- changes for revised API

- bugfixes
- ...

src/H5.c

@@ -62,7 +62,6 @@ H5OpenFile (
 	const h5_int32_t oflag,		/*!< file open flags		*/
 	const MPI_Comm comm		/*!< MPI communicator		*/
 	) {
-	
 	return h5_open_file( filename, H5_O_RDWR, comm, __func__ ); 
 }
 
@@ -99,7 +98,7 @@ H5DefineStepNameFormat (
 	) {
 	SET_FNAME ( f, __func__ );
 
-	return h5_define_stepname_fmt( f, name, width );
+	return h5_set_stepname_fmt( f, name, width );
 }
 
 /*!
@@ -188,3 +187,67 @@ H5TraverseSteps (
 
 	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();
+}
+
+/*!
+  \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/H5.h

@@ -62,4 +62,25 @@ h5_err_t
 H5TraverseSteps (
 	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
+H5GetErrno (
+	h5_file_t * const f
+	);
+
 #endif

src/H5Block.c

@@ -546,23 +546,17 @@ h5_err_t
 _release_hyperslab (
 	h5_file_t *f			/*!< IN: file handle */
 	) {
-	herr_t herr;
+	struct h5b_fdata *b = f->b;
+
+	TRY( _h5_close_dataspace( f, b->shape ) );
+	f->b->shape = -1;
+
+	TRY( _h5_close_dataspace( f, b->diskshape ) );
+	f->b->diskshape = -1;
+
+	TRY( _h5_close_dataspace( f, f->b->memshape ) );
+	f->b->memshape = -1;
 
-	if ( f->b->shape > 0 ) {
-		herr = H5Sclose ( f->b->shape );
-		if ( herr < 0 ) return H5_ERR_HDF5;
-		f->b->shape = -1;
-	}
-	if ( f->b->diskshape > 0 ) {
-		herr = H5Sclose ( f->b->diskshape );
-		if ( herr < 0 ) return H5_ERR_HDF5;
-		f->b->diskshape = -1;
-	}
-	if ( f->b->memshape > 0 ) {
-		herr = H5Sclose ( f->b->memshape );
-		if ( herr < 0 ) return H5_ERR_HDF5;
-		f->b->memshape = -1;
-	}
 	return H5_SUCCESS;
 }
 
@@ -611,8 +605,7 @@ H5BlockDefine3DFieldLayout(
 	herr = _dissolve_ghostzones ( f );
 	if ( herr < 0 ) return HANDLE_H5_LAYOUT_ERR ( f );
 
-	herr = _release_hyperslab ( f );
-	if ( herr < 0 )	return HANDLE_H5S_CLOSE_ERR ( f );
+	TRY( _release_hyperslab ( f ) );
 
 	b->have_layout = 1;
 
@@ -785,19 +778,17 @@ _open_block_group (
 	struct h5b_fdata *b = f->b;
 
 	if ( (f->step_idx != b->step_idx) && (b->blockgroup > 0) ) {
-		herr_t herr = H5Gclose ( b->blockgroup );
-		if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR ( f );
+		TRY( _h5_close_group( f, b->blockgroup ) );
 		f->b->blockgroup = -1;
 	}
 
 	if ( b->blockgroup < 0 ) {
-		hid_t herr = H5Gopen ( f->step_gid, H5BLOCK_GROUPNAME_BLOCK,
-				       H5P_DEFAULT );
-		if ( herr < 0 ) return HANDLE_H5G_OPEN_ERR (
-			f,
-			h5_get_objname(f->step_gid),
-			H5BLOCK_GROUPNAME_BLOCK );
-		b->blockgroup = herr;
+		TRY(
+			b->blockgroup = _h5_open_group (
+				f,
+				f->step_gid,
+				H5BLOCK_GROUPNAME_BLOCK )
+			);
 	}
 	b->step_idx = f->step_idx;
 
@@ -841,18 +832,12 @@ _open_field_group (
 
 	struct h5b_fdata *b = f->b;
 
-	h5_int64_t h5err = _open_block_group ( f );
-	if ( h5err < 0 ) return h5err;
+	TRY( _open_block_group ( f ) );
 
 	if ( ! _have_object ( b->blockgroup, name ) )
 		return HANDLE_H5_NOENT_ERR ( f, name );
 
-	herr_t herr = H5Gopen ( b->blockgroup, name, H5P_DEFAULT );
-	if ( herr < 0 ) return HANDLE_H5G_OPEN_ERR (
-		f,
-		h5_get_objname(b->blockgroup), name );
-
-	b->field_group_id = herr;
+	TRY( b->field_group_id = _h5_open_group( f, b->blockgroup, name ) );
 
 	return H5_SUCCESS;
 }
@@ -914,8 +899,7 @@ _select_hyperslab_for_reading (
 		p->j_end - p->j_start + 1,
 		p->i_end - p->i_start + 1 };
 
-	h5_int64_t herr = _release_hyperslab ( f );
-	if ( herr < 0 )	return HANDLE_H5S_CLOSE_ERR ( f );
+	TRY( _release_hyperslab ( f ) );
 
  	b->diskshape = H5Dget_space ( dataset );
 	if ( b->diskshape < 0 ) return HANDLE_H5D_GET_SPACE_ERR ( f );
@@ -948,7 +932,7 @@ _select_hyperslab_for_reading (
 	if ( b->memshape < 0 )
 		return HANDLE_H5S_CREATE_SIMPLE_3D_ERR ( f, part_dims );
 
-	herr = H5Sselect_hyperslab (
+	herr_t herr = H5Sselect_hyperslab (
 		b->diskshape,
 		H5S_SELECT_SET,
 		start,
@@ -992,24 +976,28 @@ _read_data (
 	) {
 
 	struct h5b_fdata *b = f->b;
-
-	hid_t dataset_id = H5Dopen ( b->field_group_id, name, H5P_DEFAULT );
-	if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( f, name );
-
-	h5_err_t herr = _select_hyperslab_for_reading ( f, dataset_id );
-	if ( herr < 0 ) return herr;
-
-	herr = H5Dread ( 
-		dataset_id,
-		type,
-		f->b->memshape,
-		f->b->diskshape,
-		H5P_DEFAULT,
-		data );
-	if ( herr < 0 ) return HANDLE_H5D_READ_ERR ( f, name );
-
-	herr = H5Dclose ( dataset_id );
-	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR ( f );
+	hid_t dataset_id;
+	TRY(
+		dataset_id = _h5_open_dataset (
+			f,
+			b->field_group_id, name
+			)
+		);
+	TRY( 
+		_select_hyperslab_for_reading ( f, dataset_id ) );
+	TRY( 
+		_h5_read_dataset(
+			f,
+			dataset_id,
+			type,
+			f->b->memshape,
+			f->b->diskshape,
+			H5P_DEFAULT,
+			data )
+		);
+	TRY(
+		_h5_close_dataset( f, dataset_id )
+		);
 
 	return H5_SUCCESS;
 }
@@ -1382,7 +1370,6 @@ _write_field_data (
 		data,
 		H5T_NATIVE_DOUBLE,
 		b->field_group_id,
-		b->shape,
 		b->memshape,
 		b->diskshape );
 }
@@ -1509,18 +1496,24 @@ _get_field_info (
 
 	hsize_t dims[16];
 	h5_id_t i, j;
+	hid_t group_id;
+	hid_t dataset_id;
 
-	h5_err_t herr = _open_block_group ( f );
-	if ( herr < 0 ) return herr;
-
-	hid_t group_id = H5Gopen ( f->b->blockgroup, field_name,
-				   H5P_DEFAULT );
-	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR (
-		f,
-		hdf5_get_objname(f->b->blockgroup), field_name );
-
-	hid_t dataset_id = H5Dopen ( group_id, "0", H5P_DEFAULT );
-	if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( f, "0" );
+	TRY(
+		_open_block_group ( f )
+		);
+	TRY(
+		group_id = _h5_open_group(
+			f,
+			f->b->blockgroup,
+			field_name )
+		);
+	TRY(
+		dataset_id = _h5_open_dataset (
+			f,
+			group_id,
+			"0" )
+		);
 
  	hid_t dataspace_id = H5Dget_space ( dataset_id );
 	if ( dataspace_id < 0 ) return HANDLE_H5D_GET_SPACE_ERR ( f );
@@ -1537,14 +1530,9 @@ _get_field_info (
 		H5G_DATASET );
 	if ( *field_dims < 0 ) return *field_dims;
 
-	herr = H5Sclose ( dataspace_id );
-	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR ( f );
-
-	herr = H5Dclose ( dataset_id );
-	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR ( f );
-
-	herr = H5Gclose ( group_id ); 
-	if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR ( f );
+	TRY( _h5_close_dataspace( f, dataspace_id ) );
+	TRY( _h5_close_dataset( f, dataset_id ) );
+	TRY( _h5_close_group( f, group_id ) ); 
 
 	return H5_SUCCESS;
 }

src/H5Fed_inquiry.c

@@ -111,7 +111,7 @@ H5FedGetNumTriangles (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, f->myproc, cur_level );
+	return h5t_get_num_elems ( f, f->myproc, cur_level );
 }
 
 /*!
@@ -129,7 +129,7 @@ H5FedGetNumTrianglesTotal (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, -1, cur_level );
+	return h5t_get_num_elems ( f, -1, cur_level );
 }
 
 
@@ -149,7 +149,7 @@ H5FedGetNumTrianglesCnode (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, cnode, cur_level );
+	return h5t_get_num_elems ( f, cnode, cur_level );
 }
 
 /******	TETRAHEDRON statistics routines **************************************/
@@ -169,7 +169,7 @@ H5FedGetNumTetrahedra (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, f->myproc, cur_level );
+	return h5t_get_num_elems ( f, f->myproc, cur_level );
 }
 
 h5_size_t
@@ -178,7 +178,7 @@ H5FedGetNumTetrahedraTotal (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, -1, cur_level );
+	return h5t_get_num_elems ( f, -1, cur_level );
 }
 
 /*!
@@ -196,7 +196,7 @@ h5_size_t H5FedGetNumTetrahedraCnode (
 	) {
 	SET_FNAME ( f, __func__ );
 	h5_id_t cur_level = h5t_get_level( f );
-	return h5t_get_num_entities ( f, cnode, cur_level );
+	return h5t_get_num_elems ( f, cnode, cur_level );
 }
 
 

src/H5Fed_map.c

@@ -28,7 +28,7 @@ H5FedMapTet2GlobalID (
 	h5_id_t * const global_vids
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_get_global_entity_id ( f, global_vids );
+	return h5t_get_global_eid ( f, global_vids );
 }
 
 

src/H5Fed_store.c

@@ -22,24 +22,31 @@
 h5_id_t
 H5FedAddTetMesh (
 	h5_file_t * const f,
+	const h5_size_t num_elems
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_open_mesh ( f, -1, H5_OID_TETRAHEDRON );
+	return h5t_add_mesh ( f, num_elems, H5_OID_TETRAHEDRON );
 }
 
 h5_id_t
 H5FedAddTriangleMesh (
-	h5_file_t * const f
+	h5_file_t * const f,
+	const h5_size_t num_elems
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_open_mesh ( f, -1, H5_OID_TRIANGLE );
+	return h5t_add_mesh ( f, num_elems, H5_OID_TRIANGLE );
 }
 
 
 /*!
   \ingroup h5fed_c_api
 
-  Add a new level.
+  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	Number of elements to add.
 
   \return ID of new level.
 
@@ -53,10 +60,12 @@ H5FedAddTriangleMesh (
 */
 h5_id_t
 H5FedAddLevel (
-	h5_file_t * const f		/*!< file handle		*/
+	h5_file_t * const f,		/*!< file handle		*/
+	const h5_size_t num_elems
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_add_level ( f );
+	h5_id_t num_vertices = (num_elems>>2)*3; /* this is an upper limit */
+	return h5t_add_level ( f, num_vertices, num_elems );
 }
 
 /*!
@@ -71,7 +80,7 @@ H5FedAddLevel (
 h5_id_t
 H5FedStoreVertex (
 	h5_file_t * const f,		/*!< file handle		*/
-	const h5_id_t id,		/*!< id from mesher or -1	*/
+	const h5_id_t vertex_id,	/*!< id from mesher or -1	*/
 	const h5_float64_t P[3]		/*!< coordinates		*/
 	) {
 
@@ -82,17 +91,7 @@ H5FedStoreVertex (
 			H5_ERR_INVAL,
 			"Vertices can be added to level 0 only!" );
 	}
-	return h5t_store_vertex ( f, id, P );
-}
-
-h5_err_t
-H5FedAddNumElements (
-	h5_file_t * const f,		/*!< file handle		*/
-	const h5_size_t num		/*!< number of additional
-					  tets on current level	*/
-	) {
-	SET_FNAME ( f, __func__ );
-	return h5t_add_num_elements ( f, num );
+	return h5t_store_vertex ( f, vertex_id, P );
 }
 
 /*!
@@ -121,14 +120,14 @@ H5FedStoreElement (
 			H5_ERR_INVAL,
 			"Tetrahedra can be added to level 0 only!" );
 	}
-	return h5t_store_element ( f, -1, local_vids );
+	return h5t_store_elem ( f, -1, local_vids );
 }
 
 h5_id_t
 H5FedRefineElement (
 	h5_file_t * const f,		/*!< file handle		*/
-	const h5_id_t local_cid		/*!< local element id		*/
+	const h5_id_t local_eid		/*!< local element id		*/
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_refine_element ( f, local_cid );
+	return h5t_refine_elem ( f, local_eid );
 }

src/H5Fed_store.h

@@ -21,17 +21,20 @@
 
 h5_id_t
 H5FedAddTetMesh (
-	h5_file_t * const f
+	h5_file_t * const f,
+	const h5_size_t num_elems
 	);
 
 h5_id_t
 H5FedAddTriangleMesh (
-	h5_file_t * const f
+	h5_file_t * const f,
+	const h5_size_t num_elems
 	);
 
 h5_id_t
 H5FedAddLevel (
-	h5_file_t * f
+	h5_file_t * f,
+	const h5_size_t num_elems
 	);
 
 h5_err_t
@@ -56,8 +59,13 @@ H5FedStoreVertex (
 h5_id_t
 H5FedStoreElement (
 	h5_file_t * f,
-	h5_id_t *vertex_ids
+	const h5_id_t local_vids[]
 	);
 
+h5_id_t
+H5FedRefineElement (
+	h5_file_t * const f,
+	const h5_id_t local_eid
+	);
 
 #endif

src/H5Part.c

@@ -125,7 +125,7 @@ H5PartDefineStepName (
 	) {
 	SET_FNAME ( f, __func__ );
 
-	return h5_define_stepname_fmt( f, name, width );
+	return h5_set_stepname_fmt( f, name, width );
 }
 
 /*!
@@ -1027,67 +1027,4 @@ H5PartReadParticleStep (
 
 /****************** error handling ******************/
 
-/*!
-  \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_int64_t
-H5PartSetVerbosityLevel (
-	const h5_int64_t level
-	) {
-
-	return h5_set_debuglevel ( level );
-}
-
-/*!
-  \ingroup h5part_c_api_errhandling
-
-  Set error handler to \c handler.
-
-  \return \c H5_SUCCESS
-*/
-h5_int64_t
-H5PartSetErrorHandler (
-	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
-H5PartGetErrorHandler (
-	void
-	) {
-	return h5_get_errorhandler();
-}
-
-/*!
-  \ingroup h5part_c_api_errhandling
-
-  Get last error code.
-
-  \return error code
-*/
-h5_int64_t
-H5PartGetErrno (
-	h5_file_t * const f
-	) {
-	return h5_get_errno( f );
-}
-/*! @} */
 

src/H5Part.h

@@ -1,10 +1,26 @@
-#ifndef _H5Part_H_
-#define _H5Part_H_
+/*
+  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 <stdlib.h>
-#include <stdarg.h>
 #include <hdf5.h>
 #include "h5_core/h5_core.h"
+#include "H5.h"
 #ifdef PARALLEL_IO
 #include <mpi.h>
 #endif
@@ -272,40 +288,6 @@ H5PartReadFileAttrib (
 	void *data
 	);
 
-h5_int64_t
-H5PartSetVerbosityLevel (
-	const h5_int64_t level
-	);
-
-h5_int64_t
-H5PartSetErrorHandler (
-	const h5_errorhandler_t handler
-	);
-
-h5_int64_t
-H5PartGetErrno (
-	h5_file_t *f
-	);
-
-h5_errorhandler_t
-H5PartGetErrorHandler (
-	void
-	);
-
-h5_int64_t
-H5PartReportErrorHandler (
-	h5_file_t *f,
-	const char *fmt,
-	...
-	);
-
-h5_int64_t
-H5PartAbortErrorHandler (
-	h5_file_t *f,
-	const char *fmt,
-	...
-	);
-
 #ifdef __cplusplus
 }
 #endif

src/bindings/Makefile.am

@@ -1 +1,2 @@
-SUBDIRS = @BINDINGS@
+#SUBDIRS = @BINDINGS@
+SUBDIRS =