include/H5_model.h
+10 -32
View File
@@ -15,13 +15,17 @@
#include "h5core/h5_debug.h"
#include "h5core/h5_model.h"
/**
\ingroup h5_c_api
\addtogroup h5_model
@{
*/
#ifdef __cplusplus
extern "C" {
#endif
/**
\ingroup h5hut_model
Define format of the step names.
Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names
@@ -43,8 +47,6 @@ H5SetStepNameFormat (
}
/**
\ingroup h5hut_model
Get format of the step names.
\return \c H5_SUCCESS on success
@@ -64,8 +66,6 @@ H5GetStepNameFormat (
}
/**
\ingroup h5hut_model
Set the current step.
\return \c H5_SUCCESS on success
@@ -83,8 +83,6 @@ H5SetStep (
}
/**
\ingroup h5hut_model
Get current step.
\return Step number
@@ -101,8 +99,6 @@ H5GetStep (
}
/**
\ingroup h5hut_model
Get the number of processors.
\return Number of processors.
@@ -119,8 +115,6 @@ H5GetNumProcs (
}
/**
\ingroup h5hut_model
Get the number of time-steps that are currently stored in the file
\c f.
@@ -141,12 +135,10 @@ H5GetNumSteps (
}
/**
\ingroup h5hut_model
Query whether a particular step already exists in the file.
\return \c H5_OK if step exists
\return \c H5NOK if step does not exist
\return true (value \c >0) if step exists
\return false (\c 0) if step does not exist
\return \c H5_FAILURE on error
*/
static inline h5_err_t
@@ -161,8 +153,6 @@ H5HasStep (
}
/**
\ingroup h5hut_model
Start traversing steps.
\note This function is not yet implemented!
@@ -181,8 +171,6 @@ H5StartTraverseSteps (
}
/**
\ingroup h5hut_model
Go to next step.
\note This function is not yet implemented!
@@ -201,8 +189,6 @@ H5TraverseSteps (
}
/**
\ingroup h5hut_model
Return number of attached files.
\return number of attachments.
@@ -219,8 +205,6 @@ H5GetNumAttachments (
}
/**
\ingroup h5hut_model
Get name and size of attachment given by index \c idx. Return the file name
in \c fname and the original size in \c fsize.
@@ -245,8 +229,6 @@ H5GetAttachmentInfoByIdx (
}
/**
\ingroup h5hut_model
Get size of attached file with name \c fname.
\return \c H5_SUCCESS on success
@@ -264,8 +246,6 @@ H5GetAttachmentInfoByName (
}
/**
\ingroup h5hut_model
Attach file \c fname.
\return \c H5_SUCCESS on success
@@ -281,8 +261,6 @@ H5AddAttachment (
}
/**
\ingroup h5hut_model
Get attachment \c fname from H5hut file and write it to disk in
the current working directory.
@@ -299,8 +277,6 @@ H5GetAttachment (
}
/**
\ingroup h5hut_model
Delete attachment \c fname.
\return \c H5_SUCCESS on success
@@ -319,6 +295,8 @@ H5DeleteAttachment (
}
#endif
///< @}
#endif
src/include/H5hut.h
+4
View File
@@ -10,6 +10,10 @@
#ifndef __H5HUT_H
#define __H5HUT_H
#if !defined(H5HUT_API_VERSION)
#define H5HUT_API_VERSION 2
#endif
#include "H5.h"
#include "H5Part.h"
#include "H5Block.h"