reorganize language bindings

src/C/H5.c

@@ -0,0 +1,268 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+/*!
+  Some conventions:
+	Functions:
+		Name:
+			thisIsAFunction()
+		Return values:
+			negative value or NULL signals an error
+
+
+	Macros:
+		UPPERCASE_WITH_UNDERSCORE
+  \note
+  In function names we use the words \b get and \b store insteed of
+  \b read and \b write, because no I/O is actually done in these
+  functions.
+*/
+
+
+/*!
+  \ingroup h5_c_api
+  \defgroup h5_c_api_general
+*/
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_core_private.h"
+#include "H5.h"
+
+/******	General routines *****************************************************/
+
+/*!
+  \ingroup h5_c_api_general
+  
+  Open file with name \c filename. This function is available in the paralell
+  and serial version. In the serial case \c comm may have any value.
+
+  \return File handle.
+  \return NULL on error.
+*/
+h5_file_t *
+H5OpenFile (
+	const char * filename,		/*!< file name			*/
+	const h5_int32_t oflag,		/*!< file open flags		*/
+	const MPI_Comm comm		/*!< MPI communicator		*/
+	) {
+	return h5_open_file( filename, H5_O_RDWR, comm, __func__ ); 
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Close file.
+
+  \return \c H5_SUCCESS or error code
+*/
+h5_err_t
+H5CloseFile (
+	h5_file_t * const f		/*!< file handle		*/
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5_close_file ( f );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Define format of the step names.
+
+  Example: ==H5FedDefineStepNameFormat( f, "Step", 6 )== defines step names 
+  like ==Step#000042==.
+
+  \return \c H5_SUCCESS or error code
+*/
+h5_err_t
+H5DefineStepNameFormat (
+	h5_file_t *f,			/*!< Handle to file		*/
+	const char *name,		/*!< Prefix			*/
+	const h5_int64_t width		/*!< Width of the number	*/
+	) {
+	SET_FNAME ( f, __func__ );
+
+	return h5_set_stepname_fmt( f, name, width );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Get format of the step names.
+
+  \return value \c >=0 on success
+  \return -1 on error
+*/
+h5_err_t
+H5GetStepNameFormat (
+	h5_file_t *f,			/*!< Handle to file		*/
+	char *name,			/*!< OUT: Prefix		*/
+	const h5_size_t l_name,		/*!< length of buffer name	*/
+	h5_size_t *width		/*!< OUT: Width of the number	*/
+	) {
+	SET_FNAME ( f, __func__ );
+
+	return h5_get_stepname_fmt( f, name, l_name, width );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Set the current step.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_err_t
+H5SetStep (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t step		/*!< [in]  Step to set. */
+	) {
+
+	SET_FNAME ( f, __func__ );
+	return h5_set_step ( f, step );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Get current step.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_id_t
+H5GetStep (
+	h5_file_t *f			/*!< Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+	return h5_get_step ( f );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Start traversing steps.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_err_t
+H5StartTraverseSteps (
+	h5_file_t *f			/*!< Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5_start_traverse_steps( f );
+}
+
+/*!
+  \ingroup h5_c_api_general
+
+  Traverse steps.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_err_t
+H5TraverseSteps (
+	h5_file_t * f			/*!< Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5_traverse_steps( f );
+}
+
+/*!
+  \ingroup h5part_c_api
+  \defgroup h5part_c_api_errhandling	Error Handling
+*/
+
+/*!
+  \ingroup h5part_c_api_errhandling
+
+  Set verbosity level to \c level.
+
+  \return \c H5_SUCCESS
+*/
+h5_err_t
+H5SetVerbosityLevel (
+	const h5_id_t level
+	) {
+
+	return h5_set_debuglevel ( level );
+}
+
+/*!
+  \ingroup h5part_c_api_errhandling
+
+  Set error handler to \c handler.
+
+  \return \c H5_SUCCESS
+*/
+h5_err_t
+H5SetErrorHandler (
+	h5_errorhandler_t handler
+	) {
+  
+	return h5_set_errorhandler( handler );
+}
+
+/*!
+  \ingroup h5part_c_api_errhandling
+
+  Get current error handler.
+
+  \return Pointer to error handler.
+*/
+h5_errorhandler_t
+H5GetErrorHandler (
+	void
+	) {
+	return h5_get_errorhandler();
+}
+
+h5_err_t
+H5ReportErrorhandler (
+	h5_file_t * const f,
+	const char *fmt,
+	va_list ap
+	) {
+	return h5_report_errorhandler ( f, fmt, ap );
+}
+
+h5_err_t
+H5AbortErrorhandler (
+	h5_file_t * const f,
+	const char *fmt,
+	va_list ap
+	) {
+	return h5_abort_errorhandler ( f, fmt, ap );
+}
+
+/*!
+  \ingroup h5part_c_api_errhandling
+
+  Get last error code.
+
+  \return error code
+*/
+h5_err_t
+H5GetErrno (
+	h5_file_t * const f
+	) {
+	return h5_get_errno( f );
+}
+/*! @} */

src/C/H5.h

@@ -0,0 +1,108 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#ifndef __H5_H
+#define __H5_H
+
+#include "H5_inquiry.h"
+
+h5_file_t *
+H5OpenFile (
+	const char * filename,
+	const h5_int32_t oflag,
+	const MPI_Comm comm
+	);
+
+h5_err_t
+H5CloseFile (
+	h5_file_t * f
+	);
+
+h5_err_t
+H5SetStepNameFormat (
+	h5_file_t *f,
+	const char *name,
+	const h5_int64_t width
+	);
+
+h5_err_t
+H5GetStepNameFormat (
+	h5_file_t *f,
+	char *name,
+	const h5_size_t l_name,
+	h5_size_t *width
+	);
+
+h5_err_t
+H5SetStep (
+	h5_file_t *f,
+	const h5_int64_t step
+	);
+
+h5_int64_t
+H5GetStep (
+	h5_file_t *f
+	);
+
+h5_err_t
+H5StartTraverseSteps (
+	h5_file_t *f
+	);
+
+h5_id_t
+H5TraverseSteps (
+	h5_file_t *f
+	);
+
+h5_err_t
+H5EndTraverseSteps (
+	h5_file_t *f
+	);
+
+h5_err_t
+H5SetVerbosityLevel (
+	const h5_id_t level
+	);
+
+h5_err_t
+H5SetErrorHandler (
+	h5_errorhandler_t handler
+	);
+
+h5_errorhandler_t
+H5GetErrorHandler (
+	void
+	);
+
+h5_err_t
+H5ReportErrorhandler (
+	h5_file_t * const f,
+	const char *fmt,
+	va_list ap
+	);
+
+h5_err_t
+H5AbortErrorhandler (
+	h5_file_t * const f,
+	const char *fmt,
+	va_list ap
+	);
+
+h5_err_t
+H5GetErrno (
+	h5_file_t * const f
+	);
+
+#endif

src/C/H5Block.h

@@ -0,0 +1,204 @@
+#ifndef __H5BLOCK_H
+#define __H5BLOCK_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! 
+  Interface for block structured field data
+
+*/
+
+h5_int64_t
+H5BlockDefine3DFieldLayout (
+	h5_file_t *f,
+	const h5_int64_t i_start,
+	const h5_int64_t i_end,
+	const h5_int64_t j_start,
+	const h5_int64_t j_end,
+	const h5_int64_t k_start,
+	const h5_int64_t k_end
+	);
+
+h5_int64_t
+H5Block3dGetPartitionOfProc (
+	h5_file_t *f,
+	const h5_int64_t proc,
+	h5_int64_t *i_start,
+	h5_int64_t *i_end,
+	h5_int64_t *j_start,
+	h5_int64_t *j_end,
+	h5_int64_t *k_start,
+	h5_int64_t *k_end
+	);
+
+h5_int64_t
+H5Block3dGetReducedPartitionOfProc (
+	h5_file_t *f,
+	h5_int64_t proc,
+	h5_int64_t *i_start, 
+	h5_int64_t *i_end,
+	h5_int64_t *j_start,
+	h5_int64_t *j_end,
+	h5_int64_t *k_start,
+	h5_int64_t *k_end
+	);
+
+h5_int64_t
+H5Block3dGetProcOf (
+	h5_file_t *f,
+	h5_int64_t i,
+	h5_int64_t j,
+	h5_int64_t k
+	);
+
+h5_int64_t
+H5Block3dWriteScalarField (
+	h5_file_t *f,
+	const char *name,
+	const h5_float64_t *data
+	);
+
+h5_int64_t
+H5Block3dReadScalarField (
+	h5_file_t *f,
+	const char *name,
+	h5_float64_t *data
+	);
+
+h5_int64_t
+H5BlockGetNumFields (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5BlockGetFieldInfo (
+	h5_file_t *f,
+	const h5_int64_t idx,
+	char *name,
+	const h5_int64_t len_name,
+	h5_int64_t *grid_rank,
+	h5_int64_t *grid_dims,
+	h5_int64_t *field_dims
+	);
+
+h5_int64_t
+H5BlockGetFieldInfoByName (
+	h5_file_t *f,
+	const char *field_name,
+	h5_int64_t *grid_rank,
+	h5_int64_t *grid_dims,
+	h5_int64_t *field_dims
+	);
+
+h5_int64_t
+H5Block3dGetFieldOrigin (
+	h5_file_t *f,
+	const char *field_name,
+	h5_float64_t *x_origin,
+	h5_float64_t *y_origin,
+	h5_float64_t *z_origin
+	);
+
+h5_int64_t
+H5Block3dSetFieldOrigin (
+	h5_file_t *f,
+	const char *field_name,
+	const h5_float64_t x_origin,
+	const h5_float64_t y_origin,
+	const h5_float64_t z_origin
+	);
+
+h5_int64_t
+H5Block3dGetFieldSpacing (
+	h5_file_t *f,
+	const char *field_name,
+	h5_float64_t *x_spacing,
+	h5_float64_t *y_spacing,
+	h5_float64_t *z_spacing
+	);
+
+h5_int64_t
+H5Block3dSetFieldSpacing (
+	h5_file_t *f,
+	const char *field_name,
+	const h5_float64_t x_spacing,
+	const h5_float64_t y_spacing,
+	const h5_float64_t z_spacing
+	);
+
+
+
+h5_int64_t
+H5Block3dWrite3dVectorField (
+	h5_file_t *f,
+	const char *name,
+	const h5_float64_t *xval,
+	const h5_float64_t *yval,
+	const h5_float64_t *zval
+	);	
+
+h5_int64_t
+H5Block3dRead3dVectorField (
+	h5_file_t *f,
+	const char *name,
+	h5_float64_t *xval,
+	h5_float64_t *yval,
+	h5_float64_t *zval
+	);
+
+h5_int64_t
+H5BlockWriteFieldAttrib (
+	h5_file_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5_int64_t attrib_type,
+	const void *attrib_value,
+	const h5_int64_t attrib_nelem
+	);
+
+h5_int64_t
+H5BlockWriteFieldAttribString (
+	h5_file_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const char *attrib_value
+	);
+
+h5_int64_t
+H5BlockGetNumFieldAttribs (
+	h5_file_t *f,
+	const char *field_name
+	);
+
+h5_int64_t
+H5BlockGetFieldAttribInfo (
+	h5_file_t *f,
+	const char *field_name,
+	const h5_int64_t attrib_idx,
+	char *attrib_name,
+	const h5_int64_t len_of_attrib_name,
+	h5_int64_t *attrib_type,
+	h5_int64_t *attrib_nelem
+	);
+
+h5_int64_t
+H5BlockReadFieldAttrib (
+	h5_file_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	void *attrib_value
+	);
+
+h5_int64_t
+H5BlockHasFieldData (
+	h5_file_t *f
+	);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

src/C/H5Fed.c

@@ -0,0 +1,54 @@
+/*
+  Copyright 2007-2009
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_core_private.h"
+#include "H5Fed.h"
+
+h5_err_t
+H5FedOpenMesh (
+	h5_file_t * const f,
+	const h5_id_t mesh_id,
+	const h5_oid_t mesh_type_id
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_open_mesh ( f, mesh_id, mesh_type_id );
+}
+
+h5_err_t
+H5FedCloseMesh (
+	h5_file_t * const f
+	) {
+	return h5_error_not_implemented ( f, __FILE__, __func__, __LINE__ );
+}
+
+h5_err_t
+H5FedSetLevel (
+	h5_file_t * const f,
+	const h5_id_t level_id
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_open_level ( f, level_id );
+}
+
+h5_err_t
+H5FedLinkMeshToStep (
+	h5_file_t * f,
+	const h5_id_t mesh_id
+	) {
+	return h5_error_not_implemented ( f, __FILE__, __func__, __LINE__ );
+}

src/C/H5Fed.h

@@ -0,0 +1,70 @@
+/*
+  Header file for declaring the H5Fed application programming
+  interface (API) in the C language.
+  
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#ifndef __H5FED_H
+#define __H5FED_H
+
+#include "H5.h"
+#include "H5Fed_adjacency.h"
+#include "H5Fed_inquiry.h"
+#include "H5Fed_map.h"
+#include "H5Fed_retrieve.h"
+#include "H5Fed_store.h"
+#include "H5Fed_tags.h"
+
+/******	General routines *****************************************************/
+
+h5_err_t
+H5FedOpenMesh (
+	h5_file_t * const f,
+	const h5_id_t mesh_id,
+	const h5_oid_t mesh_type_id
+	);
+
+h5_err_t
+H5FedCloseMesh (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedSetLevel (
+	h5_file_t * f,
+	const h5_id_t level_id
+	);
+
+h5_err_t
+H5FedLinkMeshToStep (
+	h5_file_t * f,
+	const h5_id_t mesh_id
+	);
+
+
+
+#endif
+
+
+
+
+
+
+
+
+
+
+
+

src/C/H5Fed_adjacency.c

@@ -0,0 +1,153 @@
+/*
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <hdf5.h>
+#include "h5_core/h5_types.h"
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+/******	UPWARD ADJACENCY routines *********************************************/
+
+/*!
+  \return	number of upward adjacent edges 
+ */
+h5_err_t
+H5FedGetEdgesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_edges_upadjacent_to_vertex ( f, local_vid, list );
+}
+
+h5_err_t
+H5FedGetTrianglesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_triangles_upadjacent_to_vertex ( f, local_vid, list );
+}
+
+h5_err_t
+H5FedGetTetsUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_tets_upadjacent_to_vertex ( f, local_vid, list );
+}
+
+h5_err_t
+H5FedGetTrianglesUpAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_triangles_upadjacent_to_edge ( f, local_kid, list );
+}
+
+h5_err_t
+H5FedGetTetsUpAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_tets_upadjacent_to_edge ( f, local_kid, list );
+}
+
+h5_err_t
+H5FedGetTetsUpAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_tets_upadjacent_to_triangle ( f, local_did, list );
+}
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_vertices_downadjacent_to_edge ( f, local_kid, list );
+}
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_vertices_downadjacent_to_triangle ( f, local_did, list );
+}
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_vertices_downadjacent_to_tet ( f, local_tid, list );
+}
+
+h5_err_t
+H5FedGetEdgesDownAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_edges_downadjacent_to_triangle ( f, local_did, list );
+}
+
+h5_err_t
+H5FedGetEdgesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_edges_downadjacent_to_tet ( f, local_tid, list );
+}
+
+h5_err_t
+H5FedGetTrianglesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_triangles_downadjacent_to_tet ( f, local_tid, list );
+}
+
+h5_err_t
+H5FedReleaseListOfAdjacencies (
+	h5_file_t * const f,
+	h5_idlist_t **list
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5priv_free_idlist ( f, list );
+}

src/C/H5Fed_adjacency.h

@@ -0,0 +1,94 @@
+#ifndef __H5FED_ADJACENCY_H
+#define __H5FED_ADJACENCY_H
+
+h5_err_t
+H5FedGetEdgesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTrianglesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTetsUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTrianglesUpAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTetsUpAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTetsUpAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToEdge (
+	h5_file_t * const f,
+	const h5_id_t local_kid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetVerticesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetEdgesDownAdjacentToTriangle (
+	h5_file_t * const f,
+	const h5_id_t local_did,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetEdgesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedGetTrianglesDownAdjacentToTet (
+	h5_file_t * const f,
+	const h5_id_t local_tid,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+H5FedReleaseListOfAdjacencies (
+	h5_file_t * const f,
+	h5_idlist_t **list
+	);
+
+#endif

src/C/H5Fed_inquiry.c

@@ -0,0 +1,169 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+/*!
+  \ingroup h5fed_c_api
+  \defgroup h5fed_mesh_inquiry
+*/
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+/*!
+  Get number of meshes of given type.
+
+  \param[in]	f	File handle
+  \param[in]	type_id	Type of mesh we want the number of.
+
+  \return	Number of meshes of type \c type_id or error code.
+ */
+h5_size_t
+H5FedGetNumMeshes ( 
+	h5_file_t * const f,
+	const h5_oid_t type_id
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_meshes ( f, type_id );
+}
+
+/*!
+  Get the number of hierarchical mesh levels.
+
+  \param[in]	f	File handle
+
+  \return	Number of hierarchical mesh levels or error code.
+ */
+h5_size_t
+H5FedGetNumLevels (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_levels ( f );
+}
+
+/*!
+  Get current mesh levels.
+
+  \param[in]	f	File handle
+
+  \return	ID of current mesh levels or error code.
+ */
+h5_id_t
+H5FedGetLevel (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_level ( f );
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level on this compute node.
+
+  \param[in]	f	file handle
+
+  \return	Number of vertices or error code.
+*/
+h5_size_t
+H5FedGetNumVertices (
+	h5_file_t * const f		/*!< file handle		*/
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_vertices ( f, f->myproc );
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level on compute node \c cnode.
+
+  \param[in]	f	file handle
+  \param[in]	cnode	compute node
+
+  \return	Number of vertices or error code.
+*/
+h5_size_t
+H5FedGetNumVerticesCnode (
+	h5_file_t * const f,
+	const h5_id_t cnode
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_vertices ( f, cnode );
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level overl all compute nodes.
+
+  \param[in]	f	file handle
+
+  \return	Total number of vertices or error code.
+*/
+h5_size_t
+H5FedGetNumVerticesTotal (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_vertices ( f, -1 );
+}
+
+/*!
+  Returns the number of elements present in the (sub-)mesh
+  at current level on this compute node.
+
+  \param[in]	f	file handle
+
+  \return	Number of elements or error code.
+*/
+h5_size_t
+H5FedGetNumElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_elems ( f, f->myproc );
+}
+
+/*!
+  Returns the number of elements present in the (sub-)mesh
+  at current level on compute node \c cnode.
+
+  \param[in]	f	file handle
+  \param[in]	cnode	Compute node
+
+  \return	Number of elements or error code.
+*/
+h5_size_t
+H5FedGetNumElementsCnode (
+	h5_file_t * const f,
+	const h5_id_t cnode
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_elems ( f, cnode );
+}
+/*!
+  Returns the number of elements present in the mesh
+  at current level over all compute nodes.
+
+  \param[in]	f	File handle.
+
+  \return	Number of elements or error code.
+*/
+h5_size_t
+H5FedGetNumElementsTotal (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_num_elems ( f, -1 );
+}

src/C/H5Fed_inquiry.h

@@ -0,0 +1,30 @@
+/*
+  Header file for declaring the H5Fed application programming
+  interface (API) in the C language.
+  
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+#ifndef __H5FED_INQUIRY_H
+#define __H5FED_INQUIRY_H
+
+h5_size_t H5FedGetNumMeshes ( h5_file_t * const f, const h5_oid_t type_id );
+h5_size_t H5FedGetNumLevels ( h5_file_t * const f );
+h5_id_t H5FedGetLevel ( h5_file_t * const f );
+h5_size_t H5FedGetNumVertices ( h5_file_t * const f );
+h5_size_t H5FedGetNumVerticesCnode ( h5_file_t * const f, const h5_id_t cnode );
+h5_size_t H5FedGetNumVerticesTotal ( h5_file_t * const f );
+h5_size_t H5FedGetNumElements ( h5_file_t * const f );
+h5_size_t H5FedGetNumElementsCnode ( h5_file_t * const f, const h5_id_t cnode );
+h5_size_t H5FedGetNumElementsTotal ( h5_file_t * const f );
+#endif

src/C/H5Fed_map.c

@@ -0,0 +1,53 @@
+/*
+  Copyright 2007-2009
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+/*!
+  \ingroup h5fed_c_api
+  \defgroup h5fed_map
+*/
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+h5_err_t
+H5FedLMapEdgeID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *local_vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_local_vids_of_edge ( f, local_id, local_vids );
+}
+
+h5_err_t
+H5FedLMapTriangleID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *local_vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_local_vids_of_triangle ( f, local_id, local_vids );
+}
+
+h5_err_t
+H5FedLMapTetID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *local_vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_local_vids_of_tet ( f, local_id, local_vids );
+}

src/C/H5Fed_map.h

@@ -0,0 +1,44 @@
+/*
+  Header file for declaring the H5Fed application programming
+  interface (API) in the C language.
+  
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#ifndef __H5FED_MAP_H
+#define __H5FED_MAP_H
+
+h5_err_t
+H5FedLMapEdgeID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *localvids
+	);
+
+h5_err_t
+H5FedLMapTriangleID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *localvids
+	);
+
+h5_err_t
+H5FedLMapTetID2VertexIDs (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *localvids
+	);
+
+#endif
+

src/C/H5Fed_retrieve.c

@@ -0,0 +1,238 @@
+/******	RETRIEVAL routines **************************************************/
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+
+/*!
+  Begin traverse over all vertices on this compute node. 
+  Initialize internal data structures.
+
+  \remark
+  Vertices can be on processor boundaries! Therefore the same vertex can be
+  processed on several compute nodes.
+
+  \param[in]	f	file handle
+
+  \return	H5_SUCCESS or error code
+*/
+h5_err_t
+H5FedBeginTraverseVertices (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_traverse_vertices ( f );
+}
+
+/*!
+  Get coordinates of next vertex.
+
+  \param[in]	f	file handle
+  \param[out]	P	3-dimensional coordinates
+
+  \return	Local vertex ID
+  \return	-1, if done
+  \return	error code on error
+  */
+h5_id_t
+H5FedTraverseVertices (
+	h5_file_t * const f,
+	h5_float64_t P[3]
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_traverse_vertices ( f, P );
+}
+
+/*!
+  End of traversing. Release internal data structures.
+
+  \param[in]	f	File handle
+
+  \return	H5_SUCCESS or error code
+ 
+ */
+h5_err_t
+H5FedEndTraverseVertices (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_traverse_vertices ( f );
+}
+
+/*!
+  Begin traverse over all edges on this compute node. 
+  Initialize internal data structures.
+
+  \remark
+  Edges can be on processor boundaries! Therefore the same edge can be
+  processed on several compute nodes.
+
+  \param[in]	f	file handle
+
+  \return	H5_SUCCESS or error code
+*/
+h5_err_t
+H5FedBeginTraverseEdges (
+	h5_file_t * const f  		/*!< file handle		*/
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_traverse_edges ( f );
+}
+
+/*!
+  Get local edge id and vertices of next edge.
+
+  \param[in]	f	file handle
+  \param[out]	vids	local vertex IDs
+
+  \return	Local edge ID
+  \return	-1, if done
+  \return	error code on error
+  */
+h5_id_t
+H5FedTraverseEdges (
+	h5_file_t * const f,
+	h5_id_t * const vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_traverse_edges ( f, vids );
+}
+
+/*!
+  End of traversing. Release internal data structures.
+
+  \param[in]	f	File handle
+
+  \return	H5_SUCCESS or error code
+  */
+h5_err_t
+H5FedEndTraverseEdges (
+	h5_file_t * const f		/*!< file handle		*/
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_traverse_edges ( f );
+}
+
+/*!
+  Begin traverse over all triangles on this compute node. 
+  Initialize internal data structures.
+
+  \remark
+  Triangles can be on processor boundaries! Therefore the same vertex can be
+  processed on several compute nodes.
+
+  \param[in]	f	file handle
+
+  \return	H5_SUCCESS or error code
+*/
+h5_err_t
+H5FedBeginTraverseTriangles (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_traverse_triangles ( f );
+}
+
+/*!
+  Get local triangle ID and vertices of next triangle.
+
+  \param[in]	f	file handle
+  \param[out]	vids	local vertex IDs
+
+  \return	Local triangle ID
+  \return	-1, if done
+  \return	error code on error
+  */
+h5_id_t
+H5FedTraverseTriangles (
+	h5_file_t * const f,
+	h5_id_t * const vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_traverse_triangles ( f, vids );
+}
+
+/*!
+  End of traversing. Release internal data structures.
+
+  \param[in]	f	File handle
+
+  \return	H5_SUCCESS or error code
+  */
+h5_err_t
+H5FedEndTraverseTriangles (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_traverse_triangles ( f );
+}
+
+/*!
+  Begin traverse over all elements on this compute node. 
+  Initialize internal data structures.
+
+  \remark
+  Elements are unique per compute node. Ghost elements are *not* return 
+  while traversing.
+
+  \param[in]	f	file handle
+
+  \return	H5_SUCCESS or error code
+*/
+h5_err_t
+H5FedBeginTraverseElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_traverse_elems ( f );
+}
+
+/*!
+  Get local element ID and vertices of next element.
+
+  \param[in]	f	file handle
+  \param[out]	vids	local vertex IDs
+
+  \return	Local element ID
+  \return	-1, if done
+  \return	error code on error
+  */
+h5_id_t
+H5FedTraverseElements (
+	h5_file_t * const f,
+	h5_id_t * const vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_traverse_elems ( f, vids );
+}
+
+/*!
+  End of traversing. Release internal data structures.
+
+  \param[in]	f	File handle
+
+  \return	H5_SUCCESS or error code
+  */
+h5_id_t
+H5FedEndTraverseElements (
+	h5_file_t * const f
+	) {
+	return h5t_end_traverse_elems ( f );
+}
+

src/C/H5Fed_retrieve.h

@@ -0,0 +1,33 @@
+/*
+  Copyright 2007-2009
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+#ifndef __H5FED_RETRIEVE_H
+#define __H5FED_RETRIEVE_H
+
+h5_err_t H5FedBeginTraverseVertices ( h5_file_t * const f );
+h5_id_t H5FedTraverseVertices ( h5_file_t * const f, h5_float64_t P[3] );
+h5_err_t H5FedEndTraverseVertices ( h5_file_t * const f	);
+
+h5_err_t H5FedBeginTraverseEdges ( h5_file_t * const f );
+h5_id_t H5FedTraverseEdges ( h5_file_t * const f, h5_id_t * const vids );
+h5_err_t H5FedEndTraverseEdges ( h5_file_t * const f );
+
+h5_err_t H5FedBeginTraverseTriangles ( h5_file_t * const f );
+h5_id_t H5FedTraverseTriangles ( h5_file_t * const f, h5_id_t * const vids );
+h5_err_t H5FedEndTraverseTriangles ( h5_file_t * const f );
+
+h5_err_t H5FedBeginTraverseElements ( h5_file_t * const f );
+h5_id_t H5FedTraverseElements ( h5_file_t * const f, h5_id_t * const vids );
+h5_err_t H5FedEndTraverseElements ( h5_file_t * const f );
+#endif

src/C/H5Fed_store.c

@@ -0,0 +1,171 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+
+h5_id_t
+H5FedAddMesh (
+	h5_file_t * const f,
+	const h5_oid_t mesh_type_id
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_add_mesh ( f, mesh_type_id );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Add a new level with \c num_elems elements. The number of elements must be the
+  real number of elements to add the level. If you want to refine \c n tetrahedra
+  \c n*8 elements must be added.
+
+  \param[in]	f			File handle.
+  \param[in]	num_elems_to_refine	Number of elements which will be refined.
+
+  \return ID of new level.
+
+  \note
+  values for f->t.num_levels:
+  \c -1		unknown: after opening the file. This is equivalent to
+		"topological data has not been initialized".
+  \c 0		no levels: HDF5 group for meshes may already exist but must not!
+  \c > 0	number of mesh levels
+ 
+*/
+h5_id_t
+H5FedAddLevel (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_add_level ( f );
+}
+
+h5_err_t
+H5FedBeginStoreVertices (
+	h5_file_t * const f,
+	const h5_size_t num
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_store_vertices ( f, num );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the the coordinates of a specific vertex at level \c level
+  with id \c vertex_id of the tetrahedral mesh.
+
+  \return local vertex id on success
+  \return errno on error
+*/
+h5_id_t
+H5FedStoreVertex (
+	h5_file_t * const f,		/*!< file handle		*/
+	const h5_id_t vertex_id,	/*!< id from mesher or -1	*/
+	const h5_float64_t P[3]		/*!< coordinates		*/
+	) {
+
+	SET_FNAME ( f, __func__ );
+	if ( h5t_get_level ( f ) != 0 ) {
+		return h5_error (
+			f,
+			H5_ERR_INVAL,
+			"Vertices can be added to level 0 only!" );
+	}
+	return h5t_store_vertex ( f, vertex_id, P );
+}
+
+h5_err_t
+H5FedEndStoreVertices (
+	h5_file_t * const f
+	) {
+	return h5t_end_store_vertices ( f );
+}
+
+h5_err_t
+H5FedBeginStoreElements (
+	h5_file_t * f,
+	const h5_size_t num
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_store_elems ( f, num );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the 4-tuple, that contains the specific indices describing
+  a tetrahedron with id \c tet_id at level \c level of the tetrahedral
+  mesh.
+
+  Errors:
+  * current level not yet defined
+  * to many tets stored on level
+
+  \return local tetrahedron id
+  \return \c errno on error
+*/
+h5_id_t
+H5FedStoreElement (
+	h5_file_t * const f,		/*!< file handle		*/
+	const h5_id_t local_vids[]	/*!< tuple with vertex id's	*/
+	) {
+	SET_FNAME ( f, __func__ );
+	if ( h5t_get_level ( f ) != 0 ) {
+		return h5_error (
+			f,
+			H5_ERR_INVAL,
+			"Elements can be added to level 0 only!" );
+	}
+	return h5t_store_elem ( f, -1, local_vids );
+}
+
+h5_err_t
+H5FedEndStoreElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_store_elems ( f );
+}
+
+h5_err_t
+H5FedBeginRefineElements (
+	h5_file_t * const f,
+	const h5_size_t num
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_refine_elems ( f, num );
+}
+
+h5_id_t
+H5FedRefineElement (
+	h5_file_t * const f,		/*!< file handle		*/
+	const h5_id_t local_eid		/*!< local element id		*/
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_refine_elem ( f, local_eid );
+}
+
+h5_err_t
+H5FedEndRefineElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_refine_elems ( f );
+}

src/C/H5Fed_store.h

@@ -0,0 +1,93 @@
+/*
+  Header file for declaring the H5Fed application programming
+  interface (API) in the C language.
+  
+  Copyright 2006-2009
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#ifndef __H5FED_STORE_H
+#define __H5FED_STORE_H
+
+h5_id_t
+H5FedAddMesh (
+	h5_file_t * const f,
+	const h5_oid_t mesh_type_id
+	);
+
+h5_id_t
+H5FedAddLevel (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedBeginStoreVertices (
+	h5_file_t * const f,
+	const h5_size_t num
+	);
+
+h5_id_t
+H5FedStoreVertex (
+	h5_file_t * const f,
+	const h5_id_t id,
+	const h5_float64_t P[3]
+	);
+
+h5_err_t
+H5FedEndStoreVertices (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedBeginStoreElements (
+	h5_file_t * const f,
+	const h5_size_t num
+	);
+
+
+h5_id_t
+H5FedStoreElement (
+	h5_file_t * const f,
+	const h5_id_t local_vids[]
+	);
+
+h5_err_t
+H5FedEndStoreElements (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedBeginRefineElements (
+	h5_file_t * const f,
+	const h5_size_t num
+	);
+
+h5_id_t
+H5FedRefineElement (
+	h5_file_t * const f,
+	const h5_id_t eid
+	);
+
+h5_err_t
+H5FedEndRefineElements (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedMarkRefineElement (
+	h5_file_t * const f,
+	const h5_id_t eid
+	);
+
+
+#endif

src/C/H5Fed_tags.c

@@ -0,0 +1,201 @@
+/*
+  Copyright 2007-2009
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "H5Fed.h"
+
+/*!
+  Add a tagset to the current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset
+  \param[in]	type	data type of tagset
+
+  \return	H5_SUCCESS or error code
+ */
+h5_err_t
+H5FedAddMTagset (
+	h5_file_t * const f,
+	char * name,
+	h5_id_t type
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_add_mtagset ( f, name, type );
+}
+
+/*!
+  Remove a tagset from the current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset to remove
+
+  \return	H5_SUCCESS or error code
+ */
+h5_err_t
+H5FedRemoveMTagset (
+	h5_file_t *const f,
+	char name[]
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_remove_mtagset (f, name );
+}
+
+/*!
+  Get available tagsets in current mesh.
+
+  \param[in]	f	file handle
+  \param[out]	names	names of available tagsets
+
+  \return	Number of tagsets or error code
+ */
+h5_size_t
+H5FedGetMTagsets (
+	h5_file_t *const f,
+	char **names[]
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_mtagsets ( f, names );
+}
+
+/*!
+  Get type of tagset in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset
+
+  \return	H5_SUCCESS or error code
+ */
+h5_id_t
+H5FedGetTypeOfMTagset (
+	h5_file_t *const f,
+	char name[]
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_mtagset_type_by_name ( f, name );
+}
+
+/*!
+  Set tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+  \param[in]	dim	dimension of value
+  \param[in]	val	tag value
+
+  \return	H5_SUCCESS or error code
+ */
+h5_err_t
+H5FedSetMTag (
+	h5_file_t *const f,
+	char name[],
+	h5_id_t id,
+	const size_t dims,
+	void *val 
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_set_mtag_by_name ( f, name, id, dims, val );
+}
+
+h5_err_t
+H5FedSetMTagToVertex (
+	h5_file_t *const f,
+	char name[],
+	h5_id_t id,
+	const size_t dims,
+	void *val 
+	) {
+	SET_FNAME ( f, __func__ );
+	id = h5tpriv_set_entity_type ( H5T_ETYPE_VERTEX, id );
+	return h5t_set_mtag_by_name ( f, name, id, dims, val );
+}
+
+h5_err_t
+H5FedSetMTagToEdge (
+	h5_file_t *const f,
+	char name[],
+	h5_id_t id,
+	const size_t dims,
+	void *val 
+	) {
+	SET_FNAME ( f, __func__ );
+	id = h5tpriv_set_entity_type ( H5T_ETYPE_EDGE, id );
+	return h5t_set_mtag_by_name ( f, name, id, dims, val );
+}
+
+h5_err_t
+H5FedSetMTagToTriangle (
+	h5_file_t *const f,
+	char name[],
+	h5_id_t id,
+	const size_t dims,
+	void *val 
+	) {
+	SET_FNAME ( f, __func__ );
+	id = h5tpriv_set_entity_type ( H5T_ETYPE_TRIANGLE, id );
+	return h5t_set_mtag_by_name ( f, name, id, dims, val );
+}
+
+h5_err_t
+H5FedSetMTagToTet (
+	h5_file_t *const f,
+	char name[],
+	h5_id_t id,
+	const size_t dims,
+	void *val 
+	) {
+	SET_FNAME ( f, __func__ );
+	id = h5tpriv_set_entity_type ( H5T_ETYPE_TET, id );
+	return h5t_set_mtag_by_name ( f, name, id, dims, val );
+}
+
+/*!
+  Set tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+  \param[out]	dim	dimension of value
+  \param[out]	val	tag value
+
+  \return	H5_SUCCESS or error code
+ */
+h5_err_t
+H5FedGetMTag (
+	h5_file_t* const f,
+	const char name[],
+	const h5_id_t id,
+	size_t* dim,
+	void* vals
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_mtag_by_name ( f, name, id, dim, vals );
+}
+
+/*!
+  Remove tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+*/
+h5_err_t
+H5FedRemoveMTag (
+	h5_file_t *const f,
+	const char name[],
+	const h5_id_t id
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_remove_mtag_by_name ( f, name, id );
+}

src/C/H5Fed_tags.h

@@ -0,0 +1,40 @@
+#ifndef __H5FED_TAGS_H
+#define __H5FED_TAGS_H
+h5_err_t	H5FedAddMTagset ( h5_file_t * const f,
+				  char * name,
+				  h5_id_t type );
+h5_err_t	H5FedRemoveMTagset ( h5_file_t *const f,
+				     char name[] );
+h5_size_t	H5FedGetMTagsets ( h5_file_t *const f,
+				   char **names[] );
+h5_id_t		H5FedGetTypeOfMTagset ( h5_file_t *const f,
+					char name[] );
+h5_err_t	H5FedSetMTag ( h5_file_t *const f,
+			       char name[], h5_id_t id,
+			       const size_t dims, void *val );
+h5_err_t	H5FedSetMTagToVertex ( h5_file_t *const f,
+				       char name[], h5_id_t id,
+				       const size_t dims, void *val );
+h5_err_t	H5FedSetMTagToEdge ( h5_file_t *const f,
+				     char name[], h5_id_t id,
+				     const size_t dims, void *val );
+h5_err_t	H5FedSetMTagToTriangle ( h5_file_t *const f,
+					 char name[], h5_id_t id,
+					 const size_t dims, void *val );
+h5_err_t	H5FedSetMTagToTet ( h5_file_t *const f,
+				    char name[], h5_id_t id,
+				    const size_t dims, void *val );
+
+h5_err_t	H5FedGetMTag ( h5_file_t *const f,
+			       const char name[], const h5_id_t id, 
+			       size_t *dims, void *val );
+h5_err_t	H5FedRemoveMTag ( h5_file_t *const f,
+				  const char name[], const h5_id_t id );
+
+/*
+  Get descriptor for a tagset
+  Get tag value by descriptor
+  get size of value
+  Get tagset names for specific entity
+*/
+#endif

src/C/H5Part.c

@@ -0,0 +1,974 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>	/* va_arg - System dependent ?! */
+#include <string.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <hdf5.h>
+
+#ifndef WIN32
+#include <unistd.h>
+#else /* WIN32 */
+#include <io.h>
+#define open  _open
+#define close _close
+#endif /* WIN32 */
+
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_errorhandling_private.h"
+#include "H5Part.h"
+
+/********* Private Variable Declarations *************/
+
+
+/********** Declaration of private functions ******/
+
+
+/*========== File Opening/Closing ===============*/
+
+/*!
+  \ingroup h5part_c_api
+  \defgroup h5part_c_api_openclose	File Opening and Closing
+*/
+
+/*!
+  \ingroup h5part_c_api_openclose
+
+  Opens file with specified filename. 
+
+  If you open with flag \c H5PART_WRITE, it will truncate any
+  file with the specified filename and start writing to it. If 
+  you open with \c H5PART_APPEND, then you can append new steps.
+  If you open with \c H5PART_READ, then it will open the file
+  readonly.
+
+  The typical extension for these files is \c .h5.
+  
+  h5_file should be treated as an essentially opaque
+  datastructure.  It acts as the file handle, but internally
+  it maintains several key state variables associated with 
+  the file.
+
+  \return	File handle or \c NULL
+ */
+h5_file_t *
+H5PartOpenFileParallel (
+	const char *filename,	/*!< [in] The name of the data file to open. */
+	unsigned flags,		/*!< [in] The access mode for the file. */
+	MPI_Comm comm		/*!< [in] MPI communicator */
+) {
+	return h5_open_file ( filename, flags, comm, __func__ );
+}
+
+/*!
+  \ingroup  h5part_c_api_openclose
+
+  Opens file with specified filename. 
+
+  If you open with flag \c H5PART_WRITE, it will truncate any
+  file with the specified filename and start writing to it. If 
+  you open with \c H5PART_APPEND, then you can append new steps.
+  If you open with \c H5PART_READ, then it will open the file
+  readonly.
+
+  The typical extension for these files is \c .h5.
+  
+  h5_file should be treated as an essentially opaque
+  datastructure.  It acts as the file handle, but internally
+  it maintains several key state variables associated with 
+  the file.
+
+  \return	File handle or \c NULL
+ */
+
+h5_file_t *
+H5PartOpenFile (
+	const char *filename,	/*!< [in] The name of the data file to open. */
+	unsigned flags		/*!< [in] The access mode for the file. */
+	) {
+
+	MPI_Comm comm = 0;	/* dummy */
+
+	return h5_open_file ( filename, flags, comm, __func__ );
+}
+
+/*!
+  \ingroup h5part_c_api_openclose
+
+  Closes an open file.
+
+  \return	\c H5_SUCCESS or error code
+*/
+h5_int64_t
+H5PartCloseFile (
+	h5_file_t *f		/*!< [in] filehandle of the file to close */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5_close_file( f );
+}
+
+/*============== File Writing Functions ==================== */
+
+/*!
+  \ingroup h5part_c_api
+  \defgroup h5part_c_api_write	File Writing
+*/  
+
+h5_int64_t
+H5PartDefineStepName (
+	h5_file_t *f,
+	const char *name,
+	const h5_int64_t width
+	) {
+	SET_FNAME ( f, __func__ );
+
+	return h5_set_stepname_fmt( f, name, width );
+}
+
+/*!
+  \ingroup h5part_c_api_write
+
+  Set number of particles for current time-step.
+
+  This function's sole purpose is to prevent 
+  needless creation of new HDF5 DataSpace handles if the number of 
+  particles is invariant throughout the simulation. That's its only reason 
+  for existence. After you call this subroutine, all subsequent 
+  operations will assume this number of particles will be written.
+
+
+  \return	\c H5_SUCCESS or error code
+ */
+h5_int64_t
+H5PartSetNumParticles (
+	h5_file_t *f,			/*!< [in] Handle to open file */
+	h5_int64_t nparticles	/*!< [in] Number of particles */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5u_set_num_elements( f, nparticles );
+}
+
+/*!
+  \ingroup h5part_c_api_write
+
+  Write array of 64 bit floating point data to file.
+
+  After setting the number of particles with \c H5PartSetNumParticles() and
+  the current step using \c H5PartSetStep(), you can start writing datasets
+  into the file. Each dataset has a name associated with it (chosen by the
+  user) in order to facilitate later retrieval. The name of the dataset is
+  specified in the parameter \c name, which must be a null-terminated string.
+
+  There are no restrictions on naming of datasets, but it is useful to arrive
+  at some common naming convention when sharing data with other groups.
+
+  The writing routines also implicitly store the datatype of the array so that
+  the array can be reconstructed properly on other systems with incompatible
+  type representations.
+
+  All data that is written after setting the step is associated with that
+  step. While the number of particles can change for each step, you
+  cannot change the number of particles in the middle of a given step.
+
+  The data is committed to disk before the routine returns.
+
+  \return	\c H5_SUCCESS or error code
+ */
+h5_int64_t
+H5PartWriteDataFloat64 (
+	h5_file_t *f,			/*!< [in] Handle to open file */
+	const char *name,		/*!< [in] Name to associate array with */
+	const h5_float64_t *array	/*!< [in] Array to commit to disk */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5u_write_data ( f, name, (void*)array, H5T_NATIVE_DOUBLE );
+}
+
+/*!
+  \ingroup h5part_c_api_write
+
+  Write array of 64 bit integer data to file.
+
+  After setting the number of particles with \c H5PartSetNumParticles() and
+  the current step using \c H5PartSetStep(), you can start writing datasets
+  into the file. Each dataset has a name associated with it (chosen by the
+  user) in order to facilitate later retrieval. The name of the dataset is
+  specified in the parameter \c name, which must be a null-terminated string.
+
+  There are no restrictions on naming of datasets, but it is useful to arrive
+  at some common naming convention when sharing data with other groups.
+
+  The writing routines also implicitly store the datatype of the array so that
+  the array can be reconstructed properly on other systems with incompatible
+  type representations.
+
+  All data that is written after setting the step is associated with that
+  step. While the number of particles can change for each step, you
+  cannot change the number of particles in the middle of a given step.
+
+  The data is committed to disk before the routine returns.
+
+  \return	\c H5_SUCCESS or error code
+ */
+h5_int64_t
+H5PartWriteDataInt64 (
+	h5_file_t *f,		/*!< [in] Handle to open file */
+	const char *name,	/*!< [in] Name to associate array with */
+	const h5_int64_t *array	/*!< [in] Array to commit to disk */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	return h5u_write_data ( f, name, (void*)array, H5T_NATIVE_INT64 );
+}
+
+/********************** reading and writing attribute ************************/
+
+/********************** private functions to handle attributes ***************/
+
+
+/********************** attribute API ****************************************/
+
+/*!
+  \ingroup h5part_c_api
+  \defgroup h5part_c_api_attrib	Reading and Writing Attributes
+*/
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Writes a string attribute bound to a file.
+
+  This function creates a new attribute \c name with the string \c value as
+  content. The attribute is bound to the file associated with the file handle 
+  \c f.
+
+  If the attribute already exists an error will be returned. There
+  is currently no way to change the content of an existing attribute.
+
+  \return	\c H5_SUCCESS or error code   
+*/
+h5_int64_t
+H5PartWriteFileAttribString (
+	h5_file_t *f,		/*!< [in] Handle to open file */
+	const char *attrib_name,/*!< [in] Name of attribute to create */
+	const char *attrib_value/*!< [in] Value of attribute */ 
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_write_attrib (
+		f,
+		f->root_gid,
+		attrib_name,
+		H5T_NATIVE_CHAR,
+		attrib_value,
+		strlen ( attrib_value ) + 1 );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Writes a string attribute bound to the current time-step.
+
+  This function creates a new attribute \c name with the string \c value as
+  content. The attribute is bound to the current time step in the file given
+  by the file handle \c f.
+
+  If the attribute already exists an error will be returned. There
+  is currently no way to change the content of an existing attribute.
+
+  \return	\c H5_SUCCESS or error code   
+*/
+
+h5_int64_t
+H5PartWriteStepAttribString (
+	h5_file_t *f,		/*!< [in] Handle to open file */
+	const char *attrib_name,/*!< [in] Name of attribute to create */
+	const char *attrib_value/*!< [in] Value of attribute */ 
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_write_attrib (
+		f, 
+		f->step_gid,
+		attrib_name,
+		H5T_NATIVE_CHAR,
+		attrib_value,
+		strlen ( attrib_value ) + 1 );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Writes a attribute bound to the current time-step.
+
+  This function creates a new attribute \c name with the string \c value as
+  content. The attribute is bound to the current time step in the file given
+  by the file handle \c f.
+
+  The value of the attribute is given the parameter \c type, which must be one
+  of \c H5T_NATIVE_DOUBLE, \c H5T_NATIVE_INT64 of \c H5T_NATIVE_CHAR, the array
+  \c value and the number of elements \c nelem in the array.
+
+  If the attribute already exists an error will be returned. There
+  is currently no way to change the content of an existing attribute.
+
+  \return	\c H5_SUCCESS or error code   
+*/
+
+h5_int64_t
+H5PartWriteStepAttrib (
+	h5_file_t *f,			/*!< [in] Handle to open file */
+	const char *attrib_name,	/*!< [in] Name of attribute */
+	const h5_int64_t attrib_type,/*!< [in] Type of value. */
+	const void *attrib_value,	/*!< [in] Value of attribute */ 
+	const h5_int64_t attrib_nelem/*!< [in] Number of elements */
+	){
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_write_attrib (
+		f,
+		f->step_gid,
+		attrib_name,
+		(hid_t)attrib_type,
+		attrib_value,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Writes a attribute bound to a file.
+
+  This function creates a new attribute \c name with the string \c value as
+  content. The attribute is bound to the file file given by the file handle
+  \c f.
+
+  The value of the attribute is given the parameter \c type, which must be one
+  of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64 of H5T_NATIVE_CHAR, the array \c value
+  and the number of elements \c nelem in the array.
+
+  If the attribute already exists an error will be returned. There
+  is currently no way to change the content of an existing attribute.
+
+  \return	\c H5_SUCCESS or error code   
+*/
+
+h5_int64_t
+H5PartWriteFileAttrib (
+	h5_file_t *f,			/*!< [in] Handle to open file */
+	const char *attrib_name,	/*!< [in] Name of attribute */
+	const h5_int64_t attrib_type,/*!< [in] Type of value. */
+	const void *attrib_value,	/*!< [in] Value of attribute */ 
+	const h5_int64_t attrib_nelem/*!< [in] Number of elements */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_write_attrib (
+		f,
+		f->root_gid,
+		attrib_name,
+		(hid_t)attrib_type,
+		attrib_value,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Gets the number of attributes bound to the current step.
+
+  \return	Number of attributes bound to current time step or error code.
+*/
+h5_int64_t
+H5PartGetNumStepAttribs (
+	h5_file_t *f			/*!< [in] Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_get_num_attribs ( f, f->step_gid );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Gets the number of attributes bound to the file.
+
+  \return	Number of attributes bound to file \c f or error code.
+*/
+h5_int64_t
+H5PartGetNumFileAttribs (
+	h5_file_t *f			/*!< [in] Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_get_num_attribs ( f, f->root_gid );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Gets the name, type and number of elements of the step attribute
+  specified by its index.
+
+  This function can be used to retrieve all attributes bound to the
+  current time-step by looping from \c 0 to the number of attribute
+  minus one.  The number of attributes bound to the current
+  time-step can be queried by calling the function
+  \c H5PartGetNumStepAttribs().
+
+  \return	\c H5_SUCCESS or error code 
+*/
+h5_int64_t
+H5PartGetStepAttribInfo (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t attrib_idx,/*!< [in]  Index of attribute to
+					           get infos about */
+	char *attrib_name,		/*!< [out] Name of attribute */
+	const h5_int64_t len_of_attrib_name,
+					/*!< [in]  length of buffer \c name */
+	h5_int64_t *attrib_type,	/*!< [out] Type of value. */
+	h5_int64_t *attrib_nelem	/*!< [out] Number of elements */
+	) {
+	
+	SET_FNAME ( f, __func__ );
+
+   	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno( f );
+
+	return h5_get_attrib_info (
+		f,
+		f->step_gid,
+		attrib_idx,
+		attrib_name,
+		len_of_attrib_name,
+		attrib_type,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Gets the name, type and number of elements of the file attribute
+  specified by its index.
+
+  This function can be used to retrieve all attributes bound to the
+  file \c f by looping from \c 0 to the number of attribute minus
+  one.  The number of attributes bound to file \c f can be queried
+  by calling the function \c H5PartGetNumFileAttribs().
+
+  \return	\c H5_SUCCESS or error code 
+*/
+
+h5_int64_t
+H5PartGetFileAttribInfo (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t attrib_idx,/*!< [in]  Index of attribute to get
+					           infos about */
+	char *attrib_name,		/*!< [out] Name of attribute */
+	const h5_int64_t len_of_attrib_name,
+					/*!< [in]  length of buffer \c name */
+	h5_int64_t *attrib_type,	/*!< [out] Type of value. */
+	h5_int64_t *attrib_nelem	/*!< [out] Number of elements */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return h5_get_attrib_info (
+		f,
+		f->root_gid,
+		attrib_idx,
+		attrib_name,
+		len_of_attrib_name,
+		attrib_type,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Reads an attribute bound to current time-step.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_int64_t
+H5PartReadStepAttrib (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const char *attrib_name,	/*!< [in] Name of attribute to read */
+	void *attrib_value		/*!< [out] Value of attribute */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return h5_read_attrib ( f, f->step_gid, attrib_name, attrib_value );
+}
+
+/*!
+  \ingroup h5part_c_api_attrib
+
+  Reads an attribute bound to file \c f.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_int64_t
+H5PartReadFileAttrib ( 
+	h5_file_t *f,
+	const char *attrib_name,
+	void *attrib_value
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return h5_read_attrib ( f, f->root_gid, attrib_name, attrib_value );
+}
+
+
+/*================== File Reading Routines =================*/
+
+/*!
+  \ingroup h5part_c_api
+  \defgroup h5part_c_api_read		File Reading
+*/  
+
+/*
+  H5PartSetStep:
+
+
+  So you use this to random-access the file for a particular step.
+  Failure to explicitly set the step on each read will leave you
+  stuck on the same step for *all* of your reads.  That is to say
+  the writes auto-advance the file pointer, but the reads do not
+  (they require explicit advancing by selecting a particular step).
+*/
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Set the current time-step.
+
+  When writing data to a file the current time step must be set first
+  (even if there is only one). In write-mode this function creates a new
+  time-step! You are not allowed to step to an already existing time-step.
+  This prevents you from overwriting existing data. Another consequence is,
+  that you \b must write all data before going to the next time-step.
+
+  In read-mode you can use this function to random-access the file for a
+  particular step.
+
+  \return \c H5_SUCCESS or error code 
+*/
+h5_int64_t
+H5PartSetStep (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t step	/*!< [in]  Time-step to set. */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return h5_set_step ( f, step );
+}
+
+/********************** query file structure *********************************/
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Get the number of datasets that are stored at the current time-step.
+
+  \return	number of datasets in current step or error code
+*/
+
+h5_int64_t
+H5PartGetNumDatasets (
+	h5_file_t *f			/*!< [in]  Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+
+	return hdf5_get_num_objects ( f->file, f->step_name, H5G_DATASET );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  This reads the name of a dataset specified by it's index in the current
+  time-step.
+
+  If the number of datasets is \c n, the range of \c _index is \c 0 to \c n-1.
+
+  \result	\c H5_SUCCESS
+*/
+h5_int64_t
+H5PartGetDatasetName (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t idx,	/*!< [in]  Index of the dataset */
+	char *name,			/*!< [out] Name of dataset */
+	const h5_int64_t len_of_name/*!< [in]  Size of buffer \c name */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return hdf5_get_object_name (
+		f->file,
+		f->step_name,
+		H5G_DATASET,
+		idx,
+		name,
+		len_of_name );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Gets the name, type and number of elements of a dataset specified by it's
+  index in the current time-step.
+
+  Type is one of \c H5T_NATIVE_DOUBLE or \c H5T_NATIVE_INT64.
+
+  \return	\c H5_SUCCESS
+*/
+h5_int64_t
+H5PartGetDatasetInfo (
+	h5_file_t *f,		/*!< [in]  Handle to open file */
+	const h5_int64_t idx,/*!< [in]  Index of the dataset */
+	char *dataset_name,	/*!< [out] Name of dataset */
+	const h5_int64_t len_dataset_name,
+				/*!< [in]  Size of buffer \c dataset_name */
+	h5_int64_t *type,	/*!< [out] Type of data in dataset */
+	h5_int64_t *nelem	/*!< [out] Number of elements. */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	return h5u_get_dataset_info (
+		f, idx, dataset_name, len_dataset_name, type, nelem );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  This gets the number of particles stored in the current step. 
+  It will arbitrarily select a time-step if you haven't already set
+  the step with \c H5PartSetStep().
+
+  \return	number of particles in current step or an error
+		code.
+ */
+h5_int64_t
+H5PartGetNumParticles (
+	h5_file_t *f			/*!< [in]  Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	if ( f->step_gid < 0 ) {
+		h5_int64_t herr = h5_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+
+	return h5u_get_num_elems ( f );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+*/
+h5_int64_t
+H5PartResetView (
+ 	h5_file_t *f			/*!< [in]  Handle to open file */
+	) {
+	SET_FNAME ( f, __func__ );
+
+	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
+		return h5_get_errno ( f );
+
+	CHECK_READONLY_MODE ( f );
+
+	return h5u_reset_view ( f );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+*/
+h5_int64_t
+H5PartHasView (
+ 	h5_file_t *f			/*!< [in]  Handle to open file */
+	) {
+	SET_FNAME ( f, __func__ );
+
+	CHECK_FILEHANDLE( f );
+	CHECK_READONLY_MODE ( f );
+
+	return  h5u_has_view ( f );
+}
+
+
+/*!
+  \ingroup h5part_c_api_read
+
+  For parallel I/O or for subsetting operations on the datafile, the
+  \c H5PartSetView() function allows you to define a subset of the total
+  particle dataset to read.  The concept of "view" works for both serial
+  and for parallel I/O.  The "view" will remain in effect until a new view
+  is set, or the number of particles in a dataset changes, or the view is
+  "unset" by calling \c H5PartSetView(file,-1,-1);
+
+  Before you set a view, the \c H5PartGetNumParticles() will return the
+  total number of particles in the current time-step (even for the parallel
+  reads).  However, after you set a view, it will return the number of
+  particles contained in the view.
+
+  The range is inclusive (the start and the end index).
+
+  \return	\c H5_SUCCESS or error code
+*/
+h5_int64_t
+H5PartSetView (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	const h5_int64_t start,	/*!< [in]  Start particle */
+	const h5_int64_t end	/*!< [in]  End particle */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	CHECK_FILEHANDLE( f );
+	CHECK_READONLY_MODE ( f );
+
+	if ( f->step_gid < 0 ) {
+		h5_int64_t herr = h5_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+
+	return h5u_set_view ( f, start, end );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+   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
+   total dataset.
+
+   \return       the number of elements in the view 
+*/
+h5_int64_t
+H5PartGetView (
+	h5_file_t *f,			/*!< [in]  Handle to open file */
+	h5_int64_t *start,		/*!< [out]  Start particle */
+	h5_int64_t *end		/*!< [out]  End particle */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	CHECK_FILEHANDLE( f );
+
+	if ( f->step_gid < 0 ) {
+		h5_int64_t herr = h5_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+	return h5u_get_view( f, start, end );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  If it is too tedious to manually set the start and end coordinates
+  for a view, the \c H5SetCanonicalView() will automatically select an
+  appropriate domain decomposition of the data arrays for the degree
+  of parallelism and set the "view" accordingly.
+
+  \return		H5_SUCCESS or error code
+*/
+/*
+  \note
+  There is a bug in this function:
+  If (NumParticles % f->nprocs) != 0  then
+  the last  (NumParticles % f->nprocs) particles are not handled!
+*/
+
+h5_int64_t
+H5PartSetCanonicalView (
+	h5_file_t *f			/*!< [in]  Handle to open file */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	h5_int64_t herr;
+
+	CHECK_FILEHANDLE( f );
+	CHECK_READONLY_MODE ( f )
+
+	if ( f->step_gid < 0 ) {
+		herr = h5_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+
+	return h5u_set_canonical_view ( f );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Read array of 64 bit floating point data from file.
+
+  When retrieving datasets from disk, you ask for them
+  by name. There are no restrictions on naming of arrays,
+  but it is useful to arrive at some common naming
+  convention when sharing data with other groups.
+
+  \return	\c H5_SUCCESS or error code
+*/
+h5_int64_t
+H5PartReadDataFloat64 (
+	h5_file_t *f,		/*!< [in] Handle to open file */
+	const char *name,	/*!< [in] Name to associate dataset with */
+	h5_float64_t *array	/*!< [out] Array of data */
+	) {
+
+	SET_FNAME ( f, __func__ );
+
+	CHECK_FILEHANDLE( f );
+
+	return h5u_read_elems ( f, name, array, H5T_NATIVE_DOUBLE );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Read array of 64 bit floating point data from file.
+
+  When retrieving datasets from disk, you ask for them
+  by name. There are no restrictions on naming of arrays,
+  but it is useful to arrive at some common naming
+  convention when sharing data with other groups.
+
+  \return	\c H5_SUCCESS or error code
+*/
+h5_int64_t
+H5PartReadDataInt64 (
+	h5_file_t *f,		/*!< [in] Handle to open file */
+	const char *name,	/*!< [in] Name to associate dataset with */
+	h5_int64_t *array	/*!< [out] Array of data */
+	) {
+
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE( f );
+
+	return h5u_read_elems ( f, name, array, H5T_NATIVE_INT64 );
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  This is the mongo read function that pulls in all of the data for a
+  given step in one shot. It also takes the step as an argument
+  and will call \c H5PartSetStep() internally so that you don't have to 
+  make that call separately.
+
+  \note
+  See also \c H5PartReadDataInt64() and \c H5PartReadDataFloat64() if you want
+  to just read in one of the many datasets.
+
+  \return	\c H5_SUCCESS or error code
+*/
+h5_int64_t
+H5PartReadParticleStep (
+	h5_file_t *f,		/*!< [in]  Handle to open file */
+	h5_int64_t step,	/*!< [in]  Step to read */
+	h5_float64_t *x,	/*!< [out] Buffer for dataset named "x" */
+	h5_float64_t *y,	/*!< [out] Buffer for dataset named "y" */
+	h5_float64_t *z,	/*!< [out] Buffer for dataset named "z" */
+	h5_float64_t *px,	/*!< [out] Buffer for dataset named "px" */
+	h5_float64_t *py,	/*!< [out] Buffer for dataset named "py" */
+	h5_float64_t *pz,	/*!< [out] Buffer for dataset named "pz" */
+	h5_int64_t *id	/*!< [out] Buffer for dataset named "id" */
+	) {
+
+	SET_FNAME ( f, __func__ );
+	h5_int64_t herr;
+
+	CHECK_FILEHANDLE( f );
+
+	herr = h5_set_step ( f, step );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "x", (void*)x, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "y", (void*)y, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "z", (void*)z, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "px", (void*)px, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "py", (void*)py, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "pz", (void*)pz, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = h5u_read_elems ( f, "id", (void*)id, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	return H5_SUCCESS;
+}
+
+/****************** error handling ******************/
+
+

src/C/H5Part.h

@@ -0,0 +1,285 @@
+/*
+  Header file for declaring the H5Fed application programming
+  interface (API) in the C language.
+  
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+#ifndef __H5Part_H
+#define __H5Part_H
+
+#include <hdf5.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include "h5_core/h5_core.h"
+#include "H5.h"
+#ifdef PARALLEL_IO
+#include <mpi.h>
+#endif
+
+// #define H5PART_SUCCESS		H5_SUCCESS
+#define H5PART_ERR_NOMEM	H5_ERR_NOMEM
+#define H5PART_ERR_INVAL	H5_ERR_INVAL
+#define H5PART_ERR_BADFD	H5_ERR_BADFD
+#define H5PART_ERR_LAYOUT	H5_ERR_LAYOUT
+#define H5PART_ERR_NOENT	H5_ERR_NOENT
+#define H5PART_ERR_NOENTRY	H5_ERR_NOENTRY
+
+#define H5PART_ERR_MPI		H5_ERR_MPI
+#define H5PART_ERR_HDF5		H5_ERR_HDF5
+
+#define H5PART_READ		H5_O_RDONLY
+#define H5PART_WRITE		H5_O_WRONLY
+#define H5PART_APPEND		H5_O_APPEND
+
+#define H5PART_INT64		((h5_int64_t)H5T_NATIVE_INT64)
+#define H5PART_FLOAT64		((h5_int64_t)H5T_NATIVE_DOUBLE)
+#define H5PART_CHAR		((h5_int64_t)H5T_NATIVE_CHAR)
+
+/*========== File Opening/Closing ===============*/
+h5_file_t *
+H5PartOpenFile(
+	const char *filename,
+	const unsigned flags
+	);
+
+#define H5PartOpenFileSerial(x,y) H5PartOpenFile(x,y)
+
+#ifdef PARALLEL_IO
+h5_file_t *
+H5PartOpenFileParallel (
+	const char *filename,
+	const unsigned flags,
+	MPI_Comm communicator
+	);
+#endif
+
+
+h5_int64_t
+H5PartCloseFile (
+	h5_file_t *f
+	);
+
+
+/*============== File Writing Functions ==================== */
+h5_int64_t
+H5PartDefineStepName (
+	h5_file_t *f,
+	const char *name,
+	const h5_int64_t width
+	);
+
+h5_int64_t
+H5PartSetNumParticles ( 
+	h5_file_t *f, 
+	const h5_int64_t nparticles
+	);
+
+h5_int64_t
+H5PartWriteDataFloat64 (
+	h5_file_t *f,
+	const char *name,
+	const h5_float64_t *array
+	);
+
+h5_int64_t
+H5PartWriteDataInt64 (
+	h5_file_t *f,
+	const char *name,
+	const h5_int64_t *array
+	);
+
+/*================== File Reading Routines =================*/
+h5_int64_t
+H5PartSetStep (
+	h5_file_t *f,
+	const h5_int64_t step
+	);
+
+h5_int64_t
+H5PartGetNumDatasets (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartGetDatasetName (
+	h5_file_t *f,
+	const h5_int64_t idx,
+	char *name,
+	const h5_int64_t maxlen
+	);
+
+h5_int64_t
+H5PartGetDatasetInfo (
+	h5_file_t *f,
+	const h5_int64_t idx,
+	char *name,
+	const h5_int64_t maxlen,
+	h5_int64_t *type,
+	h5_int64_t *nelem);
+
+
+h5_int64_t
+H5PartGetNumParticles (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartSetView (
+	h5_file_t *f,
+	const h5_int64_t start,
+	const h5_int64_t end
+	);
+
+
+h5_int64_t
+H5PartGetView (
+	h5_file_t *f,
+	h5_int64_t *start,
+	h5_int64_t *end
+	);
+
+h5_int64_t
+H5PartHasView (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartResetView (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartSetCanonicalView (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartReadDataFloat64(
+	h5_file_t *f,
+	const char *name,
+	h5_float64_t *array
+	);
+
+h5_int64_t
+H5PartReadDataInt64 (
+	h5_file_t *f,
+	const char *name,
+	h5_int64_t *array
+	);
+
+h5_int64_t
+H5PartReadParticleStep (
+	h5_file_t *f,
+	const h5_int64_t step,
+	h5_float64_t *x, /* particle positions */
+	h5_float64_t *y,
+	h5_float64_t *z,
+	h5_float64_t *px, /* particle momenta */
+	h5_float64_t *py,
+	h5_float64_t *pz,
+	h5_int64_t *id /* and phase */
+	);
+
+/**********==============Attributes Interface============***************/
+/* currently there is file attributes:  Attributes bound to the file
+   and step attributes which are bound to the current step.  You 
+   must set the step explicitly before writing the attributes (just
+   as you must do when you write a new dataset.  Currently there are no
+   attributes that are bound to a particular data array, but this could
+   easily be done if required.
+*/
+h5_int64_t
+H5PartWriteStepAttrib (
+	h5_file_t *f,
+	const char *attrib_name,
+	const h5_int64_t attrib_type,
+	const void *attrib_value,
+	const h5_int64_t attrib_nelem
+	);
+
+h5_int64_t
+H5PartWriteFileAttrib (
+	h5_file_t *f,
+	const char *attrib_name,
+	const h5_int64_t attrib_type,
+	const void *attrib_value,
+	const h5_int64_t attrib_nelem
+	);
+
+h5_int64_t
+H5PartWriteFileAttribString (
+	h5_file_t *f,
+	const char *name,
+	const char *attrib
+	);
+
+h5_int64_t
+H5PartWriteStepAttribString ( 
+	h5_file_t *f,
+	const char *name,
+	const char *attrib
+	);
+
+h5_int64_t
+H5PartGetNumStepAttribs ( /* for current filestep */
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartGetNumFileAttribs (
+	h5_file_t *f
+	);
+
+h5_int64_t
+H5PartGetStepAttribInfo (
+	h5_file_t *f,
+	const h5_int64_t attrib_idx,
+	char *attrib_name,
+	const h5_int64_t len_of_attrib_name,
+	h5_int64_t *attrib_type,
+	h5_int64_t *attrib_nelem
+	);
+
+h5_int64_t
+H5PartGetFileAttribInfo (
+	h5_file_t *f,
+	const h5_int64_t idx,
+	char *name,
+	const h5_int64_t maxnamelen,
+	h5_int64_t *type,
+	h5_int64_t *nelem
+	);
+
+h5_int64_t
+H5PartReadStepAttrib (
+	h5_file_t *f,
+	const char *name,
+	void *data
+	);
+
+h5_int64_t
+H5PartReadFileAttrib (
+	h5_file_t *f,
+	const char *name,
+	void *data
+	);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

src/C/H5_inquiry.c

@@ -0,0 +1,96 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+/*!
+  \ingroup h5f_c_api
+  \defgroup h5_inquiry
+*/
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_core_private.h"
+#include "H5.h"
+
+/*!
+  \ingroup h5_inquiry
+
+  Get the number of compute nodes.
+
+  \param[in]	f	File handle.
+
+  \return Number of compute notes.
+  \return \c -1 on error.
+ */
+h5_size_t
+H5GetNumNodes (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+	return (h5_size_t)f->nprocs;
+}
+
+/*!
+  \ingroup h5part_c_api_read
+
+  Get the number of time-steps that are currently stored in the file
+  \c f.
+
+  It works for both reading and writing of files, but is probably
+  only typically used when you are reading.
+
+  \param[in]	f	File handle.
+
+  \return	number of time-steps or error code
+*/
+h5_size_t
+H5GetNumSteps (
+	h5_file_t * const f
+	) {
+
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+
+	return hdf5_get_num_objects_matching_pattern (
+		f->file,
+		"/",
+		H5G_UNKNOWN,
+		f->prefix_step_name );
+}
+
+/*!
+  \ingroup h5_inquiry
+
+  Query whether a particular step already exists in the file.
+
+  \param[in]	f	File handle.
+  \param[in]	stepno	Step number to query for existence
+
+  \return      true or false
+*/
+h5_err_t
+H5HasStep (
+	h5_file_t *f,
+	h5_id_t stepno
+	) {
+  
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+
+	return h5_has_step( f, stepno );
+}
+
+
+

src/C/H5_inquiry.h

@@ -0,0 +1,19 @@
+#ifndef __H5_INQUIRY_H
+#define __H5_INQUIRY_H
+
+h5_size_t
+H5GetNumNodes (
+	h5_file_t * const f
+	);
+
+h5_size_t
+H5GetNumSteps (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5HasStep (
+	h5_file_t * const f,
+	h5_id_t step
+	);
+#endif