- neighbor information management added to elements

- prefix 'global' removed form global element struct
- global and local element data now have the same struct
- and several other changes

.gitattributes

@@ -448,6 +448,7 @@ src/h5core/h5t_readwrite_private.h -text
 src/h5core/h5t_readwrite_tetm.c -text
 src/h5core/h5t_readwrite_trim.c -text
 src/h5core/h5t_ref_elements.c -text
+src/h5core/h5t_ref_elements_private.h -text
 src/h5core/h5t_retrieve.c -text
 src/h5core/h5t_retrieve_private.h -text
 src/h5core/h5t_retrieve_tetm.c -text

src/h5core/Makefile.am

@@ -49,9 +49,11 @@ EXTRA_HEADERS =					\
 	h5t_core_private.h			\
 	h5t_errorhandling_private.h		\
 	h5t_hsearch_private.h			\
+	h5t_inquiry_private.h			\
 	h5t_map_private.h			\
 	h5t_openclose_private.h			\
 	h5t_readwrite_private.h			\
+	h5t_ref_elements_private.h		\
 	h5t_retrieve_private.h			\
 	h5t_store_private.h			\
 	h5t_store_trim_private.h		\
@@ -115,6 +117,11 @@ libH5hut_a_SOURCES =				\
 
 libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
 
+all: all-am install-libs-local
+
+install-libs-local:
+	-cp ${lib_LIBRARIES} ../lib
+
 install-exec-local:
 	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core
 	@$(INSTALL) -m644 ../include/h5core/*.h $(DESTDIR)$(includedir)/h5core/

src/h5core/h5_errorhandling.c

@@ -157,6 +157,7 @@ h5_abort_errorhandler (
 #else
 	exit (-(int)f->__errno);
 #endif
+	return -(int)f->__errno; // never executed, just to supress a warning
 }
 
 static void
@@ -167,10 +168,11 @@ _vprintf (
 	const char* fmt,
 	va_list ap
 	) {
-	char *fmt2 = (char*)malloc(
-		strlen (prefix) +
-		strlen (fmt) + 
-		strlen (__funcname) + 16);
+	size_t size = strlen (prefix);	// to avoid remark #981 with Intel CC
+	size += strlen (fmt);
+	size += strlen (__funcname) + 16;
+
+	char *fmt2 = (char*)malloc (size);
 	if (fmt2 == NULL) return;
 	sprintf (fmt2, "%s: %s: %s\n", prefix, __funcname, fmt); 
 	vfprintf (f, fmt2, ap);

src/h5core/h5_fcmp.c

@@ -3,6 +3,7 @@
 #include <math.h>
 
 #include "h5core/h5_core.h"
+#include "h5_core_private.h"
 
 /*!
   Compare two floating point numbers using integers. See

src/h5core/h5_hdf5.c

@@ -602,6 +602,7 @@ h5priv_get_base_type_name (
 	if (base_type_id == H5_FLOAT64_T)	return "H5_FLOAT64_T";
 	if (base_type_id == H5_STRING_T)	return "H5_STRING_T";
 
+	h5_warn (f, "Unknown base type id %lu", (unsigned long)base_type_id);
 	return "[unknown]";
 }
 
@@ -610,6 +611,7 @@ get_class_type_name (
 	h5_file_t* const f,
 	hid_t base_type_id
 	) {
+#pragma unused f
 	if (base_type_id == H5_COMPOUND_T)	return "H5_COMPOUND_T";
 
 	return "[unknown]";
@@ -1227,7 +1229,7 @@ _iter_op_get_obj_type (
 		herr = H5Lget_val(g_id, name, buf,
 					info->u.val_size, H5P_DEFAULT);
 		if ( herr < 0 )
-			return h5_error(f,
+			return (H5O_type_t)h5_error (f,
 				H5_ERR_HDF5,
 				"Can't get external link for object '%s'!",
 				name);
@@ -1237,7 +1239,7 @@ _iter_op_get_obj_type (
 		herr = H5Lunpack_elink_val(buf, info->u.val_size, 0,
 							&filename, &objname);
 		if ( herr < 0 )
-			return h5_error(f,
+			return (H5O_type_t)h5_error(f,
 				H5_ERR_HDF5,
 				"Can't unpack external link for object '%s'!",
 				name);
@@ -1250,7 +1252,7 @@ _iter_op_get_obj_type (
 
 		hid_t obj_id = H5Oopen(g_id, name, H5P_DEFAULT);
 		if ( obj_id < 0 )
-			return h5_error(f,
+			return (H5O_type_t)h5_error(f,
 				H5_ERR_HDF5,
 				"Can't open external link for object '%s'!",
 				name);
@@ -1261,7 +1263,7 @@ _iter_op_get_obj_type (
 	}
 	
 	if ( herr < 0 )
-		return h5_error(f,
+		return (H5O_type_t)h5_error(f,
 			H5_ERR_HDF5,
 			"Can't query object with name '%s'!", name);
 

src/h5core/h5_hsearch.c

@@ -69,7 +69,7 @@ h5priv_hcreate (
 	) {
 	/* Test for correct arguments.  */
 	if (htab == NULL || htab->table != NULL) {
-		h5_error_internal (f, __FILE__, __func__, __LINE__);
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	/* Change nel to the first prime number not smaller as nel. */
 	nel |= 1;      /* make odd */
@@ -99,7 +99,7 @@ h5priv_hresize (
 	h5_hashtable_t* htab	// hash table to resize
 	) {
 	if (htab == NULL || htab->table == NULL) {
-		h5_error_internal (f, __FILE__, __func__, __LINE__);
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	// create new hash table
 	h5_hashtable_t __htab;
@@ -138,7 +138,7 @@ h5priv_hdestroy (
 	) {
 	/* Test for correct arguments.  */
 	if (htab == NULL) {
-		h5_error_internal (f, __FILE__, __func__, __LINE__);
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 
 	/* Free used memory.  */

src/h5core/h5_maps.c

@@ -23,6 +23,7 @@ h5priv_free_idlist_items (
 	h5_file_t* const f,
 	h5_idlist_t* list
 	) {
+#pragma unused f
 	if (list->items != NULL) free (list->items);
 	list->items = NULL;
 	list->size = 0;
@@ -106,6 +107,7 @@ h5priv_sort_idlist_by_eid (
 	h5_file_t* const f,
 	h5_idlist_t* list
 	) {
+#pragma unused f
 	qsort (
 		list->items,
 		list->num_items,
@@ -124,6 +126,7 @@ h5priv_find_idlist (
 	h5_idlist_t* list,
 	h5_id_t	item
 	) {
+#pragma unused f
 	register h5_id_t low = 0;
 	register h5_id_t high = list->num_items - 1;
 	while (low <= high) {
@@ -256,8 +259,8 @@ h5priv_search_idmap (
        	return -(low+1);  // not found
 }
 
-int
-_cmp_idmap_items (
+static int
+cmp_idmap_items (
 	const void* _item1,
 	const void* _item2
 	) {
@@ -275,6 +278,6 @@ h5priv_sort_idmap (
 	h5_idmap_t* map
 	) {
 	qsort (	map->items, map->num_items, sizeof (map->items[0]),
-		_cmp_idmap_items);
+		cmp_idmap_items);
 	return H5_SUCCESS;
 }

src/h5core/h5_openclose.c

@@ -45,6 +45,7 @@ h5priv_error_handler (
 	hid_t estack_id,
 	void* __f
 	) {
+#pragma unused __f
 	if (h5_get_debuglevel() >= 5) {
 		H5Eprint (estack_id, stderr);
 	}
@@ -58,6 +59,8 @@ h5priv_error_handler (
 
   Initialize unstructured data internal data structure.
 
+  TODO: Move to file "h5u_openclose.c"
+
   \return	H5_SUCCESS or error code
 */
 static h5_err_t
@@ -86,6 +89,8 @@ h5upriv_open_file (
 
   Initialize H5Block internal structure.
 
+  TODO: Move to file "h5b_openclose.c"
+
   \return	H5_SUCCESS or error code
 */
 static h5_err_t
@@ -101,10 +106,11 @@ h5bpriv_open_file (
 	b = f->b;
 	memset (b, 0, sizeof (*b));
 
+#if defined(PARALLEL_IO)
 	size_t n = sizeof (struct h5b_partition) / sizeof (h5_int64_t);
 	TRY( h5priv_mpi_type_contiguous(f,
 			n, MPI_LONG_LONG, &b->partition_mpi_t) );
-
+#endif
 	memset (b->user_layout, 0, sizeof(*b->user_layout));
 	memset (b->write_layout, 0, sizeof(*b->write_layout));
 
@@ -130,13 +136,18 @@ h5bpriv_open_file (
   \return NULL on error.
 */
 
-h5_err_t
-h5priv_open_file (
+static h5_err_t
+open_file (
 	h5_file_t* const f,
 	const char* filename,	/*!< The name of the data file to open. */
-	char flags,		/*!< The access mode for the file. */
+	h5_int32_t flags,	/*!< The access mode for the file. */
 	MPI_Comm comm		/*!< MPI communicator */
 	) {
+
+#if !defined(PARALLEL_IO)
+#pragma unused comm
+#endif
+
 	h5_info (f, "Opening file %s.", filename);
 
 	TRY( h5priv_set_hdf5_errorhandler (f, H5E_DEFAULT, h5priv_error_handler, NULL) );
@@ -255,7 +266,7 @@ h5_open_file (
 	}
 	memset (f, 0, sizeof (h5_file_t));
 	f->__funcname = funcname;
-	if (h5priv_open_file (f, filename, flags, comm) < 0) {
+	if (open_file (f, filename, flags, comm) < 0) {
 		if (f != NULL) {
 			/* Oops, cannot open file. We release the memory allocated for
 			   f only, there is most likely more allocated memory we do
@@ -318,7 +329,9 @@ h5bpriv_close_file (
 	TRY( h5priv_close_hdf5_dataspace (f, b->diskshape) );
 	TRY( h5priv_close_hdf5_dataspace (f, b->memshape) );
 	TRY( h5priv_close_hdf5_property (f, b->dcreate_prop) );
+#if defined(PARALLEL_IO)
 	TRY( h5priv_mpi_type_free (f, &b->partition_mpi_t) );
+#endif
 	free (f->b);
 	f->b = NULL;
 
@@ -401,6 +414,10 @@ h5_get_stepname_fmt (
 	int l_name,			/*!< length of buffer name	*/
 	int* width			/*!< OUT: Width of the number	*/
 	) {
+#pragma unused f
+#pragma unused name
+#pragma unused l_name
+#pragma unused width
 	return h5_error_not_implemented (f, __FILE__, __func__, __LINE__);
 }
 

src/h5core/h5_qsort.c

@@ -38,6 +38,8 @@ static char sccsid[] = "@(#)qsort.c	8.1 (Berkeley) 6/4/93";
 
 #include <stdlib.h>
 
+#include "h5_qsort_private.h"
+
 #ifdef I_AM_QSORT_R
 typedef int		 cmp_t(void *, const void *, const void *);
 #else
@@ -53,10 +55,10 @@ static inline void	 swapfunc(char *, char *, int, int);
  */
 #define swapcode(TYPE, parmi, parmj, n) { 		\
 	long i = (n) / sizeof (TYPE); 			\
-	TYPE *pi = (TYPE *) (parmi); 		\
-	TYPE *pj = (TYPE *) (parmj); 		\
+	TYPE *pi = (TYPE *) (parmi);			\
+	TYPE *pj = (TYPE *) (parmj);			\
 	do { 						\
-		TYPE	t = *pi;		\
+		TYPE	t = *pi;			\
 		*pi++ = *pj;				\
 		*pj++ = t;				\
         } while (--i > 0);				\
@@ -66,10 +68,7 @@ static inline void	 swapfunc(char *, char *, int, int);
 	es % sizeof(long) ? 2 : es == sizeof(long)? 0 : 1;
 
 static inline void
-swapfunc(a, b, n, swaptype)
-	char *a, *b;
-	int n, swaptype;
-{
+swapfunc(char* a, char* b, int n, int swaptype) {
 	if(swaptype <= 1)
 		swapcode(long, a, b, n)
 	else

src/h5core/h5_readwrite.c

@@ -3,35 +3,6 @@
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
-/*
-  Obsolete function - still in old H5Part code !
-*/
-
-h5_err_t
-h5_write_data (
-	h5_file_t* const f,	/*!< IN: Handle to open file */
-	const char* name,	/*!< IN: Name to associate array with */
-	const void* array,	/*!< IN: Array to commit to disk */
-	const hid_t type_id,	/*!< IN: Type of data */
-	const hid_t group_id,
-	const hid_t memspace_id,
-	const hid_t diskspace_id
-	) {
-	hid_t dset_id;
-
-	h5_info (f, "Writing dataset %s/%s.", h5_get_objname(group_id), name); 
-	TRY( dset_id = h5priv_create_hdf5_dataset (
-		f,
-		group_id,
-		name,
-		type_id,
-		diskspace_id,
-		H5P_DEFAULT) );
-
-	f->empty = 0;
-
-	return H5_SUCCESS;
-}
 
 /*!
   Write data to dataset.

src/h5core/h5_syscall.c

@@ -39,6 +39,7 @@ h5priv_free (
 	h5_file_t* const f,
 	void* ptr
 	) {
+#pragma unused f
 	if (ptr) free (ptr);
 	return H5_SUCCESS;
 }
@@ -65,6 +66,7 @@ h5priv_tfind (
 	void* const* rootp,
 	int (*compar) (const void* key1, const void* key2) 
 	) {
+#pragma unused f
 	void* ptr = tfind (key, rootp, compar);
 	if (ptr == NULL) {
 		return (void*)(H5_ERR);

src/h5core/h5b_model.c

@@ -45,6 +45,7 @@ _normalize_partition (
 	}
 }
 
+#if defined(PARALLEL)
 /* MLH: this could be improved with an MPI_Reduce and MAX operator...
  * but the user_layout array-of-structs would need to be a struct-of-arrays */
 static void
@@ -72,6 +73,7 @@ _get_max_dimensions (
 			  ||   (p->k_end < q->k_start) )
 
 
+
 /*!
   \ingroup h5block_private
 
@@ -81,8 +83,8 @@ _get_max_dimensions (
 
   \return value != \c 0 if yes otherwise \c 0
 */
-static int
-_have_ghostzone (
+static inline int
+have_ghostzone (
 	const h5b_partition_t *const p,	/*!< IN: partition \c p */
 	const h5b_partition_t *const q	/*!< IN: partition \c q */
 	) {
@@ -98,8 +100,8 @@ _have_ghostzone (
 
   \return volume
 */
-static h5_int64_t
-_volume_of_partition (
+static inline h5_int64_t
+volume_of_partition (
 	const h5b_partition_t *const p	/*!< IN: partition */
 	) {
 	return (p->i_end - p->i_start)
@@ -117,8 +119,8 @@ _volume_of_partition (
 
   \return volume
 */
-static h5_int64_t
-_volume_of_ghostzone (
+static inline h5_int64_t
+volume_of_ghostzone (
 	const h5b_partition_t *const p,	/*!< IN: ptr to first partition */
 	const h5b_partition_t *const q	/*!< IN: ptr to second partition */
 	) {
@@ -248,8 +250,8 @@ _dissolve_ghostzone (
 	p_ = *p;
 	q_ = *q;
 	if ( _dissolve_X_ghostzone ( &p_, &q_ ) == 0 ) {
-		vol = _volume_of_partition ( &p_ ) 
-			+ _volume_of_partition ( &q_ );
+		vol = volume_of_partition ( &p_ ) 
+			+ volume_of_partition ( &q_ );
 		if ( vol > max_vol ) {
 			max_vol = vol;
 			p_best = p_;
@@ -260,8 +262,8 @@ _dissolve_ghostzone (
 	p_ = *p;
 	q_ = *q;
 	if ( _dissolve_Y_ghostzone ( &p_, &q_ ) == 0 ) {
-		vol = _volume_of_partition ( &p_ )
-			+ _volume_of_partition ( &q_ );
+		vol = volume_of_partition ( &p_ )
+			+ volume_of_partition ( &q_ );
 		if ( vol > max_vol ) {
 			max_vol = vol;
 			p_best = p_;
@@ -272,8 +274,8 @@ _dissolve_ghostzone (
 	q_ = *q;
 
 	if ( _dissolve_Z_ghostzone ( &p_, &q_ ) == 0 ) {
-		vol = _volume_of_partition ( &p_ )
-			+ _volume_of_partition ( &q_ );
+		vol = volume_of_partition ( &p_ )
+			+ volume_of_partition ( &q_ );
 		if ( vol > max_vol ) {
 			max_vol = vol;
 			p_best = p_;
@@ -313,7 +315,7 @@ _dissolve_ghostzone (
 
   \return H5_SUCCESS or error code.
 */
-static h5_err_t
+static inline h5_err_t
 _dissolve_ghostzones (
 	h5_file_t *const f,
 	const h5b_partition_t *const user_layout,
@@ -346,12 +348,12 @@ _dissolve_ghostzones (
 			proc_q < f->nprocs;
 			proc_q++, q++ ) {
 
-			if ( _have_ghostzone ( p, q ) ) {
+			if ( have_ghostzone ( p, q ) ) {
 				TRY( p_el = (struct list*)h5priv_alloc(f, NULL, sizeof(*p_el)) );
 
 				p_el->p = p;
 				p_el->q = q;
-				p_el->vol = _volume_of_ghostzone ( p, q );
+				p_el->vol = volume_of_ghostzone ( p, q );
 				p_el->prev = p_end;
 				p_el->next = NULL;
 				
@@ -373,8 +375,8 @@ _dissolve_ghostzones (
 		p_el = p_max = p_begin->next;
 
 		while ( p_el ) {
-			if ( _have_ghostzone ( p_el->p, p_el->q ) ) {
-				p_el->vol = _volume_of_ghostzone ( p_el->p, p_el->q );
+			if ( have_ghostzone ( p_el->p, p_el->q ) ) {
+				p_el->vol = volume_of_ghostzone ( p_el->p, p_el->q );
 				if ( p_el->vol > p_max->vol )
 					p_max = p_el;
 				p_el = p_el->next;
@@ -393,6 +395,7 @@ _dissolve_ghostzones (
 
 	return H5_SUCCESS;
 }
+#endif
 
 h5_err_t
 h5bpriv_release_hyperslab (
@@ -523,12 +526,12 @@ h5b_3d_has_view (
 h5_err_t
 h5b_3d_set_view (
 	h5_file_t *const f,		/*!< IN: File handle		*/
-	const h5_int64_t i_start,	/*!< IN: start index of \c i	*/ 
-	const h5_int64_t i_end,		/*!< IN: end index of \c i	*/  
-	const h5_int64_t j_start,	/*!< IN: start index of \c j	*/ 
-	const h5_int64_t j_end,		/*!< IN: end index of \c j	*/ 
-	const h5_int64_t k_start,	/*!< IN: start index of \c k	*/ 
-	const h5_int64_t k_end		/*!< IN: end index of \c k	*/
+	const h5_size_t i_start,	/*!< IN: start index of \c i	*/ 
+	const h5_size_t i_end,		/*!< IN: end index of \c i	*/  
+	const h5_size_t j_start,	/*!< IN: start index of \c j	*/ 
+	const h5_size_t j_end,		/*!< IN: end index of \c j	*/ 
+	const h5_size_t k_start,	/*!< IN: start index of \c k	*/ 
+	const h5_size_t k_end		/*!< IN: end index of \c k	*/
 	) {
 
 	h5b_partition_t *p = f->b->user_layout;
@@ -589,13 +592,13 @@ h5b_3d_set_view (
 
 h5_err_t
 h5b_3d_get_view (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i	*/  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j	*/ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c k	*/ 
 	) {
 
 	h5b_partition_t *p = f->b->user_layout;
@@ -612,13 +615,13 @@ h5b_3d_get_view (
 
 h5_err_t
 h5b_3d_get_reduced_view (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i	*/  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j	*/ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c k	*/ 
 	) {
 
 	h5b_partition_t *p = f->b->write_layout;
@@ -636,9 +639,9 @@ h5b_3d_get_reduced_view (
 h5_err_t
 h5b_3d_set_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
-	const h5_int64_t i,		/*!< IN: size of \c i */ 
-	const h5_int64_t j,		/*!< IN: size of \c j */  
-	const h5_int64_t k		/*!< IN: size of \c k */ 
+	const h5_size_t i,		/*!< IN: size of \c i */ 
+	const h5_size_t j,		/*!< IN: size of \c j */  
+	const h5_size_t k		/*!< IN: size of \c k */ 
 	) {
 
 	if ( i == 0 || j == 0 || k == 0 )
@@ -662,9 +665,9 @@ h5_err_t
 h5b_3d_get_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_int64_t *i,			/*!< OUT: size of \c i */ 
-	h5_int64_t *j,			/*!< OUT: size of \c j */  
-	h5_int64_t *k			/*!< OUT: size of \c k */ 
+	h5_size_t *const i,		/*!< OUT: size of \c i */ 
+	h5_size_t *const j,		/*!< OUT: size of \c j */  
+	h5_size_t *const k		/*!< OUT: size of \c k */ 
 	) {
 
 	CHECK_TIMEGROUP ( f );
@@ -696,6 +699,7 @@ h5b_3d_get_chunk (
 	return H5_SUCCESS;
 }
 
+#if defined(PARALLEL_IO)
 h5_err_t
 h5b_3d_set_grid (
 	h5_file_t *const f,		/*!< IN: File handle */
@@ -778,7 +782,6 @@ h5b_3d_set_dims (
 			(long long)dims[0], (long long)dims[1], (long long)dims[2],
 			(long long)check_dims[0], (long long)check_dims[1], (long long)check_dims[2]);
 	}
-
 	h5_int64_t coords[3];
 	TRY( h5b_3d_get_grid_coords(f,
 		f->myproc, coords+0, coords+1, coords+2) );
@@ -802,6 +805,7 @@ h5b_3d_set_dims (
 
 	return H5_SUCCESS;
 }
+#endif
 
 h5_err_t
 h5b_3d_set_halo (

src/h5core/h5b_readwrite.c

@@ -267,10 +267,9 @@ _select_hyperslab_for_reading (
 }
 
 static h5_err_t
-_read_data (
+read_data (
 	h5_file_t *const f,		/*!< IN: file handle */
-	const char *field_name,		/*!< IN: name of field */
-	const char *data_name,		/*!< IN: name of dataset */
+	const char *dataset_name,	/*!< IN: name of dataset */
 	void *data,			/*!< OUT: ptr to read buffer */
 	const hid_t type      		/*!< IN: data type */
 	) {
@@ -278,7 +277,7 @@ _read_data (
 	hid_t dataset;
 	h5b_fdata_t *b = f->b;
 
-	TRY( dataset = h5priv_open_hdf5_dataset(f, b->field_gid, data_name) );
+	TRY( dataset = h5priv_open_hdf5_dataset(f, b->field_gid, dataset_name) );
 	TRY( _select_hyperslab_for_reading(f, dataset) );
 	TRY( h5priv_read_hdf5_dataset(f,
 		dataset,
@@ -302,7 +301,7 @@ h5b_read_scalar_data (
 	CHECK_TIMEGROUP( f );
 	CHECK_LAYOUT( f );
 	TRY( h5bpriv_open_field_group(f, field_name) );
-	TRY( _read_data(f, field_name, H5_BLOCKNAME_X, data, type) );
+	TRY( read_data(f, H5_BLOCKNAME_X, data, type) );
 	return H5_SUCCESS;
 }
 
@@ -318,9 +317,9 @@ h5b_read_vector3d_data (
 	CHECK_TIMEGROUP( f );
 	CHECK_LAYOUT( f );
 	TRY( h5bpriv_open_field_group(f, field_name) );
-	TRY( _read_data(f, field_name, H5_BLOCKNAME_X, xdata, type) );
-	TRY( _read_data(f, field_name, H5_BLOCKNAME_Y, ydata, type) );
-	TRY( _read_data(f, field_name, H5_BLOCKNAME_Z, zdata, type) );
+	TRY( read_data(f, H5_BLOCKNAME_X, xdata, type) );
+	TRY( read_data(f, H5_BLOCKNAME_Y, ydata, type) );
+	TRY( read_data(f, H5_BLOCKNAME_Z, zdata, type) );
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_adjacencies.c

@@ -17,123 +17,13 @@
 #include "h5_core_private.h"
 
 h5_err_t
-h5t_get_edges_upadjacent_to_vertex (
+h5t_get_adjacencies (
 	h5_file_t* const f,
-	const h5_id_t local_vid,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
-	return (*f->t->methods.adjacency->get_edges_upadjacent_to_vertex)(
-		f, local_vid, list);
-}
-
-h5_err_t
-h5t_get_triangles_upadjacent_to_vertex (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_triangles_upadjacent_to_vertex)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_tets_upadjacent_to_vertex (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_tets_upadjacent_to_vertex)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_triangles_upadjacent_to_edge (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_triangles_upadjacent_to_edge)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_tets_upadjacent_to_edge (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_tets_upadjacent_to_edge)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_tets_upadjacent_to_triangle (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_tets_upadjacent_to_triangle)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_edge (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_vertices_downadjacent_to_edge)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_triangle (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_vertices_downadjacent_to_triangle)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_tet (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_vertices_downadjacent_to_tet)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_edges_downadjacent_to_triangle (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_edges_downadjacent_to_triangle)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_edges_downadjacent_to_tet (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_edges_downadjacent_to_tet)(
-		f, local_id, list);
-}
-
-h5_err_t
-h5t_get_triangles_downadjacent_to_tet (
-	h5_file_t* const f,
-	const h5_id_t local_id,
-	h5_idlist_t** list
-	) {
-	return (*f->t->methods.adjacency->get_triangles_downadjacent_to_tet)(
-		f, local_id, list);
+	return h5tpriv_get_adjacencies (f, entity_id, dim, list);
 }
 
 h5_err_t

src/h5core/h5t_adjacencies_private.h

@@ -4,4 +4,35 @@
 extern struct h5t_adjacency_methods h5tpriv_trim_adjacency_methods;
 extern struct h5t_adjacency_methods h5tpriv_tetm_adjacency_methods;
 
+static inline h5_err_t
+h5tpriv_get_adjacencies (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	if (f->t->methods.adjacency == NULL) {
+		h5_error_internal (f, __FILE__, __func__, __LINE__);
+	}
+	return (*f->t->methods.adjacency->get_adjacencies)(f, entity_id, dim, list);
+}
+
+static inline h5_err_t
+h5tpriv_release_adjacency_structs (
+	h5_file_t* const f
+	) {
+	if (f->t->methods.adjacency == NULL) {
+		return 0;
+	}
+	return (*f->t->methods.adjacency->release_internal_structs)(f);
+}
+
+static inline h5_err_t
+h5tpriv_update_adjacency_structs (
+	h5_file_t* const f,
+	const h5_id_t level_id
+	) {
+	return (*f->t->methods.adjacency->update_internal_structs)(f, level_id);
+}
+
 #endif

src/h5core/h5t_adjacencies_tetm.c

@@ -19,18 +19,18 @@
 /*
   compute T(V) from current level up to highest levels.
 */
-static h5_err_t
+static inline h5_err_t
 compute_elems_of_vertices (
 	h5_file_t* const f,
-	const h5_id_t from_lvl
+	const h5_id_t level_idx
 	) {
 	h5t_fdata_t* t = f->t;
-	h5_id_t idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_id_t idx = (level_idx <= 0) ? 0 : t->num_elems[level_idx-1];
 	h5_tet_t *el = &t->loc_elems.tets[idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	for (;idx < num_elems; idx++, el++) {
 		int face_idx;
-		int num_faces = t->ref_elem->num_faces[0];
+		int num_faces = h5tpriv_ref_elem_get_num_vertices(t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			h5_id_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
@@ -45,7 +45,7 @@ compute_elems_of_vertices (
 /*
   Compute T(E) from current level up to highest levels.
  */
-static h5_err_t
+static inline h5_err_t
 compute_elems_of_edges (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
@@ -57,7 +57,7 @@ compute_elems_of_edges (
 	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
 	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_elem->num_faces[1];
+		int num_faces = h5tpriv_ref_elem_get_num_edges(t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY( h5tpriv_search_te2 (
 				     f, face_idx, elem_idx, &retval) );
@@ -66,7 +66,7 @@ compute_elems_of_edges (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 compute_elems_of_triangles (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
@@ -75,10 +75,10 @@ compute_elems_of_triangles (
 	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_idlist_t *retval = NULL;
-	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
+	TRY( h5tpriv_resize_td_htab (f, 4*(num_elems-elem_idx)) );
 	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_elem->num_faces[1];
+		int num_faces = h5tpriv_ref_elem_get_num_edges (t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY( h5tpriv_search_td2 (
 				     f, face_idx, elem_idx, &retval) );
@@ -87,7 +87,7 @@ compute_elems_of_triangles (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 compute_children_of_edge (
 	h5_file_t* const f,
 	h5_id_t kid,
@@ -112,7 +112,7 @@ compute_children_of_edge (
 			TRY( h5priv_append_to_idlist (f, children, *edge) );
 		} else {
 			h5_id_t kids[2];
-			TRY( t->methods.store->get_direct_children_of_edge (
+			TRY( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
 				      tet->child_idx,
@@ -127,7 +127,7 @@ compute_children_of_edge (
 /* 
    Compute all sections of an edge.
 */
-static h5_err_t
+static inline h5_err_t
 compute_sections_of_edge (
 	h5_file_t* const f,
 	h5_id_t kid,
@@ -151,7 +151,7 @@ compute_sections_of_edge (
 		if (! h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			refined = 1;
 			h5_id_t kids[2];
-			TRY( t->methods.store->get_direct_children_of_edge (
+			TRY( h5tpriv_get_direct_children_of_edge (
 				     f,
 				     face_id,
 				     tet->child_idx,
@@ -197,7 +197,7 @@ compute_sections_of_edge (
   [4,5,7]: 0, 5       [4,6,8]: 2, 4       [5,6,9]: 1, 7       [7,8,9]: 3, 6
 
 */
-static h5_err_t
+static inline h5_err_t
 compute_direct_children_of_triangle (
 	h5_file_t* const f,
 	h5_id_t face_idx,
@@ -210,7 +210,7 @@ compute_direct_children_of_triangle (
 		{{2,0},{2,2},{2,3},{1,7}},
 		{{3,1},{3,2},{3,3},{3,6}}
 	};
-	int num_faces = f->t->ref_elem->num_faces[2];
+	int num_faces = h5tpriv_ref_elem_get_num_triangles (f->t);
 	if ((face_idx < 0) || (face_idx >= num_faces)) {
 		return h5_error_internal (f, __FILE__, __func__, __LINE__); 
 	}
@@ -225,7 +225,7 @@ compute_direct_children_of_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 compute_children_of_triangle (
 	h5_file_t* const f,
 	h5_id_t did,
@@ -264,7 +264,7 @@ compute_children_of_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 compute_sections_of_triangle (
 	h5_file_t* const f,
 	h5_id_t did,
@@ -307,8 +307,8 @@ compute_sections_of_triangle (
   map edge ID to unique ID
   if unique ID not in list: add
 */
-static h5_err_t
-_add_edge (
+static inline h5_err_t
+add_edge (
 	h5_file_t* const f,
 	h5_idlist_t* list,
 	h5_id_t face_idx,
@@ -321,8 +321,8 @@ _add_edge (
 }
 
 
-static h5_err_t
-get_edges_upadjacent_to_vertex (
+static inline h5_err_t
+get_edges_uadj_to_vertex (
 	h5_file_t* const f,
 	const h5_id_t vid,
 	h5_idlist_t** list
@@ -343,15 +343,15 @@ get_edges_upadjacent_to_vertex (
 			continue;
 		}
 		int map[4][3] = { {0,2,3}, {0,1,4}, {2,1,5}, {3,4,5} };
-		TRY( _add_edge (f, *list, map[face][0], eid) );
-		TRY( _add_edge (f, *list, map[face][1], eid) );
-		TRY( _add_edge (f, *list, map[face][2], eid) );
+		TRY( add_edge (f, *list, map[face][0], eid) );
+		TRY( add_edge (f, *list, map[face][1], eid) );
+		TRY( add_edge (f, *list, map[face][2], eid) );
 	}
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-_add_triangle (
+static inline h5_err_t
+add_triangle (
 	h5_file_t* const f,
 	h5_idlist_t* list,
 	h5_id_t face,
@@ -364,8 +364,8 @@ _add_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_triangles_upadjacent_to_vertex (
+static inline h5_err_t
+get_triangles_uadj_to_vertex (
 	h5_file_t * const f,
 	const h5_id_t vid,
 	h5_idlist_t **list
@@ -385,15 +385,15 @@ get_triangles_upadjacent_to_vertex (
 			continue;
 		}
 		int map[4][3] = { {1,2,3}, {0,2,3}, {0,1,3}, {0,1,2} };
-		TRY( _add_triangle (f, *list, map[face][0], eid) );
-		TRY( _add_triangle (f, *list, map[face][1], eid) );
-		TRY( _add_triangle (f, *list, map[face][2], eid) );
+		TRY( add_triangle (f, *list, map[face][0], eid) );
+		TRY( add_triangle (f, *list, map[face][1], eid) );
+		TRY( add_triangle (f, *list, map[face][2], eid) );
 	}
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_tets_upadjacent_to_vertex (
+static inline h5_err_t
+get_tets_uadj_to_vertex (
 	h5_file_t* const f,
 	const h5_id_t vid,
 	h5_idlist_t** list
@@ -416,8 +416,8 @@ get_tets_upadjacent_to_vertex (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_triangles_upadjacent_to_edge (
+static inline h5_err_t
+get_triangles_uadj_to_edge (
 	h5_file_t* const f,
 	const h5_id_t kid,
 	h5_idlist_t** list
@@ -432,16 +432,16 @@ get_triangles_upadjacent_to_edge (
 	for (; edge < end; edge++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*edge);
 		h5_id_t face_idx = h5tpriv_get_face_idx (*edge);
-		TRY( _add_triangle (f, *list, map[face_idx][0], eid) );
-		TRY( _add_triangle (f, *list, map[face_idx][1], eid) );
+		TRY( add_triangle (f, *list, map[face_idx][0], eid) );
+		TRY( add_triangle (f, *list, map[face_idx][1], eid) );
 	}
 	TRY( h5priv_free_idlist ( f, &children) );
 
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_tets_upadjacent_to_edge (
+static inline h5_err_t
+get_tets_uadj_to_edge (
 	h5_file_t* const f,
 	const h5_id_t kid,
 	h5_idlist_t** list
@@ -460,8 +460,8 @@ get_tets_upadjacent_to_edge (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_tets_upadjacent_to_triangle (
+static inline h5_err_t
+get_tets_uadj_to_triangle (
 	h5_file_t* const f,
 	const h5_id_t did,
 	h5_idlist_t** list
@@ -480,8 +480,8 @@ get_tets_upadjacent_to_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_vertices_downadjacent_to_edge (
+static inline h5_err_t
+get_vertices_dadj_to_edge (
 	h5_file_t* const f,
 	const h5_id_t kid,
 	h5_idlist_t** list
@@ -505,8 +505,8 @@ get_vertices_downadjacent_to_edge (
 /*
   Compute downward adjacent vertices of all edges of triangle.
  */
-static h5_err_t
-get_vertices_downadjacent_to_triangle (
+static inline h5_err_t
+get_vertices_dadj_to_triangle (
 	h5_file_t* const f,
 	const h5_id_t did,
 	h5_idlist_t** list
@@ -540,8 +540,8 @@ get_vertices_downadjacent_to_triangle (
 /*
   Compute downward adjacent vertices of all edges of tetrahedron.
  */
-static h5_err_t
-get_vertices_downadjacent_to_tet (
+static inline h5_err_t
+get_vertices_dadj_to_tet (
 	h5_file_t* const f,
 	const h5_id_t eid,
 	h5_idlist_t** list
@@ -568,8 +568,8 @@ get_vertices_downadjacent_to_tet (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_edges_downadjacent_to_triangle (
+static inline h5_err_t
+get_edges_dadj_to_triangle (
 	h5_file_t* const f,
 	const h5_id_t did,
 	h5_idlist_t** list
@@ -597,8 +597,8 @@ get_edges_downadjacent_to_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_edges_downadjacent_to_tet (
+static inline h5_err_t
+get_edges_dadj_to_tet (
 	h5_file_t* const f,
 	const h5_id_t eid,
 	h5_idlist_t** list
@@ -622,8 +622,8 @@ get_edges_downadjacent_to_tet (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_triangles_downadjacent_to_tet (
+static inline h5_err_t
+get_triangles_dadj_to_tet (
 	h5_file_t* const f,
 	const h5_id_t eid,
 	h5_idlist_t** list
@@ -647,6 +647,117 @@ get_triangles_downadjacent_to_tet (
 	return H5_SUCCESS;
 }
 
+static inline h5_err_t
+dim_error(
+	h5_file_t* const f,
+	const h5_int32_t dim
+	) {
+	return h5_error (
+		f,
+		H5_ERR_INVAL,
+		"Illegal dimension %ld", (long)dim);
+}
+
+static inline h5_err_t
+get_adjacencies_to_vertex (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 1:
+		return get_edges_uadj_to_vertex(f, entity_id, list);
+	case 2:
+		return get_triangles_uadj_to_vertex(f, entity_id, list);
+	case 3:
+		return get_tets_uadj_to_vertex(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static inline h5_err_t
+get_adjacencies_to_edge (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 0:
+		return get_vertices_dadj_to_edge(f, entity_id, list);
+	case 2:
+		return get_triangles_uadj_to_edge(f, entity_id, list);
+	case 3:
+		return get_tets_uadj_to_edge(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static inline h5_err_t
+get_adjacencies_to_triangle (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 0:
+		return get_vertices_dadj_to_triangle(f, entity_id, list);
+	case 1:
+		return get_edges_dadj_to_triangle(f, entity_id, list);
+	case 3:
+		return get_tets_uadj_to_triangle(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static inline h5_err_t
+get_adjacencies_to_tet (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 0:
+		return get_vertices_dadj_to_tet(f, entity_id, list);
+	case 1:
+		return get_edges_dadj_to_tet(f, entity_id, list);
+	case 2:
+		return get_triangles_dadj_to_tet(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static h5_err_t
+get_adjacencies (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
+	switch (entity_type) {
+	case H5T_ETYPE_VERTEX:
+		return get_adjacencies_to_vertex (f, entity_id, dim, list);
+	case H5T_ETYPE_EDGE:
+		return get_adjacencies_to_edge (f, entity_id, dim, list);
+	case H5T_ETYPE_TRIANGLE:
+		return get_adjacencies_to_triangle (f, entity_id, dim, list);
+	case H5T_ETYPE_TET:
+		return get_adjacencies_to_tet (f, entity_id, dim, list);
+	default:
+		break;
+	}
+	return h5_error_internal (f, __FILE__, __func__, __LINE__);
+}
+
+
 static h5_err_t
 update_internal_structs (
 	h5_file_t* const f,
@@ -671,11 +782,11 @@ update_internal_structs (
 	return H5_SUCCESS;
 }
 
-
 static h5_err_t
 release_internal_structs (
 	h5_file_t * const f
 	) {
+#pragma unused f
 	/* TO BE WRITTEN @@@ */
 	return H5_SUCCESS;
 }
@@ -683,17 +794,6 @@ release_internal_structs (
 struct h5t_adjacency_methods h5tpriv_tetm_adjacency_methods = {
 	update_internal_structs,
 	release_internal_structs,
-	get_edges_upadjacent_to_vertex,
-	get_triangles_upadjacent_to_vertex,
-	get_tets_upadjacent_to_vertex,
-	get_triangles_upadjacent_to_edge,
-	get_tets_upadjacent_to_edge,
-	get_tets_upadjacent_to_triangle,
-	get_vertices_downadjacent_to_edge,
-	get_vertices_downadjacent_to_triangle,
-	get_vertices_downadjacent_to_tet,
-	get_edges_downadjacent_to_triangle,
-	get_edges_downadjacent_to_tet,
-	get_triangles_downadjacent_to_tet
+	get_adjacencies,
 };
 

src/h5core/h5t_adjacencies_trim.c

@@ -19,7 +19,7 @@
 /*
   compute T(V) from current level up to highest levels.
 */
-static h5_err_t
+static inline h5_err_t
 compute_elems_of_vertices (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
@@ -30,7 +30,7 @@ compute_elems_of_vertices (
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	for (;elem_idx < num_elems; elem_idx++, el++) {
 		int face_idx;
-		int num_faces = t->ref_elem->num_faces[0];
+		int num_faces = h5tpriv_ref_elem_get_num_vertices (t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			h5_id_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
@@ -46,7 +46,7 @@ compute_elems_of_vertices (
 /*
   Compute T(E) from current level up to highest levels.
  */
-static h5_err_t
+static inline h5_err_t
 compute_elems_of_edges (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
@@ -58,7 +58,7 @@ compute_elems_of_edges (
 	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
 	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_elem->num_faces[1];
+		int num_faces = h5tpriv_ref_elem_get_num_edges (t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY ( h5tpriv_search_te2 (
 				      f, face_idx, elem_idx, &retval ) );
@@ -67,7 +67,7 @@ compute_elems_of_edges (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 compute_children_of_edge (
 	h5_file_t * const f,
 	h5_id_t kid,
@@ -94,7 +94,7 @@ compute_children_of_edge (
 				);
 		} else {
 			h5_id_t kids[2];
-			TRY ( t->methods.store->get_direct_children_of_edge (
+			TRY ( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
 				      el->child_idx,
@@ -111,7 +111,7 @@ compute_children_of_edge (
 /* 
    Compute all sections of an edge.
 */
-static h5_err_t
+static inline h5_err_t
 compute_sections_of_edge (
 	h5_file_t * const f,
 	h5_id_t kid,
@@ -136,7 +136,7 @@ compute_sections_of_edge (
 		if ( ! h5tpriv_elem_is_on_cur_level ( f, el ) == H5_OK ) {
 			refined = 1;
 			h5_id_t kids[2];
-			TRY ( t->methods.store->get_direct_children_of_edge (
+			TRY ( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_id,
 				      el->child_idx,
@@ -158,7 +158,7 @@ compute_sections_of_edge (
   map edge ID to unique ID
   if unique ID not in list: add
 */
-static h5_err_t
+static inline h5_err_t
 add_edge (
 	h5_file_t * const f,
 	h5_idlist_t *list,
@@ -172,8 +172,8 @@ add_edge (
 }
 
 
-static h5_err_t
-get_edges_upadjacent_to_vertex (
+static inline h5_err_t
+get_edges_uadj_to_vertex (
 	h5_file_t * const f,
 	const h5_id_t entity_id,
 	h5_idlist_t **list
@@ -206,8 +206,8 @@ get_edges_upadjacent_to_vertex (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_triangles_upadjacent_to_vertex (
+static inline h5_err_t
+get_triangles_uadj_to_vertex (
 	h5_file_t * const f,
 	const h5_id_t entity_id,
 	h5_idlist_t **list
@@ -230,8 +230,8 @@ get_triangles_upadjacent_to_vertex (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_triangles_upadjacent_to_edge (
+static inline h5_err_t
+get_triangles_uadj_to_edge (
 	h5_file_t * const f,
 	const h5_id_t entity_id,
 	h5_idlist_t **list
@@ -251,8 +251,8 @@ get_triangles_upadjacent_to_edge (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_vertices_downadjacent_to_edge (
+static inline h5_err_t
+get_vertices_dadj_to_edge (
 	h5_file_t * const f,
 	const h5_id_t entity_id,
 	h5_idlist_t **list
@@ -276,8 +276,8 @@ get_vertices_downadjacent_to_edge (
 /*
   Compute downward adjacent vertices of all edges of triangle.
  */
-static h5_err_t
-get_vertices_downadjacent_to_triangle (
+static inline h5_err_t
+get_vertices_dadj_to_triangle (
 	h5_file_t* const f,
 	const h5_id_t entity_id,
 	h5_idlist_t** list
@@ -288,7 +288,7 @@ get_vertices_downadjacent_to_triangle (
 	h5_id_t elem_idx = h5tpriv_get_elem_idx ( entity_id );
 	// loop over all edges of triangle
 	h5_id_t face_idx;
-	h5_id_t num_faces = f->t->ref_elem->num_faces[1];
+	h5_id_t num_faces = h5tpriv_ref_elem_get_num_edges (f->t);
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
 		TRY( compute_sections_of_edge (
 			     f,
@@ -308,8 +308,8 @@ get_vertices_downadjacent_to_triangle (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
-get_edges_downadjacent_to_triangle (
+static inline h5_err_t
+get_edges_dadj_to_triangle (
 	h5_file_t* const f,
 	const h5_id_t entity_id,
 	h5_idlist_t** list
@@ -320,7 +320,7 @@ get_edges_downadjacent_to_triangle (
 	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	// loop over all edges of triangle
 	h5_id_t face_idx;
-	h5_id_t num_faces = f->t->ref_elem->num_faces[1];
+	h5_id_t num_faces = h5tpriv_ref_elem_get_num_edges (f->t);
 	for ( face_idx = 0; face_idx < num_faces; face_idx++ ) {
 		TRY( compute_sections_of_edge (
 			     f,
@@ -337,7 +337,90 @@ get_edges_downadjacent_to_triangle (
 	return H5_SUCCESS;
 }
 
+static inline h5_err_t
+dim_error(
+	h5_file_t* const f,
+	const h5_int32_t dim
+	) {
+	return h5_error (
+		f,
+		H5_ERR_INVAL,
+		"Illegal dimension %ld", (long)dim);
+}
+
+static inline h5_err_t
+get_adjacencies_to_vertex (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 1:
+		return get_edges_uadj_to_vertex(f, entity_id, list);
+	case 2:
+		return get_triangles_uadj_to_vertex(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static inline h5_err_t
+get_adjacencies_to_edge (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 0:
+		return get_vertices_dadj_to_edge(f, entity_id, list);
+	case 2:
+		return get_triangles_uadj_to_edge(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
+static inline h5_err_t
+get_adjacencies_to_triangle (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	switch (dim) {
+	case 0:
+		return get_vertices_dadj_to_triangle(f, entity_id, list);
+	case 1:
+		return get_edges_dadj_to_triangle(f, entity_id, list);
+	default:
+		return dim_error (f, dim);
+	}
+}
+
 static h5_err_t
+get_adjacencies (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
+	) {
+	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
+	switch (entity_type) {
+	case H5T_ETYPE_VERTEX:
+		return get_adjacencies_to_vertex (f, entity_id, dim, list);
+	case H5T_ETYPE_EDGE:
+		return get_adjacencies_to_edge (f, entity_id, dim, list);
+	case H5T_ETYPE_TRIANGLE:
+		return get_adjacencies_to_triangle (f, entity_id, dim, list);
+	default:
+		break;
+	}
+	return h5_error_internal (f, __FILE__, __func__, __LINE__);
+}
+
+static inline h5_err_t
 update_internal_structs (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
@@ -356,10 +439,11 @@ update_internal_structs (
 	return H5_SUCCESS;
 }
 
-static h5_err_t
+static inline h5_err_t
 release_internal_structs (
 	h5_file_t* const f
 	) {
+#pragma unused f
 	/* TO BE WRITTEN @@@ */
 	return H5_SUCCESS;
 }
@@ -367,17 +451,6 @@ release_internal_structs (
 struct h5t_adjacency_methods h5tpriv_trim_adjacency_methods = {
 	update_internal_structs,
 	release_internal_structs,
-	get_edges_upadjacent_to_vertex,
-	get_triangles_upadjacent_to_vertex,
-	NULL,
-	get_triangles_upadjacent_to_edge,
-	NULL,
-	NULL,
-	get_vertices_downadjacent_to_edge,
-	get_vertices_downadjacent_to_triangle,
-	NULL,
-	get_edges_downadjacent_to_triangle,
-	NULL,
-	NULL
+	get_adjacencies
 };
 

src/h5core/h5t_core_private.h

@@ -3,20 +3,21 @@
 
 #define H5T_CONTAINER_GRPNAME	"Topo"
 
-
-#include "h5t_openclose_private.h"
-#include "h5t_adjacencies_private.h"
-#include "h5t_consts_private.h"
-#include "h5t_errorhandling_private.h"
-#include "h5t_hsearch_private.h"
-#include "h5t_map_private.h"
-#include "h5t_readwrite_private.h"
-#include "h5t_store_private.h"
 #include "h5t_tags_private.h"
 
 #include "h5t_types_private.h"
 
 #include "h5t_access_private.h"
+#include "h5t_adjacencies_private.h"
+#include "h5t_consts_private.h"
+#include "h5t_inquiry_private.h"
+#include "h5t_errorhandling_private.h"
+#include "h5t_hsearch_private.h"
+#include "h5t_map_private.h"
+#include "h5t_openclose_private.h"
+#include "h5t_ref_elements_private.h"
+#include "h5t_readwrite_private.h"
 #include "h5t_retrieve_private.h"
+#include "h5t_store_private.h"
 
 #endif

src/h5core/h5t_errorhandling.c

@@ -18,7 +18,7 @@ h5tpriv_error_local_elem_nexist (
 	int num_chars_printed = snprintf (s, sizeof(s), "%lld,",
 					  (long long)local_vertex_indices[0]);
 	int i;
-	int num_vertices = t->ref_elem->num_faces[0];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
 	for (i = 1; i < num_vertices; i++) {
 		num_chars_printed += snprintf (
 			s + num_chars_printed, sizeof (s) - num_chars_printed,

src/h5core/h5t_hsearch.c

@@ -244,21 +244,25 @@ h5tpriv_search_td2 (
 			     3*(num_elems-elem_idx),
 			     &a->td_hash));
 	}
-
+	/* search in directory, add if entry doen't already exists */
 	TRY( h5priv_hsearch (
 		     f,
 		     entry,
 		     H5_ENTER,
 		     &__retval,
 		     &a->td_hash) );
-	h5t_td_entry_t *te_entry = (h5t_td_entry_t *)__retval;
+
+	/* search ID in list of IDs for given triangle */
+	h5t_td_entry_t *td_entry = (h5t_td_entry_t *)__retval;
 	TRY( h5priv_search_idlist (
 		     f,
-		     &te_entry->value,
+		     &td_entry->value,
 		     h5tpriv_build_triangle_id (face_idx, elem_idx)) );
-	if (te_entry->value.num_items > 1) {
+	if (td_entry->value.num_items > 1) {
 		TRY( h5priv_free (f, entry) );
 	}
+	*retval = &td_entry->value;
+
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_inquiry.c

@@ -12,23 +12,20 @@
 h5_size_t
 h5t_get_num_meshes (
 	h5_file_t* const f,
-	const enum h5_oid type_id
+	const h5_oid_t type_id
 	) {
-	h5t_fdata_t* t = f->t;
+	hid_t topo_gid;
+	hid_t meshes_gid;
 
-	if (t->num_meshes >= 0) {
-		return t->num_meshes;
-	}
-	if (t->topo_gid < 0) {
-		TRY( h5tpriv_open_topo_group (f) );
-	}
-	TRY( t->num_meshes = h5_get_num_hdf5_groups (f, t->meshes_gid) );
+	TRY( topo_gid = h5priv_open_group (f, f->root_gid, H5T_CONTAINER_GRPNAME) );
+	TRY( meshes_gid = h5priv_open_group (
+		     f, topo_gid, h5tpriv_meshes_grpnames[type_id]) );
 
-	return t->num_meshes;
+	return h5_get_num_hdf5_groups (f, meshes_gid);
 }
 
 /*!
-  Get the number of hierarchical mesh levels.
+  Get the number of hierarchical mesh levels for the current mesh.
 
   \param[in]	f	File handle
 
@@ -78,6 +75,7 @@ h5t_get_num_elems (
 	h5_file_t* const f,
 	const h5_id_t cnode
 	) {
+#pragma unused cnode
 	h5t_fdata_t* t = f->t;
 
 	if (t->cur_mesh < 0) {
@@ -107,6 +105,7 @@ h5t_get_num_vertices (
 	h5_file_t* const f,
 	h5_id_t cnode
 	) {
+#pragma unused cnode
 	h5t_fdata_t* t = f->t;
 
 	if (t->cur_mesh < 0) {

src/h5core/h5t_map.c

@@ -112,7 +112,7 @@ cmp_elems (
 	const h5_id_t elem_idx2
 	) {
 	h5t_fdata_t* t = f->t;
-	int num_vertices = t->ref_elem->num_faces[0];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
 	h5_id_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
 	h5_id_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
 
@@ -136,7 +136,7 @@ cmp_elems1 (
 	h5_id_t elem_idx2
 	) {
 	h5t_fdata_t *t = f->t;
-	int num_vertices = t->ref_elem->num_faces[0];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
 	h5_id_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
 	h5_id_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
 
@@ -184,7 +184,7 @@ qsort_cmp_elems1 (
   binary search. 
 */
 h5_err_t
-h5tpriv_sort_elems (
+h5tpriv_sort_loc_elems (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
@@ -281,9 +281,9 @@ h5t_map_global_vertex_indices2local (
   Get local element idx of element given by its global idx.
 
   \param[in]	f		File handle
-  \param[in]	global_idx	Global element id
+  \param[in]	glb_idx		Global element index
 
-  \return	Local element id or error code.
+  \return	Local element index or error code.
 */
 h5_id_t
 h5t_map_global_elem_idx2local (
@@ -316,18 +316,24 @@ h5t_map_global_elem_indices2local (
 	return H5_SUCCESS;
 }
 
+
+/*
+
+ */
 h5_err_t
 h5tpriv_rebuild_global_2_local_map_of_vertices (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
-	h5_id_t local_vid = t->cur_level > 0 ?
-		t->num_vertices[t->cur_level-1] : 0;
-	for (; local_vid < t->num_vertices[t->num_levels-1]; local_vid++) {
-		t->map_vertex_g2l.items[local_vid].global_id =
-			t->vertices[local_vid].global_idx; 
-		t->map_vertex_g2l.items[local_vid].local_id = local_vid;
+
+	h5_loc_idx_t loc_idx = t->cur_level > 0 ? t->num_vertices[t->cur_level-1] : 0;
+	h5_loc_idx_t num_loc_vertices = t->num_vertices[t->num_levels-1];
+	h5_idmap_el_t *item = &t->map_vertex_g2l.items[loc_idx];
+
+	for (; loc_idx < num_loc_vertices; loc_idx++, item++) {
+		item->global_id = t->vertices[loc_idx].idx; 
+		item->local_id = loc_idx;
 		t->map_vertex_g2l.num_items++;
 	}
 	h5priv_sort_idmap (&t->map_vertex_g2l);
@@ -342,13 +348,13 @@ h5tpriv_rebuild_global_2_local_map_of_elems (
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
 
-	h5_id_t idx = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
-	h5_id_t num_elems = t->num_elems[t->num_levels-1];
-	h5_idmap_el_t *item = &t->map_elem_g2l.items[idx];
+	h5_id_t loc_idx = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
+	h5_id_t num_loc_elems = t->num_elems[t->num_levels-1];
+	h5_idmap_el_t *item = &t->map_elem_g2l.items[loc_idx];
 
-	for (; idx < num_elems; idx++, item++) {
-		item->global_id = h5tpriv_get_glb_elem_idx (f, idx);
-		item->local_id = idx;
+	for (; loc_idx < num_loc_elems; loc_idx++, item++) {
+		item->global_id = h5tpriv_get_glb_elem_idx (f, loc_idx);
+		item->local_id = loc_idx;
 		t->map_elem_g2l.num_items++;
 	}
 	h5priv_sort_idmap (&t->map_elem_g2l);

src/h5core/h5t_map_private.h

@@ -14,7 +14,7 @@ h5tpriv_sort_vertices (
 	);
 
 h5_err_t
-h5tpriv_sort_elems (
+h5tpriv_sort_loc_elems (
 	h5_file_t * const f
 	);
 

src/h5core/h5t_openclose.c

@@ -71,8 +71,8 @@ create_vertex_type (
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_vertex_t,
-			"global_idx",
-			HOFFSET (struct h5_vertex, global_idx),
+			"idx",
+			HOFFSET (struct h5_vertex, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
@@ -206,9 +206,9 @@ create_tet_type (
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
-			dtypes->h5_triangle_t,
+			dtypes->h5_tet_t,
 			"neighbor_indices",
-			HOFFSET(struct h5_triangle, neighbor_indices),
+			HOFFSET (struct h5_tetrahedron, neighbor_indices),
 			dtypes->h5_4id_t) );
 
 	return H5_SUCCESS;
@@ -384,6 +384,7 @@ h5_err_t
 h5tpriv_init_step (
 	h5_file_t* const f
 	) {
+#pragma unused f
 	return H5_SUCCESS;
 }
 
@@ -396,7 +397,7 @@ h5_err_t
 h5tpriv_close_step (
 	h5_file_t* const f
 	) {
-
+#pragma unused f
 	return H5_SUCCESS;
 }
 
@@ -413,7 +414,8 @@ h5tpriv_open_topo_group (
 
 h5_err_t
 h5tpriv_open_meshes_group (
-	h5_file_t* const f
+	h5_file_t* const f,
+	const h5_oid_t type_id
 	) {
 	h5t_fdata_t* t = f->t;
 
@@ -423,24 +425,34 @@ h5tpriv_open_meshes_group (
 	TRY( (t->meshes_gid = h5priv_open_group (
 		      f,
 		      t->topo_gid,
-		      h5tpriv_meshes_grpnames[t->mesh_type])) );
+		      h5tpriv_meshes_grpnames[type_id])) );
+	t->mesh_type = type_id;
 
 	return H5_SUCCESS;
 }
 
+/*
+  Open HDF5 group with specific mesh
+*/
+
 h5_err_t
 h5tpriv_open_mesh_group (
-	h5_file_t* const f
+	h5_file_t* const f,
+	const h5_oid_t type_id,
+	const h5_id_t id
 	) {
 	h5t_fdata_t* t = f->t;
 
 	if (t->meshes_gid < 0) {
-		TRY( h5tpriv_open_meshes_group (f) );
+		TRY( h5tpriv_open_meshes_group (f, type_id) );
 	}
+	snprintf (t->mesh_name, sizeof (t->mesh_name), "%lld", (long long)id);
+
 	TRY( (t->mesh_gid = h5priv_open_group (
 		      f,
 		      t->meshes_gid,
 		      t->mesh_name)) );
+	t->cur_mesh = id;
 	return H5_SUCCESS;
 }
 
@@ -451,14 +463,14 @@ h5_err_t
 h5t_open_mesh (
 	h5_file_t* const f,
 	h5_id_t id,
-	const h5_oid_t type
+	const h5_oid_t type_id
 	) {
 	h5t_fdata_t* t = f->t;
 
 	TRY( h5t_close_mesh (f) );
 
 	if (t->num_meshes < 0) {
-		h5_size_t result = h5t_get_num_meshes (f, type);
+		h5_size_t result = h5t_get_num_meshes (f, type_id);
 		t->num_meshes = (result > 0 ? result : 0);
 	}
 	if ((id < -1) || (id >= t->num_meshes)) {
@@ -467,10 +479,7 @@ h5t_open_mesh (
 	if (id == -1) {  /* append new mesh */
 		id = t->num_meshes;
 	}
-	t->mesh_type = type;
-	snprintf (t->mesh_name, sizeof (t->mesh_name), "%lld", (long long)id);
-
-	switch (type) {
+	switch (type_id) {
 	case H5_OID_TETRAHEDRON:
 		t->dsinfo_elems.type_id = t->dtypes.h5_tet_t;
 		t->methods = tet_funcs;
@@ -485,9 +494,7 @@ h5t_open_mesh (
 		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 
-	TRY( h5tpriv_open_mesh_group (f) );
-
-	t->cur_mesh = id;
+	TRY( h5tpriv_open_mesh_group (f, type_id, id) );
 
 	if (id != t->num_meshes) {	/* open existing */
 		TRY( h5tpriv_read_mesh (f) );
@@ -533,9 +540,7 @@ release_memory (
 	h5_file_t* const f
 	) {
 	TRY( h5tpriv_release_tags (f) );
-	if (f->t->methods.adjacency != NULL) {
-		TRY( (*f->t->methods.adjacency->release_internal_structs) (f) );
-	}
+	TRY( h5tpriv_release_adjacency_structs (f) );
 	TRY( release_elems (f) );
 	TRY( release_vertices (f) );
 
@@ -569,7 +574,7 @@ h5t_set_level (
 	t->cur_level = level_id;
 
 	if (level_id >= t->num_loaded_levels) {
-		TRY( (t->methods.adjacency->update_internal_structs)(f, prev_level+1) );
+		TRY( (h5tpriv_update_adjacency_structs)(f, prev_level+1) );
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_openclose_private.h

@@ -4,8 +4,8 @@
 h5_err_t h5tpriv_open_file ( h5_file_t * const f );
 h5_err_t h5tpriv_close_file ( h5_file_t * const f );
 h5_err_t h5tpriv_open_topo_group (	h5_file_t * const f );
-h5_err_t h5tpriv_open_meshes_group ( h5_file_t * const f );
-h5_err_t h5tpriv_open_mesh_group ( h5_file_t * const f );
+h5_err_t h5tpriv_open_meshes_group ( h5_file_t * const f, const h5_oid_t );
+h5_err_t h5tpriv_open_mesh_group ( h5_file_t * const f, const h5_oid_t, const h5_id_t );
 h5_err_t h5tpriv_close_step ( h5_file_t * const f );
 
 h5_err_t h5tpriv_init_fdata ( h5_file_t * const f );

src/h5core/h5t_readwrite.c

@@ -6,6 +6,8 @@ open_space_all (
 	h5_file_t* const f,
 	const hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -25,9 +27,6 @@ write_vertices (
 
 	if (t->num_vertices <= 0) return H5_SUCCESS;  /* ???? */
 
- 	if (t->mesh_gid < 0) {
-		TRY( h5tpriv_open_mesh_group (f) );
-	}
 	t->dsinfo_vertices.dims[0] = t->num_vertices[t->cur_level];
 	TRY( h5priv_write_dataset_by_name (
 		     f,
@@ -55,10 +54,6 @@ write_elems (
 	
 	if (t->num_elems <= 0) return H5_SUCCESS;
 
-	if (t->mesh_gid < 0) {
-		TRY( h5tpriv_open_mesh_group (f) );
-	}
-
 	TRY( h5priv_write_dataset_by_name (
 		     f,
 		     t->mesh_gid,
@@ -129,6 +124,8 @@ open_mem_space_vertices (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -137,6 +134,8 @@ open_file_space_vertices (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -147,7 +146,7 @@ read_num_vertices (
 	h5t_fdata_t* t = f->t;
 
  	if (t->mesh_gid < 0) {
-		TRY( h5tpriv_open_mesh_group (f) );
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	ssize_t num_bytes = t->num_levels*sizeof (t->num_vertices[0]);
 	TRY( t->num_vertices = h5priv_alloc (f, t->num_vertices, num_bytes) );
@@ -191,7 +190,7 @@ read_num_elems (
 	h5t_fdata_t* t = f->t;
 
  	if (t->mesh_gid < 0) {
-		TRY( h5tpriv_open_mesh_group (f) );
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	size_t size = t->num_levels * sizeof (t->num_elems[0]);
 	TRY( t->num_elems = h5priv_alloc (f, NULL, size) );
@@ -220,6 +219,8 @@ open_mem_space_elems (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -228,6 +229,8 @@ open_file_space_elems (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -239,8 +242,7 @@ read_elems (
 	) {
 	h5t_fdata_t* t = f->t;
 
-	TRY( (*t->methods.store->alloc_elems)(
-		     f, 0, t->num_elems[t->num_levels-1]) );
+	TRY( h5tpriv_alloc_elems(f, 0, t->num_elems[t->num_levels-1]) );
 	TRY( h5priv_read_dataset_by_name (
 		     f,
 		     t->mesh_gid,
@@ -249,9 +251,9 @@ read_elems (
 		     open_file_space_elems,
 		     t->glb_elems.data) );
 
-	TRY( h5tpriv_sort_elems (f) );
+	TRY( h5tpriv_sort_loc_elems (f) );
 	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
-	TRY( (*f->t->methods.read->init_loc_elems_struct) (f) );
+	TRY( h5tpriv_init_loc_elems_struct (f) );
 
 	return H5_SUCCESS;
 }
@@ -270,15 +272,15 @@ h5tpriv_read_mesh (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
- 	if (f->t->mesh_gid < 0) {
-		TRY( h5tpriv_open_mesh_group (f) );
+ 	if (t->mesh_gid < 0) {
+		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	TRY( read_num_levels (f) );
 	TRY( read_num_vertices (f) );
 	TRY( read_num_elems (f) );
 	TRY( read_vertices (f) );
 	TRY( read_elems (f) );
-	TRY( (t->methods.adjacency->update_internal_structs)(f, 0) );
+	TRY( h5tpriv_update_adjacency_structs (f, 0) );
 	TRY( read_mtags (f) );
 	t->num_loaded_levels = t->num_levels;
 	return H5_SUCCESS;

src/h5core/h5t_readwrite_private.h

@@ -25,4 +25,11 @@ h5tpriv_write_mesh (
 extern struct h5t_read_methods h5tpriv_read_trim_methods;
 extern struct h5t_read_methods h5tpriv_read_tetm_methods;
 
+static inline h5_err_t
+h5tpriv_init_loc_elems_struct (
+	h5_file_t* const f
+	) {
+	return (*f->t->methods.read->init_loc_elems_struct) (f);
+}
+
 #endif

src/h5core/h5t_readwrite_tetm.c

@@ -12,8 +12,8 @@ init_loc_elems_struct (
 	h5_id_t idx = 0;
 	const h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_id_t level_idx = 0;
-	int num_vertices = t->ref_elem->num_faces[0];
-	int num_edges = t->ref_elem->num_faces[1];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
+	int num_edges = h5tpriv_ref_elem_get_num_edges (t);
 	h5_tet_t* loc_elem = t->loc_elems.tets;
 	h5_tet_t* glb_elem = t->glb_elems.tets;
 

src/h5core/h5t_readwrite_trim.c

@@ -12,8 +12,8 @@ init_loc_elems_struct (
 	h5_id_t idx = 0;
 	const h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_id_t level_idx = 0;
-	int num_vertices = t->ref_elem->num_faces[0];
-	int num_edges = t->ref_elem->num_faces[1];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
+	int num_edges = h5tpriv_ref_elem_get_num_edges (t);
 	h5_triangle_t* loc_elem = t->loc_elems.tris;
 	h5_triangle_t* glb_elem = t->glb_elems.tris;
 

src/h5core/h5t_ref_elements_private.h

@@ -0,0 +1,11 @@
+#ifndef __H5T_REF_ELEMENTS_PRIVATE_H
+#define __H5T_REF_ELEMENTS_PRIVATE_H
+
+#define h5tpriv_ref_elem_get_num_vertices(this) (this->ref_elem->num_faces[0])
+#define h5tpriv_ref_elem_get_num_edges(this) (this->ref_elem->num_faces[1])
+#define h5tpriv_ref_elem_get_num_triangles(this) (this->ref_elem->num_faces[2])
+#define h5tpriv_ref_elem_get_num_faces(this, dim) (this->ref_elem->num_faces[dim])
+
+#define h5tpriv_ref_elem_get_dim(this) (this->ref_elem->dim)
+
+#endif

src/h5core/h5t_retrieve.c

@@ -68,7 +68,7 @@ h5t_begin_iterate_entities (
 	h5t_entity_iterator_t* iter,
 	const int codim
 	) {
-	return (*f->t->methods.retrieve->init_iterator)(f, iter, codim);
+	return h5tpriv_init_iterator (f, iter, codim);
 }
 
 /*!
@@ -81,8 +81,8 @@ iterate_faces (
 	) {
 	h5_idlist_t* entry;
 	h5_size_t i;
-	int dim = iter->ref_elem->dim - iter->codim;
-	int num_faces = iter->ref_elem->num_faces[dim] - 1;
+	int dim = h5tpriv_ref_elem_get_dim (iter) - iter->codim;
+	int num_faces = h5tpriv_ref_elem_get_num_faces (iter, dim) - 1;
 	do {
 		if (iter->face_idx >= num_faces) {
 			if (h5tpriv_skip_to_next_elem_on_level (f, iter) == H5_NOK) {
@@ -143,6 +143,7 @@ h5t_end_iterate_entities (
 	h5_file_t* const f,
 	h5t_entity_iterator_t* iter
 	) {
+#pragma unused f
 	iter->face_idx = -1;
 	iter->elem_idx = -1;
 	iter->codim = -1;

src/h5core/h5t_retrieve_private.h

@@ -16,4 +16,13 @@ h5tpriv_elem_is_on_cur_level (
 extern struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods;
 extern struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods;
 
+static inline h5_err_t
+h5tpriv_init_iterator (
+	h5_file_t* f,
+	h5t_entity_iterator_t* const iter,
+	const int codim
+	) {
+	return (*f->t->methods.retrieve->init_iterator) (f, iter, codim);
+}
+
 #endif

src/h5core/h5t_retrieve_trim.c

@@ -13,7 +13,7 @@ begin_iterate_entities (
 	iter->elem_idx = -1;
 	iter->codim = codim;
 	iter->ref_elem = f->t->ref_elem;
-	switch (iter->ref_elem->dim - codim) {
+	switch (h5tpriv_ref_elem_get_dim (iter) - codim) {
 	case 0: // iterate vertices
 		iter->find = h5tpriv_find_tv2;
 		return h5tpriv_skip_to_next_elem_on_level (f, iter);

src/h5core/h5t_store.c

@@ -42,7 +42,7 @@ assign_global_vertex_indices (
 	for (local_idx = 0;
 	     local_idx < t->num_vertices[t->num_levels-1];
 	     local_idx++) {
-		t->vertices[local_idx].global_idx = local_idx;
+		t->vertices[local_idx].idx = local_idx;
 	}
 
 	return H5_SUCCESS;
@@ -52,7 +52,7 @@ assign_global_vertex_indices (
  Assign unique global indices to new elements.
 */
 static h5_err_t
-assign_global_elem_indices (
+assign_glb_elem_indices (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* const t = f->t;
@@ -62,32 +62,55 @@ assign_global_elem_indices (
 	/*
 	  simple in serial runs: global index = local index
 	*/
-	h5_id_t local_idx = (t->cur_level == 0) ? 0 : t->num_elems[t->cur_level-1];
-	int num_vertices = t->ref_elem->num_faces[0];
+	h5_loc_idx_t loc_idx = (t->cur_level == 0) ? 0 : t->num_elems[t->cur_level-1];
 	
-	for (; local_idx < t->num_elems[t->cur_level]; local_idx++) {
-		h5_generic_elem_t *loc_elem = h5tpriv_get_loc_elem (f, local_idx);
-		h5_generic_elem_t *glb_elem = h5tpriv_get_glb_elem (f, local_idx);
+	for (; loc_idx < t->num_elems[t->cur_level]; loc_idx++) {
+		h5_generic_elem_t *glb_elem = h5tpriv_get_glb_elem (f, loc_idx);
+
+		glb_elem->idx = loc_idx;
+	}
+
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+assign_glb_elem_data (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t* const t = f->t;
+
+	if (t->cur_level < 0) return H5_SUCCESS; /* no level defined */
+
+	/*
+	  simple in serial runs: global index = local index
+	*/
+	h5_loc_idx_t loc_idx = (t->cur_level == 0) ? 0 : t->num_elems[t->cur_level-1];
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
+	int dim = h5tpriv_ref_elem_get_dim (t) - 1;
+	int num_faces = h5tpriv_ref_elem_get_num_faces(t, dim);
+	for (; loc_idx < t->num_elems[t->cur_level]; loc_idx++) {
+		h5_generic_elem_t *loc_elem = h5tpriv_get_loc_elem (f, loc_idx);
+		h5_generic_elem_t *glb_elem = h5tpriv_get_glb_elem (f, loc_idx);
 
-		glb_elem->idx = local_idx;
 		glb_elem->parent_idx = loc_elem->parent_idx;
 		glb_elem->child_idx = loc_elem->child_idx;
 
-		h5_id_t* glb_indices = h5tpriv_get_glb_elem_vertex_indices (f, local_idx);
-		h5_id_t* loc_indices = h5tpriv_get_loc_elem_vertex_indices (f, local_idx);
+		h5_id_t* glb_indices = h5tpriv_get_glb_elem_vertex_indices (f, loc_idx);
+		h5_id_t* loc_indices = h5tpriv_get_loc_elem_vertex_indices (f, loc_idx);
 
 		memcpy (glb_indices, loc_indices, num_vertices*sizeof(*glb_indices));
 
-		glb_indices = h5tpriv_get_glb_elem_neighbor_indices (f, local_idx);
-		loc_indices = h5tpriv_get_loc_elem_neighbor_indices (f, local_idx);
+		glb_indices = h5tpriv_get_glb_elem_neighbor_indices (f, loc_idx);
+		loc_indices = h5tpriv_get_loc_elem_neighbor_indices (f, loc_idx);
 
-		memcpy (glb_indices, loc_indices, num_vertices*sizeof(*glb_indices));
+		memcpy (glb_indices, loc_indices, num_faces*sizeof(*glb_indices));
 
 	}
 
 	return H5_SUCCESS;
 }
 
+
 h5_id_t
 h5t_add_level (
 	h5_file_t* const f
@@ -150,7 +173,7 @@ h5t_begin_store_vertices (
 h5_id_t
 h5t_store_vertex (
 	h5_file_t* const f,		/*!< file handle		*/
-	const h5_id_t global_idx,     	/*!< global vertex id or -1	*/
+	const h5_id_t glb_idx,     	/*!< global vertex id or -1	*/
 	const h5_float64_t P[3]		/*!< coordinates		*/
 	) {
 	h5t_fdata_t* const t = f->t;
@@ -170,7 +193,7 @@ h5t_store_vertex (
 
 	h5_id_t local_idx = ++t->last_stored_vid;
 	h5_vertex_t *vertex = &t->vertices[local_idx];
-	vertex->global_idx = global_idx;     /* ID from mesher, replaced later!*/
+	vertex->idx = glb_idx;     /* ID from mesher, replaced later!*/
 	memcpy (&vertex->P, P, sizeof (vertex->P));
 	return local_idx;
 }
@@ -214,7 +237,7 @@ h5t_begin_store_elems (
 	 */
 	size_t nel = 2097152 > 5*new ? 2097152 : 5*new;
 	TRY( h5tpriv_resize_te_htab (f, nel) );
-	return (*t->methods.store->alloc_elems) (f, cur, new);
+	return h5tpriv_alloc_elems (f, cur, new);
 }
 
 
@@ -261,14 +284,14 @@ h5t_store_elem (
 	h5tpriv_set_loc_elem_child_idx (f, elem_idx, -1);
 	h5tpriv_set_loc_elem_level_idx (f, elem_idx, t->cur_level);
 
-	h5_id_t* loc_elem_vertex_indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
-	int num_vertices = t->ref_elem->num_faces[0];
-	memcpy (loc_elem_vertex_indices, vertex_indices, sizeof (*vertex_indices) * num_vertices);
-	h5tpriv_sort_local_vertex_indices (f, loc_elem_vertex_indices, num_vertices);
+	h5_id_t* loc_vertex_indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
+	memcpy (loc_vertex_indices, vertex_indices, sizeof (*vertex_indices)*num_vertices);
+	h5tpriv_sort_local_vertex_indices (f, loc_vertex_indices, num_vertices);
 
-	/* add edges to directory which maps edges to elements */
+	/* add edges to map  edges -> elements */
 	h5_id_t face_idx;
-	int num_faces = t->ref_elem->num_faces[1];
+	int num_faces = h5tpriv_ref_elem_get_num_edges (t);
 	h5_idlist_t* retval;
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
 		// add edges to neighbour struct
@@ -288,13 +311,21 @@ h5t_end_store_elems (
 	h5t_fdata_t* const t = f->t;
 
 	t->num_elems[t->cur_level] = t->last_stored_eid+1;
-	TRY( assign_global_elem_indices (f) );
 
-	TRY( h5tpriv_sort_elems (f) );
+	TRY( h5tpriv_sort_loc_elems (f) );
+
+	/* assign global indices to new indices */
+	TRY( assign_glb_elem_indices (f) );
+
+	/* rebuild map: global index -> local_index */
 	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
 
+	/* mesh specific finalize */
 	TRY( (t->methods.store->end_store_elems)(f) );
 
+	/* setup global element data */
+	TRY( assign_glb_elem_data (f) );
+
 	return H5_SUCCESS;
 }
 
@@ -362,13 +393,13 @@ h5t_pre_refine (
   Refine previously marked elements.
 */
 h5_err_t
-h5t_refine (
+h5t_refine_marked_elems (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* const t = f->t;
 	int i;
 	for (i = 0; i < t->marked_entities.num_items; i++) {
-		TRY( h5t_refine_elem (f, t->marked_entities.items[i]) );
+		TRY( h5tpriv_refine_elem (f, t->marked_entities.items[i]) );
 	}
 	return H5_SUCCESS;
 }
@@ -399,25 +430,12 @@ h5t_begin_refine_elems (
 }
 
 
-/*!
-  Refine element \c elem_id. Actually we set a mark only ...
-
-  \return local id of first new element or \c -1
-*/
-h5_id_t
-h5t_refine_elem (
-	h5_file_t* const f,
-	const h5_id_t elem_id
-	) {
-	return h5t_mark_entity (f, elem_id);
-}
-
 h5_err_t
 h5t_end_refine_elems (
 	h5_file_t* const f
 	) {
 	TRY( h5t_pre_refine (f) );
-	TRY( h5t_refine (f) );
+	TRY( h5t_refine_marked_elems (f) );
 	TRY( h5t_post_refine (f) );
 
 	return H5_SUCCESS;

src/h5core/h5t_store_private.h

@@ -4,4 +4,32 @@
 extern struct h5t_store_methods h5tpriv_trim_store_methods;
 extern struct h5t_store_methods h5tpriv_tetm_store_methods;
 
+static inline h5_err_t
+h5tpriv_get_direct_children_of_edge (
+	h5_file_t* const f,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
+	h5_loc_id_t children[2]
+	) {
+	return (*f->t->methods.store->get_direct_children_of_edge) (
+		f, face_idx, elem_idx, children);
+}
+
+static inline h5_err_t
+h5tpriv_alloc_elems (
+	h5_file_t* const f,
+	const size_t cur,
+	const size_t new
+	) {
+	return (*f->t->methods.store->alloc_elems) (f, cur, new);
+}
+
+static inline h5_id_t
+h5tpriv_refine_elem (
+	h5_file_t * const f,
+	const h5_id_t local_eid
+	) {
+	return (*f->t->methods.store->refine_elem)(f, local_eid);
+}
+
 #endif

src/h5core/h5t_store_tetm.c

@@ -41,9 +41,9 @@ alloc_tets (
 static h5_err_t
 get_direct_children_of_edge (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
-	h5_id_t	children[2]
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
+	h5_loc_id_t children[2]
 	) {
 	/*
 	  Please read the note about the offsets in the corresponding file
@@ -56,8 +56,8 @@ get_direct_children_of_edge (
 			   {1,3}, // edge 4
 			   {2,3}  // edge 5
 	};
-	int num_faces = f->t->ref_elem->num_faces[1];
-	if ((face_idx < 0) || ( face_idx >= num_faces)) {
+	h5_loc_idx_t num_faces = h5tpriv_ref_elem_get_num_edges (f->t);
+	if ((face_idx < 0) || (face_idx >= num_faces)) {
 		return h5_error_internal (f, __FILE__, __func__, __LINE__); 
 	}
 	children[0] = h5tpriv_build_edge_id (face_idx, elem_idx+offs[face_idx][0]);
@@ -75,8 +75,8 @@ get_direct_children_of_edge (
 static h5_id_t
 bisect_edge (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx
 	) {
 	h5t_fdata_t* t = f->t;
 	h5_idlist_t* retval;
@@ -88,17 +88,18 @@ bisect_edge (
 	  check wether one of the found elements has been refined
 	 */
 	size_t i;
-	for ( i = 0; i < retval->num_items; i++ ) {
-		h5_id_t idx = h5tpriv_get_elem_idx ( retval->items[i] );
+	for (i = 0; i < retval->num_items; i++) {
+		h5_id_t idx = h5tpriv_get_elem_idx (retval->items[i]);
 		h5_id_t child_idx = h5tpriv_get_loc_elem_child_idx (f, idx);
-		if ( child_idx >= 0 ) {
+		if (child_idx >= 0) {
 			/*
 			  this element has been refined!
 			  return bisecting point
 			 */
-			h5_id_t	face_id = h5tpriv_get_face_idx (
-				retval->items[i] );
-			h5_id_t kids[2], edge0[2], edge1[2];
+			h5_loc_idx_t face_id = h5tpriv_get_face_idx (
+				retval->items[i]);
+			h5_loc_id_t kids[2];
+			h5_loc_idx_t edge0[2], edge1[2];
 			TRY( get_direct_children_of_edge (
 				     f,
 				     face_id,
@@ -115,17 +116,17 @@ bisect_edge (
 	/*
 	  None of the elements has been refined -> add new vertex.
 	 */
-	h5_id_t indices[2];
+	h5_loc_idx_t indices[2];
 	TRY( h5t_get_vertex_indices_of_edge2 (f, face_idx, elem_idx, indices) );
-	h5_float64_t *P0 = t->vertices[indices[0]].P;
-	h5_float64_t *P1 = t->vertices[indices[1]].P;
+	h5_float64_t* P0 = t->vertices[indices[0]].P;
+	h5_float64_t* P1 = t->vertices[indices[1]].P;
 	h5_float64_t P[3];
 
-	P[0] = ( P0[0] + P1[0] ) / 2.0;
-	P[1] = ( P0[1] + P1[1] ) / 2.0;
-	P[2] = ( P0[2] + P1[2] ) / 2.0;
+	P[0] = (P0[0] + P1[0]) / 2.0;
+	P[1] = (P0[1] + P1[1]) / 2.0;
+	P[2] = (P0[2] + P1[2]) / 2.0;
 
-	return h5t_store_vertex ( f, -1, P );
+	return h5t_store_vertex (f, -1, P);
 }
 
 /*!
@@ -136,11 +137,11 @@ bisect_edge (
 static h5_id_t
 refine_tet (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	h5t_fdata_t* t = f->t;
-	h5_id_t vertices[10];
-	h5_id_t elem_idx_of_first_child;
+	h5_loc_idx_t vertices[10];
+	h5_loc_idx_t elem_idx_of_first_child;
 	h5_tet_t* el = &t->loc_elems.tets[elem_idx];
 
 	if ( el->child_idx >= 0 )
@@ -164,7 +165,7 @@ refine_tet (
 	/* 
 	   add new tets
 	*/
-	h5_id_t new_elem[4];
+	h5_loc_idx_t new_elem[4];
 
 	new_elem[0] = vertices[0]; // child 0
 	new_elem[1] = vertices[4];
@@ -214,17 +215,92 @@ refine_tet (
 	new_elem[3] = vertices[9];
 	TRY( h5t_store_elem (f, elem_idx, new_elem) );
 
-	t->glb_elems.tets[elem_idx].child_idx = elem_idx_of_first_child;
+	// t->glb_elems.tets[elem_idx].child_idx = elem_idx_of_first_child;
 	t->loc_elems.tets[elem_idx].child_idx = elem_idx_of_first_child;
 	t->num_elems_on_level[t->cur_level]--;
 
 	return elem_idx_of_first_child;
 }
 
-h5_err_t
-end_store_elems (
-	h5_file_t* f
+static inline h5_loc_idx_t
+compute_neighbor_of_face (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
+
+	h5t_fdata_t * const t = f->t;
+	h5_idlist_t* td;
+	h5_loc_idx_t neighbor_idx = -2;
+
+	do {
+		TRY( h5tpriv_find_td2 (
+			     f,
+			     face_idx,
+			     elem_idx,
+			     &td) );
+		if (td == NULL) {
+			return h5_error_internal (
+				f, __FILE__, __func__, __LINE__);
+		}
+		if (td->num_items == 1) {
+			// neighbor is coarser or face is on the border
+			elem_idx = t->loc_elems.tets[elem_idx].parent_idx;
+			if (elem_idx == -1) {
+				// we are on the level of the macro grid
+				neighbor_idx = -1;
+			}
+		} else if (td->num_items == 2) {
+			// neighbor has same level of coarsness
+			if (h5tpriv_get_elem_idx(td->items[0]) == elem_idx) {
+				neighbor_idx = h5tpriv_get_elem_idx (td->items[1]);
+			} else {
+				neighbor_idx = h5tpriv_get_elem_idx (td->items[0]);
+			}
+			
+		} else {
+			return h5_error_internal (
+				f, __FILE__, __func__, __LINE__);
+		}
+	} while (neighbor_idx < -1);
+	return neighbor_idx;
+}
+
+/*
+  New level has been added, compute neighbores for new elements.
+ */
+static inline h5_err_t
+compute_neighbors_of_new_elems (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t * const t = f->t;
+	if (t->cur_level < 0) {
+		// or should we consider this as an error?
+		return H5_SUCCESS;
+	}
+	h5_loc_idx_t elem_idx = t->cur_level == 0 ? 0 : t->num_elems[t->cur_level-1];
+	const h5_loc_idx_t last_idx = t->num_elems[t->cur_level] - 1;
+	h5_tet_t *el = &t->loc_elems.tets[elem_idx];
+	while (elem_idx <= last_idx) {
+		h5_loc_idx_t face_idx = 0;
+		for (; face_idx < 4; face_idx++) {
+			el->neighbor_indices[face_idx] = 
+				compute_neighbor_of_face (f, elem_idx, face_idx);
+		}
+		elem_idx++;
+		el++;
+	}
+
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+end_store_elems (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t* const t = f->t;
+	TRY( h5tpriv_update_adjacency_structs (f, t->cur_level) );
+	TRY( compute_neighbors_of_new_elems (f) );
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_store_trim.c

@@ -40,11 +40,10 @@ alloc_triangles (
 static h5_err_t
 get_direct_children_of_edge (
 	h5_file_t * const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx, // index of the first child!
-	h5_id_t	children[2]
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx,
+	h5_loc_id_t children[2]
 	) {
-	int num_faces = f->t->ref_elem->num_faces[1];
 	/*
 	  Please note: The face index of the children and the father is
 	  always the same. The only think we have to know, is the offset
@@ -60,22 +59,25 @@ get_direct_children_of_edge (
 			  {0,2}, // edge 1
 			  {1,2}  // edge 2
 	};
-
-	if ( ( face_idx < 0 ) || ( face_idx >= num_faces ) ) {
-		return  h5_error_internal ( f, __FILE__, __func__, __LINE__ ); 
+	h5_loc_idx_t num_faces = h5tpriv_ref_elem_get_num_edges (f->t);
+	if ((face_idx < 0) || (face_idx >= num_faces)) {
+		return  h5_error_internal (f, __FILE__, __func__, __LINE__); 
 	}
-	children[0] = h5tpriv_build_edge_id ( face_idx, elem_idx+off[face_idx][0] );
-	children[1] = h5tpriv_build_edge_id ( face_idx, elem_idx+off[face_idx][1] );
+	children[0] = h5tpriv_build_edge_id (face_idx, elem_idx+off[face_idx][0]);
+	children[1] = h5tpriv_build_edge_id (face_idx, elem_idx+off[face_idx][1]);
 	return H5_SUCCESS;
 }
 
-static h5_id_t
+/*
+  Bisect edge and return local vertex index of the bisecting point.
+*/
+static h5_loc_idx_t
 bisect_edge (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx
 	) {
-	h5t_fdata_t* t = f->t;
+	h5t_fdata_t* const t = f->t;
 	h5_idlist_t* retval;
 	/*
 	  get all elements sharing the given edge
@@ -85,25 +87,25 @@ bisect_edge (
 	  check wether one of the found elements has been refined
 	 */
 	size_t i;
-	for ( i = 0; i < retval->num_items; i++ ) {
-		h5_id_t idx = h5tpriv_get_elem_idx ( retval->items[i] );
-		h5_id_t child_idx = h5tpriv_get_loc_elem_child_idx (f, idx);
-		if ( child_idx >= 0 ) {
+	for (i = 0; i < retval->num_items; i++) {
+		h5_loc_idx_t idx = h5tpriv_get_elem_idx (retval->items[i]);
+		h5_loc_idx_t child_idx = h5tpriv_get_loc_elem_child_idx (f, idx);
+		if (child_idx >= 0) {
 			/*
 			  this element has been refined!
 			  return bisecting point
 			 */
-			h5_id_t	face_id = h5tpriv_get_face_idx (
-				retval->items[i] );
-			h5_id_t kids[2], edge0[2], edge1[2];
-			TRY ( get_direct_children_of_edge (
+			h5_loc_id_t kids[2];
+			TRY( get_direct_children_of_edge (
 				      f,
-				      face_id,
+				      h5tpriv_get_face_idx (retval->items[i]),
 				      child_idx,
 				      kids ) );
-			TRY ( h5t_get_vertex_indices_of_edge ( f, kids[0], edge0 ) );
-			TRY ( h5t_get_vertex_indices_of_edge ( f, kids[1], edge1 ) );
-			if ( (edge0[0] == edge1[0]) || (edge0[0] == edge1[1]) )
+
+			h5_loc_idx_t edge0[2], edge1[2];
+			TRY( h5t_get_vertex_indices_of_edge ( f, kids[0], edge0 ) );
+			TRY( h5t_get_vertex_indices_of_edge ( f, kids[1], edge1 ) );
+			if ((edge0[0] == edge1[0]) || (edge0[0] == edge1[1]))
 				return edge0[0];
 			else
 				return edge0[1];
@@ -112,50 +114,50 @@ bisect_edge (
 	/*
 	  None of the elements has been refined -> add new vertex.
 	 */
-	h5_id_t indices[2];
+	h5_loc_idx_t indices[2];
 	TRY( h5t_get_vertex_indices_of_edge2 (f, face_idx, elem_idx, indices) );
-	h5_float64_t *P0 = t->vertices[indices[0]].P;
-	h5_float64_t *P1 = t->vertices[indices[1]].P;
+	h5_float64_t* P0 = t->vertices[indices[0]].P;
+	h5_float64_t* P1 = t->vertices[indices[1]].P;
 	h5_float64_t P[3];
 
-	P[0] = ( P0[0] + P1[0] ) / 2.0;
-	P[1] = ( P0[1] + P1[1] ) / 2.0;
-	P[2] = ( P0[2] + P1[2] ) / 2.0;
+	P[0] = (P0[0] + P1[0]) / 2.0;
+	P[1] = (P0[1] + P1[1]) / 2.0;
+	P[2] = (P0[2] + P1[2]) / 2.0;
 
-	return h5t_store_vertex ( f, -1, P );
+	return h5t_store_vertex (f, -1, P);
 }
 
 /*!
   Refine triangle \c local_eid
 
-  \return Local id of first new triangle or \c -1
+  \return Local index of first new triangle or \c H5_ERR
 */
-static h5_id_t
+static h5_loc_idx_t
 refine_triangle (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_id_t vertices[6];	// local vertex indices
-	h5_id_t elem_idx_of_first_child;
-	h5_triangle_t *el = &t->loc_elems.tris[elem_idx];
+	h5t_fdata_t* const t = f->t;
+	h5_loc_idx_t vertices[6];	// local vertex indices
+	h5_loc_idx_t elem_idx_of_first_child;
+	h5_triangle_t* el = &t->loc_elems.tris[elem_idx];
 
-	if ( el->child_idx >= 0 )
+	if (el->child_idx >= 0)
 		return h5_error (
 			f,
 			H5_ERR_INVAL,
 			"Element %lld already refined.",
-			(long long)elem_idx );
+			(long long)elem_idx);
 
 	vertices[0] = el->vertex_indices[0];
 	vertices[1] = el->vertex_indices[1];
 	vertices[2] = el->vertex_indices[2];
 
-	vertices[3] = bisect_edge( f, 0, elem_idx );
-	vertices[4] = bisect_edge( f, 1, elem_idx );
-	vertices[5] = bisect_edge( f, 2, elem_idx );
+	vertices[3] = bisect_edge (f, 0, elem_idx);
+	vertices[4] = bisect_edge (f, 1, elem_idx);
+	vertices[5] = bisect_edge (f, 2, elem_idx);
 
-	h5_id_t new_elem[3];
+	h5_loc_idx_t new_elem[3];
 
 	new_elem[0] = vertices[0]; // V[0] < V[3] , V[4]
 	new_elem[1] = vertices[3]; 
@@ -184,54 +186,75 @@ refine_triangle (
 	return elem_idx_of_first_child;
 }
 
-/*
-  Compute the neighbors in the macro-grid. 
- */
-static h5_err_t
-compute_neighbors_in_macrogrid (
-	h5_file_t* const f
+static inline h5_loc_idx_t
+compute_neighbor_of_face (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_id_t elem_idx = 0;
-	h5_triangle_t *el = &t->loc_elems.tris[0];
-	h5_id_t num_elems = t->num_elems[0];
-	for (;elem_idx < num_elems; elem_idx++, el++) {
-		int face_idx = 0;
-		for (; face_idx < 3; face_idx++) {
-			h5_idlist_t* te;
 
-			TRY( h5tpriv_find_te2 (
-				     f,
-				     face_idx,
-				     elem_idx,
-				     &te) );
-			if (te == NULL) {
-			} else {
-			}
+	h5t_fdata_t * const t = f->t;
+	h5_idlist_t* te;
+	h5_loc_idx_t neighbor_idx = -2;
+
+	do {
+		TRY( h5tpriv_find_te2 (
+			     f,
+			     face_idx,
+			     elem_idx,
+			     &te) );
+		if (te == NULL) {
+			return h5_error_internal (
+				f, __FILE__, __func__, __LINE__);
 		}
-	}
-	return H5_SUCCESS;
+		if (te->num_items == 1) {
+			// neighbor is coarser or face is on the border
+			elem_idx = t->loc_elems.tris[elem_idx].parent_idx;
+			if (elem_idx == -1) {
+				// we are on the level of the macro grid
+				neighbor_idx = -1;
+			}
+		} else if (te->num_items == 2) {
+			// neighbor has same level of coarsness
+			if (h5tpriv_get_elem_idx(te->items[0]) == elem_idx) {
+				neighbor_idx = h5tpriv_get_elem_idx (te->items[1]);
+			} else {
+				neighbor_idx = h5tpriv_get_elem_idx (te->items[0]);
+			}
+			
+		} else {
+			return h5_error_internal (
+				f, __FILE__, __func__, __LINE__);
+		}
+	} while (neighbor_idx < -1);
+	return neighbor_idx;
 }
 
-static h5_err_t
-compute_neighbors_for_refined_elems (
+/*
+  New level has been added, compute neighbores for new elements.
+ */
+static inline h5_err_t
+compute_neighbors_of_new_elems (
 	h5_file_t* const f
 	) {
-	h5t_fdata_t *t = f->t;
-	return H5_SUCCESS;
-}
-
-static h5_err_t
-compute_neighbors (
-	h5_file_t* const f
-	) {
-	h5t_fdata_t *t = f->t;
-
-	if (t->cur_level == 0) {
-		TRY( compute_neighbors_in_macrogrid (f) );
-	} else {
-		TRY( compute_neighbors_for_refined_elems (f) );
+	h5t_fdata_t * const t = f->t;
+	if (t->cur_level < 0) {
+		// or should we consider this as an error?
+		return H5_SUCCESS;
 	}
+	h5_loc_idx_t elem_idx = t->cur_level == 0 ? 0 : t->num_elems[t->cur_level-1];
+	const h5_loc_idx_t last_idx = t->num_elems[t->cur_level] - 1;
+	h5_triangle_t *el = &t->loc_elems.tris[elem_idx];
+	while (elem_idx <= last_idx) {
+		h5_loc_idx_t face_idx = 0;
+		for (; face_idx < 3; face_idx++) {
+			el->neighbor_indices[face_idx] = 
+				compute_neighbor_of_face (f, elem_idx, face_idx);
+		}
+		elem_idx++;
+		el++;
+	}
+
 	return H5_SUCCESS;
 }
 
@@ -239,10 +262,10 @@ static h5_err_t
 end_store_elems (
 	h5_file_t* const f
 	) {
-	h5t_fdata_t *t = f->t;
+	h5t_fdata_t* t = f->t;
 
-	TRY( (t->methods.adjacency->update_internal_structs)(f, t->cur_level) );
-	TRY( compute_neighbors (f) );
+	TRY( h5tpriv_update_adjacency_structs (f, t->cur_level) );
+	TRY( compute_neighbors_of_new_elems (f) );
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_tags.c

@@ -25,8 +25,8 @@ init_container (
 /*
   Initialize tag container for current mesh and level.
  */
-h5_err_t
-h5tpriv_init_mtagsets (
+static h5_err_t
+init_mtagsets (
 	h5_file_t * const f,
 	size_t ntags
 	) {
@@ -106,8 +106,8 @@ h5tpriv_release_tags (
 
   \return	H5_SUCCESS or error code
 */
-h5_err_t
-h5tpriv_add_mtagset (
+static h5_err_t
+add_mtagset (
 	h5_file_t * const f,
 	char * name,
 	h5_id_t type,
@@ -119,7 +119,7 @@ h5tpriv_add_mtagset (
 	  Initialize data structure for m-tagsets, if not already done.
 	*/
 	if ( t->mtags.names == NULL ) {
-		TRY ( h5tpriv_init_mtagsets ( f, 521 ) );
+		TRY( init_mtagsets (f, 521) );
 	}
 	/*
 	  ToDo: Resize!
@@ -171,7 +171,7 @@ h5t_add_mtagset (
 	char * name,
 	h5_id_t type
 	) {
-	return h5tpriv_add_mtagset ( f, name, type, 0 );
+	return add_mtagset ( f, name, type, 0 );
 }
 
 
@@ -347,8 +347,8 @@ h5t_get_mtagset_info (
 
   \return	H5_SUCCESS or error code
  */
-h5_err_t
-h5tpriv_set_mtag (
+static h5_err_t
+set_mtag (
 	h5_file_t *const f,
 	H5T_Tagset *tagset,
 	const h5_id_t id,
@@ -433,16 +433,17 @@ h5t_set_mtag_by_name (
 	) {
 	H5T_Tagset *tagset;
 	TRY ( h5t_open_mtagset ( f, name, &tagset ) );
-	return h5tpriv_set_mtag ( f, tagset, id, size, val );
+	return set_mtag ( f, tagset, id, size, val );
 }
 
 static h5_err_t
-_get_tag_valp (
-	h5_file_t *const f,
-	const H5T_Tagset *tagset,
+get_tag_valp (
+	h5_file_t* const f,
+	const H5T_Tagset* tagset,
 	const h5_id_t entity_id,
-	h5t_tagval_t **valp
+	h5t_tagval_t** const valp
 	) {
+#pragma unused f
 	h5_id_t el_idx = h5tpriv_get_elem_idx ( entity_id );
 	h5_id_t subentity_id = h5tpriv_get_face_idx ( entity_id );
 	h5_id_t type_id = h5tpriv_get_entity_type ( entity_id );
@@ -458,7 +459,7 @@ _get_tag_valp (
 		return H5_NOK; /* no value set for this subentity */
 	}
 	size_t k = tagselem->idx[i];
-	valp = &tagselem->valp[k];
+	*valp = tagselem->valp[k];
 
 	return H5_SUCCESS;
 }
@@ -479,11 +480,11 @@ h5t_get_tag (
 	h5_file_t *const f,
 	const H5T_Tagset *tagset,
 	const h5_id_t entity_id,
-	size_t *dim,
-	void *vals
+	size_t* const dim,
+	void* const vals
 	) {
 	h5t_tagval_t *tagval;
-	TRY ( _get_tag_valp ( f, tagset, entity_id, &tagval ) );
+	TRY ( get_tag_valp ( f, tagset, entity_id, &tagval ) );
 
 	if ( (*dim > tagval->size) || (vals == NULL) ) {
 		*dim = tagval->size;
@@ -527,8 +528,8 @@ h5t_get_mtag_by_name (
 */
 h5_err_t
 h5t_remove_mtag (
-	h5_file_t *const f,
-	H5T_Tagset *tagset,
+	h5_file_t* const f,
+	H5T_Tagset* tagset,
 	const h5_id_t id
 	) {
 	h5_id_t el_idx = h5tpriv_get_elem_idx ( id );
@@ -586,8 +587,10 @@ h5t_remove_mtag_by_name (
 static hid_t
 open_space_all (
 	h5_file_t * const f,
-	hid_t dataset_id
+	const hid_t dataset_id
 	) {
+#pragma unused f
+#pragma unused dataset_id
 	return H5S_ALL;
 }
 
@@ -860,11 +863,11 @@ read_tagset (
 	  add tagset and set values
 	*/
 	H5T_Tagset* tagset;
-	TRY( h5tpriv_add_mtagset (f, name, type, &tagset) );
+	TRY( add_mtagset (f, name, type, &tagset) );
 	for (ent_idx = 0; ent_idx < num_entities; ent_idx++) {
 		h5t_tag_idx_t *entity = &entities[ent_idx];
 		size_t dim = (entity+1)->idx - entity->idx;
-		TRY( h5tpriv_set_mtag (
+		TRY( set_mtag (
 			     f,
 			     tagset,
 			     entity->eid,
@@ -909,8 +912,8 @@ h5tpriv_read_tag_container (
 
   \return	number of tagsets
  */
-h5_ssize_t
-h5tpriv_get_tagset_names_of_entity (
+static h5_ssize_t
+get_tagset_names_of_entity (
 	h5_file_t * const f,
 	h5t_tagcontainer_t *ctn,
 	h5_id_t entity_id,
@@ -928,7 +931,7 @@ h5tpriv_get_tagset_names_of_entity (
 				  &ctn->sets));
 		H5T_Tagset *tset = (H5T_Tagset*)__retval;
 		h5t_tagval_t *tval;
-		if (_get_tag_valp (f, tset, entity_id, &tval) != H5_SUCCESS) {
+		if (get_tag_valp (f, tset, entity_id, &tval) != H5_SUCCESS) {
 			continue;
 		}
 		if ( (names != NULL) && (_dim <= dim) ) {
@@ -941,11 +944,10 @@ h5tpriv_get_tagset_names_of_entity (
 
 h5_ssize_t
 h5t_get_mtagset_names_of_entity (
-	h5_file_t * const f,
-	h5_id_t entity_id,
+	h5_file_t* const f,
+	const h5_id_t entity_id,
 	char *names[],
-	h5_size_t dim
+	const h5_size_t dim
 	) {
-	return h5tpriv_get_tagset_names_of_entity (
-		     f, &f->t->mtags, entity_id, names, dim);
+	return get_tagset_names_of_entity (f, &f->t->mtags, entity_id, names, dim);
 }

src/h5core/h5t_types_private.h

@@ -2,7 +2,7 @@
 #define __H5T_TYPES_PRIVATE_H
 
 typedef struct h5_vertex {
-	h5_id_t		global_idx;
+	h5_id_t		idx;
 	h5_coord3d_t	P;
 } h5_vertex_t;
 
@@ -71,7 +71,6 @@ struct h5t_retrieve_methods {
 	h5_err_t (*init_iterator)(h5_file_t* const, h5t_entity_iterator_t*, const int);
 };
 
-
 struct h5t_access_methods {
 	h5_generic_elem_t* (*get_loc_elem)(
 		h5_file_t* const, const h5_id_t);
@@ -126,7 +125,6 @@ struct h5t_access_methods {
 		h5_file_t* const, const h5_id_t, const h5_id_t);
 	h5_id_t (*set_glb_elem_neighbor_idx)(
 		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
-
 };
 
 struct h5t_read_methods {
@@ -136,30 +134,8 @@ struct h5t_read_methods {
 struct h5t_adjacency_methods {
 	h5_err_t (*update_internal_structs)(h5_file_t* const, h5_id_t);
 	h5_err_t (*release_internal_structs)(h5_file_t* const);
-	h5_err_t (*get_edges_upadjacent_to_vertex)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_triangles_upadjacent_to_vertex)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_tets_upadjacent_to_vertex)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_triangles_upadjacent_to_edge)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_tets_upadjacent_to_edge)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_tets_upadjacent_to_triangle)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_vertices_downadjacent_to_edge)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_vertices_downadjacent_to_triangle)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_vertices_downadjacent_to_tet)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_edges_downadjacent_to_triangle)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_edges_downadjacent_to_tet)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
-	h5_err_t (*get_triangles_downadjacent_to_tet)(
-		h5_file_t * const, const h5_id_t, h5_idlist_t**);
+	h5_err_t (*get_adjacencies)(
+		h5_file_t * const, const h5_id_t, const h5_int32_t, h5_idlist_t**);
 };
 
 typedef struct h5t_methods {

src/h5core/h5u_model.c

@@ -115,6 +115,7 @@ h5u_set_num_particles (
 	}
 
 #ifndef PARALLEL_IO
+#pragma unused total
 	count = u->nparticles;
 	TRY( u->shape = h5priv_create_hdf5_dataspace(f, 1, &count, NULL) );
 	u->viewstart = 0;
@@ -436,11 +437,13 @@ h5u_get_dataset_info (
 		     dataset_name, len_dataset_name) );
 
 	if ( nelem ) {
-		TRY( *nelem = h5priv_get_npoints_of_hdf5_dataset_by_name (
+		h5_ssize_t nelem_;
+		TRY( nelem_ = h5priv_get_npoints_of_hdf5_dataset_by_name (
 			f,
 			f->step_gid,
 			dataset_name) );
-		if ( *nelem < 0 ) return *nelem;
+		if ( nelem_ < 0 ) return nelem_;
+		*nelem = nelem_;
 	}
 
 	if ( type ) {

src/h5core/h5u_readwrite.c

@@ -28,20 +28,19 @@ h5u_read_data (
 
 	/* default spaces, if not using a view selection */
 	memspace_id = H5S_ALL;
-	TRY ( space_id = h5priv_get_hdf5_dataset_space(f, dataset_id) );
+	TRY( space_id = h5priv_get_hdf5_dataset_space(f, dataset_id) );
 
 	/* get the number of elements on disk for the datset */
 	TRY ( ndisk = h5priv_get_npoints_of_hdf5_dataspace(f, space_id) );
 
-	if ( u->diskshape != H5S_ALL )
-	{
-		TRY ( nread = h5priv_get_npoints_of_hdf5_dataspace(f, u->diskshape) );
+	if (u->diskshape != H5S_ALL) {
+		TRY( nread = h5priv_get_npoints_of_hdf5_dataspace(f, u->diskshape) );
 
 		/* make sure the disk space selected by the view doesn't
 		 * exceed the size of the dataset */
-		if ( nread <= ndisk ) {
+		if (nread <= ndisk) {
 			/* we no longer need the dataset space... */
-			TRY ( h5priv_close_hdf5_dataspace(f, space_id) );
+			TRY( h5priv_close_hdf5_dataspace(f, space_id) );
 			/* ...because it's safe to use the view selection */
 			space_id = f->u->diskshape;
 		} else {
@@ -55,20 +54,18 @@ h5u_read_data (
 					name2, (long long)ndisk, (long long)nread );
 			nread = ndisk;
 		}
-	}
-	else {
+	} else {
 		/* since the view selection is H5S_ALL, we will
 		 * read all available elements in the dataset space */
 		nread = ndisk;
 	}
 
-	if ( u->memshape != H5S_ALL )
-	{
-		TRY ( nread = h5priv_get_npoints_of_hdf5_dataspace(f, u->memshape) );
+	if (u->memshape != H5S_ALL) {
+		TRY( nmem = h5priv_get_npoints_of_hdf5_dataspace(f, u->memshape) );
 
 		/* make sure the memory space selected by the view has
 		 * enough capacity for the read */
-		if ( nmem >= nread ) {
+		if (nmem >= nread) {
 			memspace_id = f->u->memshape;
 		} else {
 			/* the view selection is too small?

src/include/H5.h

@@ -107,14 +107,14 @@ H5GetErrorHandler (
 
 h5_err_t
 H5ReportErrorhandler (
-	h5_file_t * const f,
+	const h5_file_t * const f,
 	const char *fmt,
 	va_list ap
 	);
 
 h5_err_t
 H5AbortErrorhandler (
-	h5_file_t * const f,
+	const h5_file_t * const f,
 	const char *fmt,
 	va_list ap
 	);

src/include/H5Block.h

@@ -19,41 +19,44 @@ H5Block3dSetView (
 
 h5_err_t
 H5Block3dGetView (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i	*/  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j	*/ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c k	*/ 
 	);
 
 h5_err_t
 H5Block3dGetReducedView (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i */ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i */  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j */ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j */ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c j */ 
-	h5_size_t *k_end	/*!< OUT: end index of \c j */ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i */ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i */  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j */ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j */ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c j */ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c j */ 
 	);
 
 h5_err_t
 H5Block3dSetChunk (
 	h5_file_t *const f,		/*!< IN: File handle */
-	const h5_int64_t i,		/*!< IN: size of \c i */ 
-	const h5_int64_t j,		/*!< IN: size of \c j */  
-	const h5_int64_t k		/*!< IN: size of \c k */ 
+	const h5_size_t i,		/*!< IN: size of \c i */ 
+	const h5_size_t j,		/*!< IN: size of \c j */  
+	const h5_size_t k		/*!< IN: size of \c k */ 
 	);
 
 h5_err_t
 H5Block3dGetChunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_size_t *dims			/*!< OUT: array containing the chunk dimensions */
+	h5_size_t *const i,		/*!< OUT: size of i */
+	h5_size_t *const j,		/*!< OUT: size of j */
+	h5_size_t *const k		/*!< OUT: size of k */
 	);
 
+#if defined(PARALLEL_IO)
 h5_err_t
 H5Block3dSetGrid (
 	h5_file_t *const f,		/*!< IN: File handle */
@@ -66,9 +69,9 @@ h5_err_t
 H5Block3dGetGridCoords (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const int proc,			/*!< IN: MPI processor */
-	h5_int64_t *i,			/*!< OUT: index in \c i */ 
-	h5_int64_t *j,			/*!< OUT: index in \c j */  
-	h5_int64_t *k			/*!< OUT: index in \c k */ 
+	h5_size_t *const i,		/*!< OUT: index in \c i */ 
+	h5_size_t *const j,		/*!< OUT: index in \c j */  
+	h5_size_t *const k		/*!< OUT: index in \c k */ 
 	);
 
 h5_err_t
@@ -78,6 +81,7 @@ H5Block3dSetDims (
 	const h5_size_t j,		/*!< IN: dimension in \c j */  
 	const h5_size_t k		/*!< IN: dimension in \c k */ 
 	);
+#endif
 
 h5_err_t
 H5Block3dSetHalo (
@@ -94,59 +98,59 @@ H5BlockGetNumFields (
 
 h5_err_t
 H5BlockGetFieldInfo (
-	h5_file_t *const f,			/*!< IN: file handle */
-	const h5_size_t idx,			/*!< IN: index of field */
-	char *name,				/*!< OUT: field name */
-	const h5_size_t len_name,		/*!< IN: buffer size */
-	h5_size_t *field_rank,			/*!< OUT: field rank */
-	h5_size_t *field_dims,			/*!< OUT: field dimensions */
-	h5_size_t *elem_rank,			/*!< OUT: element rank */
-	h5_int64_t *type			/*!< OUT: datatype */
+	h5_file_t *const f,		/*!< IN: file handle */
+	const h5_size_t idx,		/*!< IN: index of field */
+	char *name,			/*!< OUT: field name */
+	const h5_size_t len_name,	/*!< IN: buffer size */
+	h5_size_t *const field_rank,	/*!< OUT: field rank */
+	h5_size_t *const field_dims,	/*!< OUT: field dimensions */
+	h5_size_t *const elem_rank,	/*!< OUT: element rank */
+	h5_int64_t *const type		/*!< OUT: datatype */
 	);
 
 h5_err_t
 H5BlockGetFieldInfoByName (
 	h5_file_t *const f,		/*!< IN: file handle */
 	const char *name,		/*!< IN: field name */
-	h5_size_t *field_rank,			/*!< OUT: field rank */
-	h5_size_t *field_dims,			/*!< OUT: field dimensions */
-	h5_size_t *elem_rank,			/*!< OUT: element rank */
-	h5_int64_t *type		/*!< OUT: datatype */
+	h5_size_t *const field_rank,	/*!< OUT: field rank */
+	h5_size_t *const field_dims,	/*!< OUT: field dimensions */
+	h5_size_t *const elem_rank,	/*!< OUT: element rank */
+	h5_int64_t *const type		/*!< OUT: datatype */
 	);
 
 h5_err_t
 H5BlockWriteFieldAttribString (
-	h5_file_t *const f,			/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	const char *attrib_name,		/*!< IN: attribute name */
-	const char *value			/*!< IN: attribute value */
+	h5_file_t *const f,		/*!< IN: file handle */
+	const char *const field_name,	/*!< IN: field name */
+	const char *const attrib_name,	/*!< IN: attribute name */
+	const char *const value		/*!< IN: attribute value */
 	);
 
 h5_err_t
 H5BlockReadFieldAttribString (
-	h5_file_t *const f,			/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	const char *attrib_name,		/*!< IN: attribute name */
-	char *buffer			        /*!< OUT: attribute value */
+	h5_file_t *const f,		/*!< IN: file handle */
+	const char *const field_name,	/*!< IN: field name */
+	const char *const attrib_name,	/*!< IN: attribute name */
+	char *const buffer		/*!< OUT: attribute value */
 	);
 
 h5_ssize_t
 H5BlockGetNumFieldAttribs (
-	h5_file_t *const f,			/*<! IN: file handle */
-	const char *field_name			/*<! IN: field name */
+	h5_file_t *const f,		/*<! IN: file handle */
+	const char *const field_name	/*<! IN: field name */
 	);
 
 h5_int64_t
 H5BlockGetFieldAttribInfo (
 	h5_file_t *const f,		/*<! IN: Handle to open file */
-	const char *field_name,		/*<! IN: field name */
+	const char *const field_name,	/*<! IN: field name */
 	const h5_size_t attrib_idx,	/*<! IN: Index of attribute to
 					           get infos about */
-	char *attrib_name,		/*<! OUT: Name of attribute */
+	char *const attrib_name,	/*<! OUT: Name of attribute */
 	const h5_size_t len_of_attrib_name,
 					/*<! IN: length of buffer \c name */
-	h5_int64_t *attrib_type,	/*<! OUT: Type of value. */
-	h5_size_t *attrib_nelem         /*<! OUT: Number of elements */
+	h5_int64_t *const attrib_type,	/*<! OUT: Type of value. */
+	h5_size_t *const attrib_nelem         /*<! OUT: Number of elements */
 	);
 
 

src/include/H5Fed_adjacency.h

@@ -2,87 +2,11 @@
 #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
+H5FedGetAdjacencies (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
+	h5_idlist_t** list
 	);
 
 h5_err_t

src/include/H5Fed_retrieve.h

@@ -31,13 +31,13 @@ H5FedEndTraverseEntities (
 	h5t_entity_iterator_t* iter
 	);
 h5_err_t
-H5FedGetVertexCoordByIndex (
+H5FedGetVertexCoordsByIndex (
 	h5_file_t* const f,
 	h5_id_t vertex_index,
 	h5_float64_t P[3]
 	);
 h5_err_t
-H5FedGetVertexCoordByID (
+H5FedGetVertexCoordsByID (
 	h5_file_t* const f,
 	h5_id_t vertex_id,
 	h5_float64_t P[3]

src/include/h5core/h5_readwrite.h

@@ -1,17 +1,6 @@
 #ifndef __H5_READWRITE_H
 #define __H5_READWRITE_H
 
-h5_int64_t
-h5_write_data (
-	h5_file_t *f,
-	const char *name,
-	const void *array,
-	const hid_t type_id,
-	const hid_t group_id,
-	const hid_t memspace_id,
-	const hid_t diskspace_id
-	) ;
-
 h5_int64_t
 h5_set_step (
 	h5_file_t * const f,

src/include/h5core/h5_types.h

@@ -39,6 +39,10 @@ typedef __int64			int64_t;
 typedef int64_t			h5_int64_t;
 typedef int32_t			h5_int32_t;
 typedef int64_t			h5_id_t;
+typedef int64_t			h5_glb_idx_t;	// type for a global index
+typedef int64_t			h5_loc_idx_t;	// type for a local index
+typedef int64_t			h5_glb_id_t;	// type for a global ID
+typedef int64_t			h5_loc_id_t;	// type for a local ID
 typedef uint64_t		h5_size_t;	/* size in number of elements */
 typedef int64_t			h5_ssize_t;	/* size in number of elements */
 typedef int64_t			h5_err_t;
@@ -60,12 +64,13 @@ struct h5_file;
 typedef struct h5_file h5_file_t;
 
 typedef h5_err_t (*h5_errorhandler_t)(
-	const struct h5_file * const,
+	const h5_file_t * const,
 	const char*,
 	va_list ap );
 
 #ifndef PARALLEL_IO
 typedef unsigned long		MPI_Comm;
+typedef unsigned long		MPI_Datatype;
 #endif
 
 typedef struct h5_idlist {

src/include/h5core/h5b_model.h

@@ -37,53 +37,54 @@ h5b_3d_has_view (
 h5_err_t
 h5b_3d_set_view (
 	h5_file_t *const f,		/*!< IN: File handle		*/
-	const h5_int64_t i_start,	/*!< IN: start index of \c i	*/ 
-	const h5_int64_t i_end,		/*!< IN: end index of \c i	*/  
-	const h5_int64_t j_start,	/*!< IN: start index of \c j	*/ 
-	const h5_int64_t j_end,		/*!< IN: end index of \c j	*/ 
-	const h5_int64_t k_start,	/*!< IN: start index of \c k	*/ 
-	const h5_int64_t k_end		/*!< IN: end index of \c k	*/
+	const h5_size_t i_start,	/*!< IN: start index of \c i	*/ 
+	const h5_size_t i_end,		/*!< IN: end index of \c i	*/  
+	const h5_size_t j_start,	/*!< IN: start index of \c j	*/ 
+	const h5_size_t j_end,		/*!< IN: end index of \c j	*/ 
+	const h5_size_t k_start,	/*!< IN: start index of \c k	*/ 
+	const h5_size_t k_end		/*!< IN: end index of \c k	*/
 	);
 
 h5_err_t
 h5b_3d_get_view (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i	*/  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j	*/ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c k	*/ 
 	);
 
 h5_err_t
 h5b_3d_get_reduced_view (
-	h5_file_t *const f,	/*!< IN: File handle */
-	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_file_t *const f,		/*!< IN: File handle */
+	h5_size_t *const i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_size_t *const i_end,		/*!< OUT: end index of \c i	*/  
+	h5_size_t *const j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_size_t *const j_end,		/*!< OUT: end index of \c j	*/ 
+	h5_size_t *const k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_size_t *const k_end		/*!< OUT: end index of \c k	*/ 
 	);
 
 h5_err_t
 h5b_3d_set_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
-	const h5_int64_t i,		/*!< IN: size of \c i */ 
-	const h5_int64_t j,		/*!< IN: size of \c j */  
-	const h5_int64_t k		/*!< IN: size of \c k */ 
+	const h5_size_t i,		/*!< IN: size of \c i */ 
+	const h5_size_t j,		/*!< IN: size of \c j */  
+	const h5_size_t k		/*!< IN: size of \c k */ 
 	);
 
 h5_err_t
 h5b_3d_get_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_int64_t *i,			/*!< OUT: size of \c i */ 
-	h5_int64_t *j,			/*!< OUT: size of \c j */  
-	h5_int64_t *k			/*!< OUT: size of \c k */ 
+	h5_size_t *const i,		/*!< OUT: size of \c i */ 
+	h5_size_t *const j,		/*!< OUT: size of \c j */  
+	h5_size_t *const k		/*!< OUT: size of \c k */ 
 	);
 
+#if defined(PARALLEL_IO)
 h5_err_t
 h5b_3d_set_grid (
 	h5_file_t *const f,		/*!< IN: File handle */
@@ -96,9 +97,9 @@ h5_err_t
 h5b_3d_get_grid_coords (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const int proc,			/*!< IN: MPI processor */
-	h5_int64_t *i,			/*!< OUT: index in \c i */ 
-	h5_int64_t *j,			/*!< OUT: index in \c j */  
-	h5_int64_t *k			/*!< OUT: index in \c k */ 
+	h5_size_t *const i,		/*!< OUT: index in \c i */ 
+	h5_size_t *const j,		/*!< OUT: index in \c j */  
+	h5_size_t *const k		/*!< OUT: index in \c k */ 
 	);
 
 h5_err_t
@@ -108,6 +109,7 @@ h5b_3d_set_dims (
 	const h5_size_t j,		/*!< IN: dimension in \c j */  
 	const h5_size_t k		/*!< IN: dimension in \c k */ 
 	);
+#endif
 
 h5_err_t
 h5b_3d_set_halo (
@@ -126,10 +128,10 @@ h5_err_t
 h5b_get_field_info_by_name (
 	h5_file_t *const f,			/*!< IN: file handle */
 	const char *name,			/*!< OUT: field name */
-	h5_size_t *field_rank,			/*!< OUT: field rank */
-	h5_size_t *field_dims,			/*!< OUT: field dimensions */
-	h5_size_t *elem_rank,			/*!< OUT: element rank */
-	h5_int64_t *type			/*!< OUT: datatype */
+	h5_size_t *const field_rank,		/*!< OUT: field rank */
+	h5_size_t *const field_dims,		/*!< OUT: field dimensions */
+	h5_size_t *const elem_rank,		/*!< OUT: element rank */
+	h5_int64_t *const type			/*!< OUT: datatype */
 	);
 
 h5_err_t
@@ -138,10 +140,10 @@ h5b_get_field_info (
 	const h5_size_t idx,			/*!< IN: index of field */
 	char *name,				/*!< OUT: field name */
 	const h5_size_t len_name,		/*!< IN: buffer size */
-	h5_size_t *field_rank,			/*!< OUT: field rank */
-	h5_size_t *field_dims,			/*!< OUT: field dimensions */
-	h5_size_t *elem_rank,			/*!< OUT: element rank */
-	h5_int64_t *type			/*!< OUT: datatype */
+	h5_size_t *const field_rank,		/*!< OUT: field rank */
+	h5_size_t *const field_dims,		/*!< OUT: field dimensions */
+	h5_size_t *const elem_rank,		/*!< OUT: element rank */
+	h5_int64_t *const type			/*!< OUT: datatype */
 	);
 
 

src/include/h5core/h5t_adjacencies.h

@@ -2,86 +2,10 @@
 #define __H5T_ADJACENCIES_H
 
 h5_err_t
-h5t_get_edges_upadjacent_to_vertex (
+h5t_get_adjacencies (
 	h5_file_t * const f,
-	const h5_id_t local_vid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_triangles_upadjacent_to_vertex (
-	h5_file_t * const f,
-	const h5_id_t local_vid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_tets_upadjacent_to_vertex (
-	h5_file_t * const f,
-	const h5_id_t local_vid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_triangles_upadjacent_to_edge (
-	h5_file_t * const f,
-	const h5_id_t local_kid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_tets_upadjacent_to_edge (
-	h5_file_t * const f,
-	const h5_id_t local_kid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_tets_upadjacent_to_triangle (
-	h5_file_t * const f,
-	const h5_id_t local_did,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_edge (
-	h5_file_t * const f,
-	const h5_id_t local_kid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_triangle (
-	h5_file_t * const f,
-	const h5_id_t local_did,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_vertices_downadjacent_to_tet (
-	h5_file_t * const f,
-	const h5_id_t local_tid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_edges_downadjacent_to_triangle (
-	h5_file_t * const f,
-	const h5_id_t local_did,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_edges_downadjacent_to_tet (
-	h5_file_t * const f,
-	const h5_id_t local_tid,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5t_get_triangles_downadjacent_to_tet (
-	h5_file_t * const f,
-	const h5_id_t local_tid,
+	const h5_id_t entity_id,
+	const h5_int32_t dim,
 	h5_idlist_t **list
 	);
 

src/include/h5core/h5t_map.h

@@ -2,7 +2,7 @@
 #define __H5T_MAP_H
 
 h5_id_t
-h5t_map_global_vertex_index2local (
+h5t_map_global_vertex_idx2local (
 	h5_file_t * const f,
 	h5_id_t global_idx
 	);

src/include/h5core/h5t_openclose.h

@@ -7,6 +7,7 @@ h5_err_t h5t_open_mesh ( h5_file_t * const f, const h5_id_t id,
 h5_err_t h5t_set_level ( h5_file_t * const f, const h5_id_t id );
 h5_err_t h5t_close_mesh ( h5_file_t * const f );
 
+#if 0
 h5_err_t h5tpriv_open_file ( h5_file_t * const f );
 h5_err_t h5tpriv_close_file ( h5_file_t * const f );
 h5_err_t h5tpriv_open_topo_group (	h5_file_t * const f );
@@ -25,3 +26,4 @@ h5_err_t h5tpriv_alloc_tets ( h5_file_t * const f, const size_t cur,
 			   const size_t new_size );
 
 #endif
+#endif

src/include/h5core/h5t_retrieve.h

@@ -53,7 +53,7 @@ h5t_get_vertex_coords_by_index (
 	);
 
 h5_err_t
-h5t_get_vertrex_coords_by_id (
+h5t_get_vertex_coords_by_id (
 	h5_file_t* const f,
 	h5_id_t vertex_id,
 	h5_float64_t P[3]

src/include/h5core/h5t_storemesh.h

@@ -54,13 +54,33 @@ h5t_begin_refine_elems (
 	);
 
 h5_id_t
-h5t_refine_elem (
-	h5_file_t * const f,
-	const h5_id_t local_eid
+h5t_refine_marked_elems (
+	h5_file_t * const f
 	);
 
 h5_err_t
 h5t_end_refine_elems (
 	h5_file_t * const f
 	);
+
+h5_err_t
+h5t_mark_entity (
+	h5_file_t* const f,
+	const h5_id_t entity_id
+	);
+
+h5_err_t
+h5t_pre_refine (
+	h5_file_t* const f
+	);
+
+h5_err_t
+h5t_refine (
+	h5_file_t* const f
+	);
+
+h5_err_t
+h5t_post_refine (
+	h5_file_t* const f
+	);
 #endif

src/include/h5core/h5t_tags.h

@@ -1,4 +1,4 @@
-#ifndef __H5T_TAGS_H
+#ifndef __H5T_TAGS_H 
 #define __H5T_TAGS_H
 
 typedef struct h5t_tagset H5T_Tagset;
@@ -19,7 +19,35 @@ h5_err_t h5t_set_mtag_by_name ( h5_file_t* const f, char name[], const h5_id_t i
 h5_err_t h5t_get_mtag_by_name ( h5_file_t* const f, const char name[],
 				const h5_id_t id, size_t* dim, void* vals );
 
-h5_err_t h5t_remove_mtag_by_name ( h5_file_t* const f, const char name[],
-			   const h5_id_t id );
+h5_err_t
+h5t_remove_mtag_by_name (
+	h5_file_t* const f,
+	const char name[],
+	const h5_id_t id
+	);
+
+h5_ssize_t
+h5t_get_tag (
+	h5_file_t *const f,
+	const H5T_Tagset *tagset,
+	const h5_id_t entity_id,
+	size_t* const dim,
+	void* const vals
+	);
+
+h5_err_t
+h5t_remove_mtag (
+	h5_file_t* const f,
+	H5T_Tagset* tagset,
+	const h5_id_t id
+	);
+
+h5_ssize_t
+h5t_get_mtagset_names_of_entity (
+	h5_file_t* const f,
+	const h5_id_t entity_id,
+	char *names[],
+	const h5_size_t dim
+	);
 
 #endif