- introduced types for local and global indices and ID's

- bugfixes

.gitattributes

@@ -406,6 +406,7 @@ src/h5core/h5_hsearch_private.h -text
 src/h5core/h5_lustre.c -text
 src/h5core/h5_lustre_private.h -text
 src/h5core/h5_maps.c -text
+src/h5core/h5_maps_private.h -text
 src/h5core/h5_model.c -text
 src/h5core/h5_mpi.c -text
 src/h5core/h5_mpi_private.h -text

src/C/H5Fed.c

@@ -29,6 +29,7 @@ h5_err_t
 H5FedCloseMesh (
 	h5_file_t* const f
 	) {
+	SET_FNAME (f, __func__);
 	return h5t_close_mesh (f);
 }
 

src/C/H5Fed_adjacency.c

@@ -38,5 +38,5 @@ H5FedReleaseListOfAdjacencies (
 	h5_idlist_t** list
 	) {
 	SET_FNAME (f, __func__);
-	return h5priv_free_idlist (f, list);
+	return h5t_release_list_of_adjacencies (f, list);
 }

src/C/H5Fed_tags.c

@@ -107,58 +107,6 @@ H5FedSetMTag (
 	return h5t_set_mtag_by_name (f, name, id, dims, val);
 }
 
-h5_err_t
-H5FedSetMTagToVertex (
-	h5_file_t* const f,
-	char name[],
-	h5_id_t id,
-	const size_t dims,
-	void* val 
-	) {
-	SET_FNAME (f, __func__);
-	id = h5tpriv_set_entity_type (H5T_ETYPE_VERTEX, id);
-	return h5t_set_mtag_by_name (f, name, id, dims, val);
-}
-
-h5_err_t
-H5FedSetMTagToEdge (
-	h5_file_t* const f,
-	char name[],
-	h5_id_t id,
-	const size_t dims,
-	void* val 
-	) {
-	SET_FNAME (f, __func__);
-	id = h5tpriv_set_entity_type (H5T_ETYPE_EDGE, id);
-	return h5t_set_mtag_by_name (f, name, id, dims, val);
-}
-
-h5_err_t
-H5FedSetMTagToTriangle (
-	h5_file_t* const f,
-	char name[],
-	h5_id_t id,
-	const size_t dims,
-	void* val 
-	) {
-	SET_FNAME (f, __func__);
-	id = h5tpriv_set_entity_type (H5T_ETYPE_TRIANGLE, id);
-	return h5t_set_mtag_by_name (f, name, id, dims, val);
-}
-
-h5_err_t
-H5FedSetMTagToTet (
-	h5_file_t* const f,
-	char name[],
-	h5_id_t id,
-	const size_t dims,
-	void* val 
-	) {
-	SET_FNAME (f, __func__);
-	id = h5tpriv_set_entity_type (H5T_ETYPE_TET, id);
-	return h5t_set_mtag_by_name (f, name, id, dims, val);
-}
-
 /*!
   Set tag for entity in current mesh.
 

src/h5core/h5_core_private.h

@@ -18,6 +18,7 @@
 #include "h5_fcmp_private.h"
 #include "h5_hdf5_private.h"
 #include "h5_hsearch_private.h"
+#include "h5_maps_private.h"
 #include "h5_mpi_private.h"
 #include "h5_qsort_private.h"
 #include "h5_readwrite_private.h"

src/h5core/h5_errorhandling.c

@@ -6,7 +6,7 @@
 #include "h5_core_private.h"
 
 static h5_errorhandler_t	h5priv_errhandler	= h5_report_errorhandler;
-static h5_int32_t		h5priv_debug_level	= 1;
+h5_int32_t			h5priv_debug_level	= 1;
 
 /*!
   \ingroup h5_core
@@ -160,8 +160,8 @@ h5_abort_errorhandler (
 	return -(int)f->__errno; // never executed, just to supress a warning
 }
 
-static void
-_vprintf (
+void
+h5priv_vprintf (
 	FILE* f,
 	const char* prefix,
 	const char* __funcname,
@@ -216,7 +216,7 @@ h5_verror (
 	) {
 
 	if (h5priv_debug_level < 1) return;
-	_vprintf (stderr, "E", f->__funcname, fmt, ap);
+	h5priv_vprintf (stderr, "E", f->__funcname, fmt, ap);
 }
 
 
@@ -232,7 +232,7 @@ h5_vwarn (
 	va_list ap
 	) {
 	if (h5priv_debug_level < 2) return;
-	_vprintf (stderr, "W", f->__funcname, fmt, ap);
+	h5priv_vprintf (stderr, "W", f->__funcname, fmt, ap);
 }
 
 /*!
@@ -252,69 +252,6 @@ h5_warn (
 	va_end (ap);
 }
 
-/*!
-  \ingroup h5_core_errorhandling
-
-  Print an informational message to \c stdout.
-*/
-void
-h5_vinfo (
-	const h5_file_t* const f,
-	const char* fmt,
-	va_list ap
-	) {
-	if (h5priv_debug_level < 3) return;
-	_vprintf (stdout, "I", f->__funcname, fmt, ap);
-}
-
-/*!
-  \ingroup h5_core_errorhandling
-
-  Print an informational message to \c stdout.
-*/
-void
-h5_info (
-	const h5_file_t* const f,
-	const char* fmt,
-	...
-	) {
-	va_list ap;
-	va_start (ap, fmt);
-	h5_vinfo (f, fmt, ap);
-	va_end (ap);
-}
-
-/*!
-  \ingroup h5_core_errorhandling
-
-  Print a debug message to \c stdout.
-*/
-void
-h5_vdebug (
-	const h5_file_t* const f,
-	const char* fmt,
-	va_list ap
-	) {
-	if (h5priv_debug_level < 4) return;
-	_vprintf (stdout, "D", f->__funcname, fmt, ap);
-}
-
-/*!
-  \ingroup h5_core_errorhandling
-
-  Print a debug message to \c stdout.
-*/
-void
-h5_debug (
-	const h5_file_t* const f,
-	const char* fmt,
-	...
-	) {
-	va_list ap;
-	va_start (ap, fmt);
-	h5_vdebug (f, fmt, ap);
-	va_end (ap);
-}
 
 /*!
   \ingroup h5_core_errorhandling

src/h5core/h5_hdf5.c

@@ -13,6 +13,9 @@ h5priv_open_hdf5_group (
 	const hid_t loc_id,
 	const char* const group_name
 	) {
+	h5_debug (f, "%s (loc_id=%lld, group_name=\"%s/%s\")", 
+		  __func__, (long long)loc_id,
+		  h5_get_objname (loc_id), group_name);
 	hid_t group_id = H5Gopen (loc_id, group_name, H5P_DEFAULT);
 	if (group_id < 0)
 		return h5_error (
@@ -21,6 +24,7 @@ h5priv_open_hdf5_group (
 			"Cannot open group \"%s/%s\".",
 			h5_get_objname (loc_id),
 			group_name);
+	h5_debug (f, "%s (): return group id: %lld", __func__, (long long)group_id);
 	return group_id;
 }
 
@@ -30,6 +34,9 @@ h5priv_create_hdf5_group (
 	const hid_t loc_id,
 	const char* const group_name
 	) {
+	h5_debug (f, "%s (loc_id=%lld, group_name=\"%s/%s\")", 
+		  __func__, (long long)loc_id,
+		  h5_get_objname (loc_id), group_name);
 	hid_t group_id = H5Gcreate (
 		loc_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 	if (group_id < 0)
@@ -39,6 +46,7 @@ h5priv_create_hdf5_group (
 			"Cannot create group \"%s/%s\".",
 			h5_get_objname (loc_id),
 			group_name);
+	h5_debug (f, "%s (): return group id: %lld", __func__, (long long)group_id);
 	return group_id;
 }
 
@@ -69,29 +77,11 @@ h5priv_open_group (
         h5_err_t exists;
         TRY( exists = h5priv_hdf5_link_exists(f, loc_id, group_name) );
 	if (exists > 0) {
-		h5_info (
-			f,
-			"Opening group %s/%s.",
-			h5_get_objname (loc_id),
-			group_name);
-		group_id = H5Gopen (loc_id, group_name, H5P_DEFAULT);
+		TRY( group_id = h5priv_open_hdf5_group (f, loc_id, group_name) );
 	} else {
 		CHECK_WRITABLE_MODE (f);
-		h5_info (
-			f,
-			"Creating group %s/%s.",
-			h5_get_objname (loc_id),
-			group_name);
-		group_id = H5Gcreate (loc_id, group_name, 0,
-				  H5P_DEFAULT, H5P_DEFAULT);
+		TRY( group_id = h5priv_create_hdf5_group (f, loc_id, group_name) );
 	}
-	if (group_id < 0)
-		return h5_error (
-			f,
-			H5_ERR_HDF5,
-			"Cannot open or create group %s/%s.",
-			h5_get_objname (loc_id),
-			group_name);
 
 	return group_id;
 }
@@ -107,6 +97,12 @@ h5priv_close_hdf5_group (
 	h5_file_t* const f,
 	const hid_t group_id
 	) {
+	h5_debug (f, "%s (group_id=%lld, group_name=\"%s\")", 
+		  __func__,
+		  (long long)group_id,
+		  h5_get_objname (group_id));
+
+	h5_debug (f, "%s (group_id=%lld)", __func__, (long long)group_id);
 	if (group_id <= 0) return H5_SUCCESS; 
 	if (H5Gclose (group_id) < 0 ) {
 		return h5_error (
@@ -187,6 +183,10 @@ h5priv_open_hdf5_dataset (
 	const hid_t loc_id,
 	const char* const dataset_name
 	) {
+	h5_debug (f, "%s (loc_id=%lld, dataset_name=\"%s/%s\")", 
+		  __func__, (long long)loc_id,
+		  h5_get_objname (loc_id), dataset_name);
+
 	hid_t dataset_id;
 
 	dataset_id = H5Dopen ( 
@@ -198,7 +198,7 @@ h5priv_open_hdf5_dataset (
 			f,
 			H5_ERR_HDF5,
 			"Cannot open dataset \"%s\".", dataset_name);
-
+	h5_debug (f, "%s (): return dataset id: %lld", __func__, (long long)dataset_id);
 	return dataset_id;
 }
 
@@ -222,6 +222,10 @@ h5priv_create_hdf5_dataset (
 	const hid_t dataspace_id,
 	const hid_t create_proplist
 	) {
+	h5_debug (f, "%s (loc_id=%lld, dataset_name=\"%s/%s\")", 
+		  __func__, (long long)loc_id,
+		  h5_get_objname (loc_id), dataset_name);
+	
 	hid_t dataset_id = H5Dcreate ( 
 		loc_id,
 		dataset_name,
@@ -237,6 +241,7 @@ h5priv_create_hdf5_dataset (
 			"Cannot create dataset %s/%s",
 			h5_get_objname (loc_id),
 			dataset_name);
+	h5_debug (f, "%s (): return dataset id: %lld", __func__, (long long)dataset_id);
 	return dataset_id;
 }
 
@@ -252,6 +257,10 @@ h5priv_close_hdf5_dataset (
 	const hid_t dset_id
 	) {
 	if (dset_id == 0 || dset_id == -1) return H5_SUCCESS; 
+	h5_debug (f, "%s (dataset_id=%lld, dataset_name=\"%s\")", 
+		  __func__,
+		  (long long)dset_id,
+		  h5_get_objname (dset_id));
 
 	if (H5Dclose (dset_id) < 0) {
 		return 	h5_error(

src/h5core/h5_hsearch.c

@@ -299,19 +299,19 @@ h5priv_hcreate_string_keyed (
 }
 
 static int
-_hcmp_id_keyed (
+hcmp_loc_id_keyed (
 	const void* __a,
 	const void* __b
 	) {
-	return memcmp (__a, __b, sizeof(h5_id_t));
+	return memcmp (__a, __b, sizeof(h5_loc_id_t));
 }
 
 static unsigned int
-_hcompute_id_keyed (
+hcompute_loc_id_keyed (
 	const void*__item
 	) {
 	char* key = (char*)__item;
-	unsigned int count = sizeof (h5_id_t);
+	unsigned int count = sizeof (h5_loc_id_t);
 	unsigned int hval = count;
 	while (count-- > 0) {
 		if (key[count]) {
@@ -323,11 +323,11 @@ _hcompute_id_keyed (
 }
 
 h5_err_t
-h5priv_hcreate_id_keyed (
+h5priv_hcreate_loc_id_keyed (
 	h5_file_t* const f,
 	size_t nel,
 	h5_hashtable_t* htab 
 	) {
 	return h5priv_hcreate (f, nel, htab,
-			       _hcmp_id_keyed, _hcompute_id_keyed);
+			       hcmp_loc_id_keyed, hcompute_loc_id_keyed);
 }

src/h5core/h5_hsearch_private.h

@@ -68,7 +68,7 @@ h5priv_hcreate_string_keyed (
 	);
 
 h5_err_t
-h5priv_hcreate_id_keyed (
+h5priv_hcreate_loc_id_keyed (
 	h5_file_t* const f,
 	size_t nel,
 	h5_hashtable_t* htab 

src/h5core/h5_maps.c

@@ -8,7 +8,7 @@ h5_err_t
 h5priv_alloc_idlist_items (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	const h5_size_t	size
+	const h5_size_t	size	// new size of list
 	) {
 	int new = (list->items == NULL);
 	size_t size_in_bytes = size * sizeof (list->items[0]);
@@ -61,7 +61,7 @@ h5_err_t
 h5priv_append_to_idlist (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_id_t id
+	h5_loc_id_t id
 	) {
 	if (list->num_items == list->size) {
 		h5_size_t size = list->size;
@@ -81,8 +81,8 @@ h5priv_cmp_ids_by_eid (
 	const void* _id1,
 	const void* _id2
 	) {
-	h5_id_t	id1 = h5tpriv_get_elem_idx (*(h5_id_t*)_id1); 
-	h5_id_t	id2 = h5tpriv_get_elem_idx (*(h5_id_t*)_id2); 
+	h5_loc_id_t	id1 = h5tpriv_get_elem_idx (*(h5_loc_id_t*)_id1); 
+	h5_loc_id_t	id2 = h5tpriv_get_elem_idx (*(h5_loc_id_t*)_id2); 
 	
 	if (id1 < id2) return -1;
 	if (id1 > id2) return 1;
@@ -94,8 +94,8 @@ h5priv_cmp_ids (
 	const void* _id1,
 	const void* _id2
 	) {
-	h5_id_t	*id1 = (h5_id_t*)_id1;
-	h5_id_t	*id2 = (h5_id_t*)_id2;
+	h5_loc_id_t	*id1 = (h5_loc_id_t*)_id1;
+	h5_loc_id_t	*id2 = (h5_loc_id_t*)_id2;
 	
 	if (*id1 < *id2) return -1;
 	if (*id1 > *id2) return 1;
@@ -120,18 +120,18 @@ h5priv_sort_idlist_by_eid (
 /*
   Find ID in sorted list
 */
-h5_id_t
+h5_loc_id_t
 h5priv_find_idlist (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_id_t	item
+	h5_loc_id_t item
 	) {
 #pragma unused f
-	register h5_id_t low = 0;
-	register h5_id_t high = list->num_items - 1;
+	register h5_loc_idx_t low = 0;
+	register h5_loc_idx_t high = list->num_items - 1;
 	while (low <= high) {
-		register h5_id_t mid = (low + high) / 2;
-		register h5_id_t diff = list->items[mid] - item;
+		register h5_loc_idx_t mid = (low + high) / 2;
+		register h5_loc_id_t diff = list->items[mid] - item;
            	if ( diff > 0 )
                		high = mid - 1;
            	else if ( diff < 0 )
@@ -145,12 +145,12 @@ h5priv_find_idlist (
 /*
   Add item to list at position given by \c idx.
 */
-h5_id_t
+h5_loc_idx_t
 h5priv_insert_idlist (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_id_t	item,
-	h5_id_t idx
+	h5_loc_id_t item,
+	h5_loc_idx_t idx
 	) {
 	if (list->num_items == list->size) {
 		h5_size_t size = list->size;
@@ -173,13 +173,13 @@ h5priv_insert_idlist (
 /*
   Search in sorted list. If item is not in list, add it.
  */
-h5_id_t
+h5_loc_idx_t
 h5priv_search_idlist (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_id_t	item
+	h5_loc_id_t item
 	) {
-	h5_id_t idx = h5priv_find_idlist (f, list, item);
+	h5_loc_idx_t idx = h5priv_find_idlist (f, list, item);
 	if (idx < 0) {
 		idx = -(idx+1);
 		idx = h5priv_insert_idlist (f, list, item, idx);
@@ -187,10 +187,11 @@ h5priv_search_idlist (
 	return idx;
 }
 
+
 h5_err_t
-h5priv_alloc_idmap (
+h5priv_alloc_idxmap (
 	h5_file_t* const f,
-	h5_idmap_t* map,
+	h5_idxmap_t* map,
 	const h5_size_t	size
 	) {
 	int new = (map->items == NULL);
@@ -202,16 +203,16 @@ h5priv_alloc_idmap (
 }
 
 h5_err_t
-h5priv_insert_idmap (
+h5priv_insert_idxmap (
 	h5_file_t* const f,
-	h5_idmap_t* map,
-	h5_id_t global_id,
-	h5_id_t local_id
+	h5_idxmap_t* map,
+	h5_glb_idx_t glb_idx,
+	h5_loc_idx_t loc_idx
 	) {
 	if (map->num_items == map->size)
 		return HANDLE_H5_OVERFLOW_ERR (f, "g2lmap", (long long)map->size);
 
-	h5_id_t i = h5priv_search_idmap (map, global_id);
+	h5_loc_idx_t i = h5priv_search_idxmap (map, glb_idx);
 	if (i >= 0)			/* global id already in use ? */
 		return -1;
 
@@ -221,8 +222,8 @@ h5priv_insert_idmap (
 		&map->items[i+1],
 		&map->items[i],
 		(map->num_items - i) * sizeof(map->items[0]));
-	map->items[i].global_id = global_id;
-	map->items[i].local_id = local_id;
+	map->items[i].glb_idx = glb_idx;
+	map->items[i].loc_idx = loc_idx;
 	map->num_items++;
 
 	return H5_SUCCESS;
@@ -238,17 +239,17 @@ h5priv_insert_idmap (
   where \c value must be inserted.
 
  */
-h5_id_t
-h5priv_search_idmap (
-	h5_idmap_t* map,
-	h5_id_t value
+h5_loc_idx_t
+h5priv_search_idxmap (
+	h5_idxmap_t* map,
+	h5_glb_idx_t value
 	) {
 
-	register int low = 0;
-	register int high = map->num_items - 1;
+	register h5_loc_idx_t low = 0;
+	register h5_loc_idx_t high = map->num_items - 1;
 	while (low <= high) {
-		register int mid = (low + high) / 2;
-		register h5_id_t diff = map->items[mid].global_id - value;
+		register h5_loc_idx_t mid = (low + high) / 2;
+		register h5_glb_idx_t diff = map->items[mid].glb_idx - value;
            	if ( diff > 0 )
                		high = mid - 1;
            	else if ( diff < 0 )
@@ -260,24 +261,24 @@ h5priv_search_idmap (
 }
 
 static int
-cmp_idmap_items (
+cmp_idxmap_items (
 	const void* _item1,
 	const void* _item2
 	) {
-	h5_idmap_el_t* item1 = (h5_idmap_el_t*)_item1;
-	h5_idmap_el_t* item2 = (h5_idmap_el_t*)_item2;
+	h5_idxmap_el_t* item1 = (h5_idxmap_el_t*)_item1;
+	h5_idxmap_el_t* item2 = (h5_idxmap_el_t*)_item2;
 
-	if (item1->global_id < item2->global_id) return -1;
-	if (item1->global_id > item2->global_id) return 1;
+	if (item1->glb_idx < item2->glb_idx) return -1;
+	if (item1->glb_idx > item2->glb_idx) return 1;
 	
 	return 0;
 }
 
 h5_err_t
-h5priv_sort_idmap (
-	h5_idmap_t* map
+h5priv_sort_idxmap (
+	h5_idxmap_t* map
 	) {
 	qsort (	map->items, map->num_items, sizeof (map->items[0]),
-		cmp_idmap_items);
+		cmp_idxmap_items);
 	return H5_SUCCESS;
 }

src/h5core/h5_maps_private.h

@@ -0,0 +1,103 @@
+#ifndef __H5_MAPS_PRIVATE_H
+#define __H5_MAPS_PRIVATE_H
+
+h5_err_t
+h5priv_alloc_idlist (
+	h5_file_t * const f,
+	h5_idlist_t **list,
+	const h5_size_t	size
+	);
+
+h5_err_t
+h5priv_free_idlist (
+	h5_file_t * const f,
+	h5_idlist_t **list
+	);
+
+h5_err_t
+h5priv_alloc_idlist_items (
+	h5_file_t * const f,
+	h5_idlist_t *list,
+	const h5_size_t	size
+	);
+
+h5_err_t
+h5priv_free_idlist_items (
+	h5_file_t * const f,
+	h5_idlist_t *list
+	);
+
+h5_err_t
+h5priv_append_to_idlist (
+	h5_file_t * const f,
+	h5_idlist_t *list,
+	h5_loc_id_t id
+	);
+
+int
+h5priv_cmp_ids_by_eid (
+	const void *_id1,
+	const void *_id2
+	);
+
+int
+h5priv_cmp_ids (
+	const void *_id1,
+	const void *_id2
+	);
+
+h5_err_t
+h5priv_sort_idlist_by_eid (
+	h5_file_t * const f,
+	h5_idlist_t *list
+	);
+
+h5_loc_id_t
+h5priv_find_idlist (
+	h5_file_t * const f,
+	h5_idlist_t *list,
+	h5_loc_id_t item
+	);
+
+h5_loc_idx_t
+h5priv_insert_idlist (
+	h5_file_t * const f,
+	h5_idlist_t *list,
+	h5_loc_id_t	item,
+	h5_loc_idx_t idx
+	);
+
+h5_loc_idx_t
+h5priv_search_idlist (
+	h5_file_t * const f,
+	h5_idlist_t *list,
+	h5_loc_id_t item
+	);
+
+h5_err_t
+h5priv_alloc_idxmap (
+	h5_file_t * const f,
+	h5_idxmap_t *map,
+	const h5_size_t	size
+	);
+
+h5_err_t
+h5priv_insert_idxmap (
+	h5_file_t * const f,
+	h5_idxmap_t *map,
+	h5_glb_idx_t glb_idx,
+	h5_loc_idx_t loc_idx
+	);
+
+h5_loc_idx_t
+h5priv_search_idxmap (
+	h5_idxmap_t *map,
+	h5_glb_idx_t value
+	);
+
+h5_err_t
+h5priv_sort_idxmap (
+	h5_idxmap_t *map
+	);
+
+#endif

src/h5core/h5_openclose.c

@@ -351,6 +351,7 @@ h5_err_t
 h5_close_file (
 	h5_file_t* const f	/*!< file handle */
 	) {
+	h5_debug (f, "%s ()", __func__);
 	f->__errno = H5_SUCCESS;
 
 	CHECK_FILEHANDLE (f);
@@ -369,7 +370,7 @@ h5_close_file (
 	TRY( h5priv_close_hdf5_file (f, f->file) );
 
 	free (f);
-
+	h5_debug (f, "%s (): done", __func__);
 	return H5_SUCCESS;
 }
 

src/h5core/h5_types_private.h

@@ -44,15 +44,15 @@ struct h5_file {
 	struct h5t_fdata *t;
 };
 
-struct h5_idmap_el {
-	h5_id_t	global_id;
-	h5_id_t	local_id;
+struct h5_idxmap_el {
+	h5_glb_idx_t	glb_idx;
+	h5_loc_idx_t	loc_idx;
 };
-typedef struct h5_idmap_el h5_idmap_el_t;
+typedef struct h5_idxmap_el h5_idxmap_el_t;
 
-struct h5_idmap {
+struct h5_idxmap {
 	h5_size_t	size;		/* allocated space in number of items */
 	h5_size_t	num_items;	/* stored items	*/
-	h5_idmap_el_t*  items;
+	h5_idxmap_el_t*  items;
 };
 #endif

src/h5core/h5t_access_private.h

@@ -4,95 +4,253 @@
 extern struct h5t_access_methods h5tpriv_access_trim_methods;
 extern struct h5t_access_methods h5tpriv_access_tetm_methods;
 
-#define h5tpriv_get_loc_elem(f, elem_idx)			\
-	(*f->t->methods.access->get_loc_elem)(f, elem_idx)
+static inline h5_generic_loc_elem_t*
+h5tpriv_get_loc_elem (
+	h5_file_t* const f,
+	const h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem)(f, elem_idx);
+}
 
-#define h5tpriv_get_loc_elem_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_loc_elem_idx)(f, elem_idx)
+static inline h5_loc_idx_t
+h5tpriv_get_loc_elem_parent_idx (
+	h5_file_t* const f,
+	const h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_parent_idx)(f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_loc_elem_idx)(f, elem_idx, idx)
+static inline h5_loc_idx_t
+h5tpriv_set_loc_elem_parent_idx (
+	h5_file_t* const f,
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t parent_idx
+	) {
+	return (*f->t->methods.access->set_loc_elem_parent_idx)(
+		f, elem_idx, parent_idx);
+}
 
-#define h5tpriv_get_loc_elem_parent_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_loc_elem_parent_idx)(f, elem_idx)
+static inline h5_loc_idx_t
+h5tpriv_get_loc_elem_child_idx (
+	h5_file_t* const f,
+	const h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_child_idx)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_parent_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_loc_elem_parent_idx)(f, elem_idx, idx)
+static inline h5_loc_idx_t
+h5tpriv_set_loc_elem_child_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t child_idx) {
+	return (*f->t->methods.access->set_loc_elem_child_idx)(
+		f, elem_idx, child_idx);
+}
 
-#define h5tpriv_get_loc_elem_child_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_loc_elem_child_idx)(f, elem_idx)
+static inline h5_id_t
+h5tpriv_get_loc_elem_level_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_level_idx)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_child_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_loc_elem_child_idx)(f, elem_idx, idx)
+static inline h5_id_t
+h5tpriv_set_loc_elem_level_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_id_t lvl_idx
+	) {
+	return (*f->t->methods.access->set_loc_elem_level_idx)(
+		f, elem_idx, lvl_idx);
+}
 
-#define h5tpriv_get_loc_elem_level_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_loc_elem_level_idx)(f, elem_idx)
+static inline h5_loc_idx_t*
+h5tpriv_get_loc_elem_vertex_indices (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_vertex_indices)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_level_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_loc_elem_level_idx)(f, elem_idx, idx)
+static inline h5_loc_idx_t
+h5tpriv_get_loc_elem_vertex_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_vertex_idx)(
+	f, elem_idx, face_idx);
+}
 
-#define h5tpriv_get_loc_elem_vertex_indices(f, elem_idx)		\
-	(*f->t->methods.access->get_loc_elem_vertex_indices)(f, elem_idx)
+static inline h5_loc_idx_t
+h5tpriv_set_loc_elem_vertex_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t vertex_idx
+	) {
+	return (*f->t->methods.access->set_loc_elem_vertex_idx)(
+		f, elem_idx, face_idx, vertex_idx);
+}
 
-#define h5tpriv_get_loc_elem_vertex_idx(f, elem_idx, face_idx)	\
-	(*f->t->methods.access->get_loc_elem_vertex_idx)(f, elem_idx, face_idx)
+static inline h5_loc_idx_t*
+h5tpriv_get_loc_elem_neighbor_indices (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_neighbor_indices)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_vertex_idx(f, elem_idx, face_idx, idx)	\
-	(*f->t->methods.access->get_loc_elem_vertex_idx)(f, elem_idx, face_idx, idx)
+static inline h5_loc_idx_t
+h5tpriv_get_loc_elem_neighbor_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx
+	) {
+	return (*f->t->methods.access->get_loc_elem_neighbor_idx)(
+		f, elem_idx, face_idx);
+}
 
-#define h5tpriv_get_loc_elem_neighbor_indices(f, elem_idx)		\
-	(*f->t->methods.access->get_loc_elem_neighbor_indices)(f, elem_idx)
+static inline h5_loc_idx_t
+h5tpriv_set_loc_elem_neighbor_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t idx
+	) {
+	return (*f->t->methods.access->set_loc_elem_neighbor_idx)(
+		f, elem_idx, face_idx, idx);
+}
 
-#define h5tpriv_get_loc_elem_neighbor_idx(f, elem_idx, face_idx)	\
-	(*f->t->methods.access->get_loc_elem_neighbor_idx)(f, elem_idx, face_idx)
+static inline h5_generic_glb_elem_t*
+h5tpriv_get_glb_elem (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_loc_elem_neighbor_idx(f, elem_idx, face_idx, idx)	\
-	(*f->t->methods.access->get_loc_elem_neighbor_idx)(f, elem_idx, face_idx, idx)
+static inline h5_glb_idx_t
+h5tpriv_get_glb_elem_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_idx)(
+		f, elem_idx);
+}
 
-#define h5tpriv_get_glb_elem(f, elem_idx)			\
-	(*f->t->methods.access->get_glb_elem)(f, elem_idx)
+static inline h5_glb_idx_t
+h5tpriv_set_glb_elem_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_glb_idx_t idx
+	) {
+	return (*f->t->methods.access->set_glb_elem_idx)(
+		f, elem_idx, idx);
+}
 
-#define h5tpriv_get_glb_elem_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_glb_elem_idx)(f, elem_idx)
+static inline h5_glb_idx_t
+h5tpriv_get_glb_elem_parent_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_parent_idx)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_glb_elem_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_glb_elem_idx)(f, elem_idx, idx)
+static inline h5_glb_idx_t
+h5tpriv_set_glb_elem_parent_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_glb_idx_t idx
+	) {
+	return (*f->t->methods.access->set_glb_elem_parent_idx)(
+		f, elem_idx, idx);
+}
 
-#define h5tpriv_get_glb_elem_parent_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_glb_elem_parent_idx)(f, elem_idx)
+static inline h5_glb_idx_t
+h5tpriv_get_glb_elem_child_idx(
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_child_idx)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_glb_elem_parent_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_glb_elem_parent_idx)(f, elem_idx, idx)
+static inline h5_glb_idx_t
+h5tpriv_set_glb_elem_child_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_glb_idx_t idx
+	) {
+	return (*f->t->methods.access->set_glb_elem_child_idx)(
+		f, elem_idx, idx);
+}
 
-#define h5tpriv_get_glb_elem_child_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_glb_elem_child_idx)(f, elem_idx)
+static inline h5_glb_idx_t*
+h5tpriv_get_glb_elem_vertex_indices (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_vertex_indices)(
+		f, elem_idx);
+}
 
-#define h5tpriv_set_glb_elem_child_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_glb_elem_child_idx)(f, elem_idx, idx)
+static inline h5_glb_idx_t
+h5tpriv_get_glb_elem_vertex_idx(
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_vertex_idx)(
+		f, elem_idx, face_idx);
+}
 
-#define h5tpriv_get_glb_elem_level_idx(f, elem_idx)			\
-	(*f->t->methods.access->get_glb_elem_level_idx)(f, elem_idx)
+static inline h5_glb_idx_t
+ h5tpriv_set_glb_elem_vertex_idx(
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_glb_idx_t idx
+	) {
+	return (*f->t->methods.access->set_glb_elem_vertex_idx)(
+		f, elem_idx, face_idx, idx);
+}
 
-#define h5tpriv_set_glb_elem_level_idx(f, elem_idx, idx)		\
-	(*f->t->methods.access->set_glb_elem_level_idx)(f, elem_idx, idx)
+static inline h5_glb_idx_t*
+h5tpriv_get_glb_elem_neighbor_indices(
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_neighbor_indices)(
+		f, elem_idx);
+}
 
-#define h5tpriv_get_glb_elem_vertex_indices(f, elem_idx)		\
-	(*f->t->methods.access->get_glb_elem_vertex_indices)(f, elem_idx)
-
-#define h5tpriv_get_glb_elem_vertex_idx(f, elem_idx, face_idx)	\
-	(*f->t->methods.access->get_glb_elem_vertex_idx)(f, elem_idx, face_idx)
-
-#define h5tpriv_set_glb_elem_vertex_idx(f, elem_idx, face_idx, idx)	\
-	(*f->t->methods.access->get_glb_elem_vertex_idx)(f, elem_idx, face_idx, idx)
-
-#define h5tpriv_get_glb_elem_neighbor_indices(f, elem_idx)		\
-	(*f->t->methods.access->get_glb_elem_neighbor_indices)(f, elem_idx)
-
-#define h5tpriv_get_glb_elem_neighbor_idx(f, elem_idx, face_idx)	\
-	(*f->t->methods.access->get_glb_elem_neighbor_idx)(f, elem_idx, face_idx)
-
-#define h5tpriv_set_glb_elem_neighbor_idx(f, elem_idx, face_idx, idx)	\
-	(*f->t->methods.access->get_glb_elem_neighbor_idx)(f, elem_idx, face_idx, idx)
+static inline h5_glb_idx_t
+h5tpriv_get_glb_elem_neighbor_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx
+	) {
+	return (*f->t->methods.access->get_glb_elem_neighbor_idx)(
+		f, elem_idx, face_idx);
+}
 
+static inline h5_glb_idx_t
+h5tpriv_set_glb_elem_neighbor_idx (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_glb_idx_t idx
+	) {
+	return (*f->t->methods.access->set_glb_elem_neighbor_idx)(
+		f, elem_idx, face_idx, idx);
+}
 
 #endif

src/h5core/h5t_access_tetm.c

@@ -2,45 +2,45 @@
 #include "h5_core_private.h"
 
 /*** op's on local elements ***/
-static h5_generic_elem_t*
+static h5_generic_loc_elem_t*
 get_loc_elem (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
-	return (h5_generic_elem_t*)&f->t->loc_elems.tets[elem_idx];
+	return (h5_generic_loc_elem_t*)&f->t->loc_elems.tets[elem_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].parent_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t parent_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t parent_idx
 	) {
 	f->t->loc_elems.tets[elem_idx].parent_idx = parent_idx;
 	return parent_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].child_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t child_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t child_idx
 	) {
 	f->t->loc_elems.tets[elem_idx].child_idx = child_idx;
 	return child_idx;
@@ -49,7 +49,7 @@ set_loc_elem_child_idx (
 static h5_id_t
 get_loc_elem_level_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].idx;
 }
@@ -57,64 +57,64 @@ get_loc_elem_level_idx (
 static h5_id_t
 set_loc_elem_level_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
+	const h5_loc_idx_t elem_idx,
 	const h5_id_t level_idx
 	) {
 	f->t->loc_elems.tets[elem_idx].idx = level_idx;
 	return level_idx;
 }
 
-static h5_id_t*
+static h5_loc_idx_t*
 get_loc_elem_vertex_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].vertex_indices;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].vertex_indices[face_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t vertex_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t vertex_idx
 	) {
 	f->t->loc_elems.tets[elem_idx].vertex_indices[face_idx] = vertex_idx;
 	return vertex_idx;
 }
 
-static h5_id_t*
+static h5_loc_idx_t*
 get_loc_elem_neighbor_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].neighbor_indices;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->loc_elems.tets[elem_idx].neighbor_indices[face_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t neighbor_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t neighbor_idx
 	) {
 	f->t->loc_elems.tets[elem_idx].neighbor_indices[face_idx] = neighbor_idx;
 	return neighbor_idx;
@@ -122,119 +122,119 @@ set_loc_elem_neighbor_idx (
 
 
 /*** op's on global elements ***/
-static h5_generic_elem_t*
+static h5_generic_glb_elem_t*
 get_glb_elem (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
-	return (h5_generic_elem_t*)&f->t->glb_elems.tets[elem_idx];
+	return (h5_generic_glb_elem_t*)&f->t->glb_elems.tets[elem_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_idx_t idx
 	) {
 	f->t->glb_elems.tets[elem_idx].idx = idx;
 	return idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].parent_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t parent_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_idx_t parent_idx
 	) {
 	f->t->glb_elems.tets[elem_idx].parent_idx = parent_idx;
 	return parent_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].child_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t child_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_idx_t child_idx
 	) {
 	f->t->glb_elems.tets[elem_idx].child_idx = child_idx;
 	return child_idx;
 }
 
-static h5_id_t*
+static h5_glb_idx_t*
 get_glb_elem_vertex_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].vertex_indices;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].vertex_indices[face_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t vertex_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_glb_idx_t vertex_idx
 	) {
 	f->t->glb_elems.tets[elem_idx].vertex_indices[face_idx] = vertex_idx;
 	return vertex_idx;
 }
 
-static h5_id_t*
+static h5_glb_idx_t*
 get_glb_elem_neighbor_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].neighbor_indices;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->glb_elems.tets[elem_idx].neighbor_indices[face_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t neighbor_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_glb_idx_t neighbor_idx
 	) {
 	f->t->glb_elems.tets[elem_idx].neighbor_indices[face_idx] = neighbor_idx;
 	return neighbor_idx;

src/h5core/h5t_access_trim.c

@@ -2,45 +2,45 @@
 #include "h5_core_private.h"
 
 /*** op's on local elements ***/
-static h5_generic_elem_t*
+static h5_generic_loc_elem_t*
 get_loc_elem (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
-	return (h5_generic_elem_t*)&f->t->loc_elems.tris[elem_idx];
+	return (h5_generic_loc_elem_t*)&f->t->loc_elems.tris[elem_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].parent_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t parent_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t parent_idx
 	) {
 	f->t->loc_elems.tris[elem_idx].parent_idx = parent_idx;
 	return parent_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].child_idx;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t child_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t child_idx
 	) {
 	f->t->loc_elems.tris[elem_idx].child_idx = child_idx;
 	return child_idx;
@@ -49,7 +49,7 @@ set_loc_elem_child_idx (
 static h5_id_t
 get_loc_elem_level_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].idx;
 }
@@ -57,64 +57,64 @@ get_loc_elem_level_idx (
 static h5_id_t
 set_loc_elem_level_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t level_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t level_idx
 	) {
 	f->t->loc_elems.tris[elem_idx].idx = level_idx;
 	return level_idx;
 }
 
-static h5_id_t*
+static h5_loc_idx_t*
 get_loc_elem_vertex_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].vertex_indices;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].vertex_indices[face_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t vertex_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t vertex_idx
 	) {
 	f->t->loc_elems.tris[elem_idx].vertex_indices[face_idx] = vertex_idx;
 	return vertex_idx;
 }
 
-static h5_id_t*
+static h5_loc_idx_t*
 get_loc_elem_neighbor_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].neighbor_indices;
 }
 
-static h5_id_t
+static h5_loc_idx_t
 get_loc_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->loc_elems.tris[elem_idx].neighbor_indices[face_idx];
 }
 
-static h5_id_t
+static h5_loc_idx_t
 set_loc_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t neighbor_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t neighbor_idx
 	) {
 	f->t->loc_elems.tris[elem_idx].neighbor_indices[face_idx] = neighbor_idx;
 	return neighbor_idx;
@@ -122,119 +122,119 @@ set_loc_elem_neighbor_idx (
 
 
 /*** op's on global elements ***/
-static h5_generic_elem_t*
+static h5_generic_glb_elem_t*
 get_glb_elem (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
-	return (h5_generic_elem_t*)&f->t->glb_elems.tris[elem_idx];
+	return (h5_generic_glb_elem_t*)&f->t->glb_elems.tris[elem_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_idx_t idx
 	) {
 	f->t->glb_elems.tris[elem_idx].idx = idx;
 	return idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].parent_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_parent_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t parent_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_id_t parent_idx
 	) {
 	f->t->glb_elems.tris[elem_idx].parent_idx = parent_idx;
 	return parent_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].child_idx;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_child_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t child_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_glb_idx_t child_idx
 	) {
 	f->t->glb_elems.tris[elem_idx].child_idx = child_idx;
 	return child_idx;
 }
 
-static h5_id_t*
+static h5_glb_idx_t*
 get_glb_elem_vertex_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].vertex_indices;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].vertex_indices[face_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_vertex_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t vertex_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_glb_idx_t vertex_idx
 	) {
 	f->t->glb_elems.tris[elem_idx].vertex_indices[face_idx] = vertex_idx;
 	return vertex_idx;
 }
 
-static h5_id_t*
+static h5_glb_idx_t*
 get_glb_elem_neighbor_indices (
 	h5_file_t* const f,
-	const h5_id_t elem_idx
+	const h5_loc_idx_t elem_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].neighbor_indices;
 }
 
-static h5_id_t
+static h5_glb_idx_t
 get_glb_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx
 	) {
 	return f->t->glb_elems.tris[elem_idx].neighbor_indices[face_idx];
 }
 
-static h5_id_t
+static h5_glb_idx_t
 set_glb_elem_neighbor_idx (
 	h5_file_t* const f,
-	const h5_id_t elem_idx,
-	const h5_id_t face_idx,
-	const h5_id_t neighbor_idx
+	const h5_loc_idx_t elem_idx,
+	const h5_loc_idx_t face_idx,
+	const h5_glb_idx_t neighbor_idx
 	) {
 	f->t->glb_elems.tris[elem_idx].neighbor_indices[face_idx] = neighbor_idx;
 	return neighbor_idx;

src/h5core/h5t_adjacencies.c

@@ -19,7 +19,7 @@
 h5_err_t
 h5t_get_adjacencies (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {

src/h5core/h5t_adjacencies_private.h

@@ -7,7 +7,7 @@ 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_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -21,6 +21,7 @@ static inline h5_err_t
 h5tpriv_release_adjacency_structs (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s ()", __func__);
 	if (f->t->methods.adjacency == NULL) {
 		return 0;
 	}
@@ -32,6 +33,7 @@ h5tpriv_update_adjacency_structs (
 	h5_file_t* const f,
 	const h5_id_t level_id
 	) {
+	h5_debug (f, "%s (%lld)", __func__, level_id);
 	return (*f->t->methods.adjacency->update_internal_structs)(f, level_id);
 }
 

src/h5core/h5t_adjacencies_tetm.c

@@ -20,20 +20,14 @@
 
 static inline h5_err_t
 alloc_tv (
-	h5_file_t* const f,
-	const h5_loc_idx_t level_idx
-
+	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
-	h5_loc_idx_t idx = (level_idx <= 0) ? 0 : t->num_vertices[level_idx-1];
-	h5_loc_idx_t last = t->num_vertices[t->num_levels-1];
+	h5_loc_idx_t num_vertices = t->num_vertices[t->num_levels-1];
 
 	h5t_adjacencies_t* adj = &t->adjacencies;
-	adj->tv.size = last;
-	size_t size = last * sizeof(adj->tv.v[0]);
-	TRY( adj->tv.v = h5priv_alloc (f, adj->tv.v, size) );
-	size = (last-idx) * sizeof(adj->tv.v[0]);
-	memset (&adj->tv.v[idx], 0, size);
+	// allocate one ID list per vertex
+	TRY( adj->tv.v = h5priv_calloc (f, num_vertices, sizeof(*adj->tv.v)) );
 
 	return H5_SUCCESS;
 }
@@ -65,18 +59,18 @@ compute_elems_of_vertices (
 	const h5_id_t from_lvl
 	) {
 	/* expand structure */
-	TRY( alloc_tv (f, from_lvl) );
+	TRY( alloc_tv (f) );
 
 	/* loop over all elements in current level */
 	h5t_fdata_t* t = f->t;
 	h5_loc_idx_t idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
 	h5_loc_idx_t last = t->num_elems[t->num_levels-1];
-	h5_tet_t *el = &t->loc_elems.tets[idx];
+	h5_loc_tet_t *el = &t->loc_elems.tets[idx];
 	for (;idx < last; idx++, el++) {
 		int face_idx;
 		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];
+			h5_loc_idx_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
 				     f,
 				     &t->adjacencies.tv.v[vidx],
@@ -104,8 +98,8 @@ compute_elems_of_edges (
 	const h5_id_t from_lvl
 	) {
 	h5t_fdata_t *t = f->t;
-	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_loc_idx_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_loc_idx_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)) );
 	for (;elem_idx < num_elems; elem_idx++) {
@@ -134,8 +128,8 @@ compute_elems_of_triangles (
 	const h5_id_t from_lvl
 	) {
 	h5t_fdata_t* t = f->t;
-	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_loc_idx_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 	h5_idlist_t *retval = NULL;
 	TRY( h5tpriv_resize_td_htab (f, 4*(num_elems-elem_idx)) );
 	for (;elem_idx < num_elems; elem_idx++) {
@@ -152,7 +146,7 @@ compute_elems_of_triangles (
 static inline h5_err_t
 compute_children_of_edge (
 	h5_file_t* const f,
-	h5_id_t kid,
+	h5_loc_id_t kid,
 	h5_idlist_t* children
 	) {
 	h5t_fdata_t* t = f->t;
@@ -164,16 +158,16 @@ compute_children_of_edge (
 		     h5tpriv_get_elem_idx (kid),
 		     &te ) 
 		);
-	h5_id_t* edge = te->items;
-	h5_id_t* end = te->items+te->num_items;
+	h5_loc_id_t* edge = te->items;
+	h5_loc_id_t* end = te->items+te->num_items;
 	for (; edge < end; edge++) {
-		h5_id_t elem_idx = h5tpriv_get_elem_idx (*edge);
-		h5_id_t face_idx =  h5tpriv_get_face_idx (*edge);
-		h5_tet_t* tet = &t->loc_elems.tets[elem_idx];
-		if (h5tpriv_elem_is_on_cur_level (f, (h5_generic_elem_t*)tet) == H5_OK ) {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge);
+		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx (*edge);
+		h5_loc_tet_t* tet = &t->loc_elems.tets[elem_idx];
+		if (h5tpriv_elem_is_on_cur_level (f, (h5_generic_loc_elem_t*)tet) == H5_OK ) {
 			TRY( h5priv_append_to_idlist (f, children, *edge) );
 		} else {
-			h5_id_t kids[2];
+			h5_loc_id_t kids[2];
 			TRY( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
@@ -192,7 +186,7 @@ compute_children_of_edge (
 static inline h5_err_t
 compute_sections_of_edge (
 	h5_file_t* const f,
-	h5_id_t kid,
+	h5_loc_id_t kid,
 	h5_idlist_t* children
 	) {
 	h5t_fdata_t* t = f->t;
@@ -203,16 +197,16 @@ compute_sections_of_edge (
 		     h5tpriv_get_face_idx (kid),
 		     h5tpriv_get_elem_idx (kid),
 		     &te ) );
-	h5_id_t* edge = te->items;
-	h5_id_t* end = te->items+te->num_items;
+	h5_loc_id_t* edge = te->items;
+	h5_loc_id_t* end = te->items+te->num_items;
 	int refined = 0;
 	for (; edge < end; edge++) {
-		h5_id_t eid = h5tpriv_get_elem_idx (*edge);
-		h5_id_t face_id =  h5tpriv_get_face_idx (*edge);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
+		h5_loc_idx_t eid = h5tpriv_get_elem_idx (*edge);
+		h5_loc_idx_t face_id =  h5tpriv_get_face_idx (*edge);
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[eid];
 		if (! h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			refined = 1;
-			h5_id_t kids[2];
+			h5_loc_id_t kids[2];
 			TRY( h5tpriv_get_direct_children_of_edge (
 				     f,
 				     face_id,
@@ -262,11 +256,11 @@ compute_sections_of_edge (
 static inline h5_err_t
 compute_direct_children_of_triangle (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
-	h5_id_t	children[4]
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
+	h5_loc_id_t children[4]
 	) {
-	h5_id_t map[4][4][2] = {
+	h5_loc_idx_t map[4][4][2] = {
 		{{0,0},{0,1},{0,2},{0,5}},
 		{{1,0},{1,1},{1,3},{2,4}},
 		{{2,0},{2,2},{2,3},{1,7}},
@@ -290,7 +284,7 @@ compute_direct_children_of_triangle (
 static inline h5_err_t
 compute_children_of_triangle (
 	h5_file_t* const f,
-	h5_id_t did,
+	h5_loc_id_t did,
 	h5_idlist_t* children 
 	) {
 
@@ -302,16 +296,16 @@ compute_children_of_triangle (
 		     h5tpriv_get_face_idx (did),
 		     h5tpriv_get_elem_idx (did),
 		     &td) );
-	h5_id_t* tri = td->items;
-	h5_id_t* end = td->items+td->num_items;
+	h5_loc_id_t* tri = td->items;
+	h5_loc_id_t* end = td->items+td->num_items;
 	for (; tri < end; tri++) {
-		h5_id_t eid = h5tpriv_get_elem_idx (*tri);
-		h5_id_t face_idx =  h5tpriv_get_face_idx (*tri);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
+		h5_loc_idx_t eid = h5tpriv_get_elem_idx (*tri);
+		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx (*tri);
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[eid];
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			TRY( h5priv_append_to_idlist (f, children, *tri) );
 		} else {
-			h5_id_t dids[4];
+			h5_loc_id_t dids[4];
 			TRY( compute_direct_children_of_triangle (
 				      f,
 				      face_idx,
@@ -329,7 +323,7 @@ compute_children_of_triangle (
 static inline h5_err_t
 compute_sections_of_triangle (
 	h5_file_t* const f,
-	h5_id_t did,
+	h5_loc_id_t did,
 	h5_idlist_t* children
 	) {
 	h5t_fdata_t* t = f->t;
@@ -339,16 +333,16 @@ compute_sections_of_triangle (
 		     f,
 		     h5tpriv_get_face_idx (did),
 		     h5tpriv_get_elem_idx (did), &td) );
-	h5_id_t* tri = td->items;
-	h5_id_t* end = td->items+td->num_items;
+	h5_loc_id_t* tri = td->items;
+	h5_loc_id_t* end = td->items+td->num_items;
 	int refined = 0;
 	for (; tri < end; tri++) {
-		h5_id_t eid = h5tpriv_get_elem_idx (*tri);
-		h5_id_t face_idx =  h5tpriv_get_face_idx (*tri);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
+		h5_loc_idx_t eid = h5tpriv_get_elem_idx (*tri);
+		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx (*tri);
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[eid];
 		if (! h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			refined = 1;
-			h5_id_t dids[4];
+			h5_loc_id_t dids[4];
 			TRY( compute_direct_children_of_triangle (
 				     f,
 				     face_idx,
@@ -399,11 +393,11 @@ get_edges_uadj_to_vertex (
 	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
 	h5_size_t i;
 
-	h5_id_t* vidp = tv->items;	// ptr to upward adjacent elements
+	h5_loc_id_t* vidp = tv->items;	// ptr to upward adjacent elements
 	for (i = 0; i < tv->num_items; i++, vidp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
 		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*vidp);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[elem_idx];
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK ) {
 			continue;
@@ -423,11 +417,11 @@ static inline h5_err_t
 add_triangle (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_id_t face,
-	h5_id_t eid
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx
 	) {
 	h5_idlist_t* td;
-	TRY( h5tpriv_find_td2 (f, face, eid, &td) );
+	TRY( h5tpriv_find_td2 (f, face_idx, elem_idx, &td) );
 	TRY( h5priv_search_idlist (f, list, td->items[0]) );
 
 	return H5_SUCCESS;
@@ -452,11 +446,11 @@ get_triangles_uadj_to_vertex (
 	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
-	h5_id_t* vidp = tv->items;
+	h5_loc_id_t* vidp = tv->items;
 	for (i = 0; i < tv->num_items; i++, vidp++) {
-		h5_id_t elem_idx = h5tpriv_get_elem_idx (*vidp);
-		h5_id_t face_idx = h5tpriv_get_face_idx (*vidp);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[elem_idx];
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*vidp);
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK) {
 			continue;
@@ -486,10 +480,10 @@ get_tets_uadj_to_vertex (
 	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
 	h5_size_t i;
 
-	h5_id_t* vidp = tv->items;
+	h5_loc_id_t* vidp = tv->items;
 	for (i = 0; i < tv->num_items; i++, vidp++) {
-		h5_id_t elem_idx = h5tpriv_get_elem_idx (*vidp);
-		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[elem_idx];
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
+		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK) {
 			continue;
@@ -503,21 +497,21 @@ get_tets_uadj_to_vertex (
 static inline h5_err_t
 get_triangles_uadj_to_edge (
 	h5_file_t* const f,
-	const h5_id_t kid,
+	const h5_loc_id_t kid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
 	TRY( compute_children_of_edge (f, kid, children) );
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t* edge = children->items;
-	h5_id_t* end = children->items+children->num_items;
+	h5_loc_id_t* edge = children->items;
+	h5_loc_id_t* end = children->items+children->num_items;
 	int map[6][2] = { {2,3}, {0,3}, {1,3}, {1,2}, {0,2}, {0,1} };
 	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) );
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge);
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*edge);
+		TRY( add_triangle (f, *list, map[face_idx][0], elem_idx) );
+		TRY( add_triangle (f, *list, map[face_idx][1], elem_idx) );
 	}
 	TRY( h5priv_free_idlist ( f, &children) );
 
@@ -527,7 +521,7 @@ get_triangles_uadj_to_edge (
 static inline h5_err_t
 get_tets_uadj_to_edge (
 	h5_file_t* const f,
-	const h5_id_t kid,
+	const h5_loc_id_t kid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
@@ -535,10 +529,10 @@ get_tets_uadj_to_edge (
 	TRY( compute_children_of_edge (f, kid, children) );
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	int i;
-	h5_id_t* kidp = children->items;
+	h5_loc_id_t* kidp = children->items;
 	for (i = 0; i < children->num_items; i++, kidp++) {
-		h5_id_t eid = h5tpriv_get_elem_idx (*kidp);
-		TRY( h5priv_search_idlist (f, *list, eid) );
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*kidp);
+		TRY( h5priv_search_idlist (f, *list, elem_idx) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -547,7 +541,7 @@ get_tets_uadj_to_edge (
 static inline h5_err_t
 get_tets_uadj_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t did,
+	const h5_loc_id_t did,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
@@ -555,10 +549,10 @@ get_tets_uadj_to_triangle (
 	TRY( compute_children_of_triangle (f, did, children) );
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	int i;
-	h5_id_t *didp = children->items;
+	h5_loc_id_t *didp = children->items;
 	for (i = 0; i < children->num_items; i++ , didp++) {
-		h5_id_t eid = h5tpriv_get_elem_idx (*didp);
-		TRY( h5priv_search_idlist (f, *list, eid) );
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*didp);
+		TRY( h5priv_search_idlist (f, *list, elem_idx) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -567,7 +561,7 @@ get_tets_uadj_to_triangle (
 static inline h5_err_t
 get_vertices_dadj_to_edge (
 	h5_file_t* const f,
-	const h5_id_t kid,
+	const h5_loc_id_t kid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
@@ -575,12 +569,12 @@ get_vertices_dadj_to_edge (
 	TRY( compute_sections_of_edge (f, kid, children) );
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	int i;
-	h5_id_t* kidp = children->items;
+	h5_loc_id_t* kidp = children->items;
 	for (i = 0; i < children->num_items; i++, kidp++) {
-		h5_id_t vids[2];
-		TRY( h5t_get_vertex_indices_of_edge (f, *kidp, vids) );
-		TRY( h5priv_search_idlist (f, *list, vids[0]) );
-		TRY( h5priv_search_idlist (f, *list, vids[1]) );
+		h5_loc_idx_t vertex_indices[2];
+		TRY( h5t_get_vertex_indices_of_edge (f, *kidp, vertex_indices) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -592,61 +586,62 @@ get_vertices_dadj_to_edge (
 static inline h5_err_t
 get_vertices_dadj_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t did,
+	const h5_loc_id_t did,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
 
 	int map[4][3] = { {1,4,5}, {2,3,5}, {0,3,4}, {0,1,2} };
-	h5_id_t face = h5tpriv_get_face_idx (did);
-	h5_id_t eid = h5tpriv_get_elem_idx (did);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (did);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (did);
 
-	h5_id_t i;
+	int i;
 	for (i = 0; i < 3; i++) {
 		TRY( compute_sections_of_edge (
 			     f,
-			     h5tpriv_build_edge_id (map[face][i], eid),
+			     h5tpriv_build_edge_id (map[face_idx][i], elem_idx),
 			     children) );
 	}
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t* kid = children->items;
+	h5_loc_id_t* kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
-		h5_id_t vids[2];
-		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vids) );
-		TRY( h5priv_search_idlist (f, *list, vids[0]) );
-		TRY( h5priv_search_idlist (f, *list, vids[1]) );
+		h5_loc_idx_t vertex_indices[2];
+		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vertex_indices) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
 }
 
 /*
-  Compute downward adjacent vertices of all edges of tetrahedron.
+  Compute downward adjacent vertices to tetrahedron given by ID.
  */
 static inline h5_err_t
 get_vertices_dadj_to_tet (
 	h5_file_t* const f,
-	const h5_id_t eid,
+	const h5_loc_id_t eid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (eid);
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
 
-	h5_id_t i;
+	int i;
 	for (i = 0; i < 6; i++) {
 		TRY( compute_sections_of_edge (
 			     f,
-			     h5tpriv_build_edge_id ( i, eid ),
+			     h5tpriv_build_edge_id ( i, elem_idx ),
 			     children) );
 	}
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t *kid = children->items;
+	h5_loc_id_t *kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
-		h5_id_t vids[2];
-		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vids) );
-		TRY( h5priv_search_idlist (f, *list, vids[0]) );
-		TRY( h5priv_search_idlist (f, *list, vids[1]) );
+		h5_loc_idx_t vertex_indices[2];
+		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vertex_indices) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -655,25 +650,25 @@ get_vertices_dadj_to_tet (
 static inline h5_err_t
 get_edges_dadj_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t did,
+	const h5_loc_id_t did,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
 
 	int map[4][3] = { {1,4,5}, {2,3,5}, {0,3,4}, {0,1,2} };
-	h5_id_t face_idx = h5tpriv_get_face_idx (did);
-	h5_id_t eid = h5tpriv_get_elem_idx (did);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (did);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (did);
 
-	h5_id_t i;
+	int i;
 	for (i = 0; i < 3; i++) {
 		TRY( compute_sections_of_edge (
 			     f,
-			     h5tpriv_build_edge_id ( map[face_idx][i], eid ),
+			     h5tpriv_build_edge_id ( map[face_idx][i], elem_idx ),
 			     children) );
 	}
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t *kid = children->items;
+	h5_loc_id_t *kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
 		TRY( h5priv_search_idlist (f, *list, *kid) );
 	}
@@ -684,21 +679,22 @@ get_edges_dadj_to_triangle (
 static inline h5_err_t
 get_edges_dadj_to_tet (
 	h5_file_t* const f,
-	const h5_id_t eid,
+	const h5_loc_id_t eid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (eid);
 
-	h5_id_t i;
+	int i;
 	for (i = 0; i < 6; i++) {
 		TRY( compute_sections_of_edge (
 			     f,
-			     h5tpriv_build_edge_id ( i, eid ),
+			     h5tpriv_build_edge_id ( i, elem_idx ),
 			     children) );
 	}
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t* kid = children->items;
+	h5_loc_id_t* kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
 		TRY( h5priv_search_idlist (f, *list, *kid) );
 	}
@@ -709,21 +705,22 @@ get_edges_dadj_to_tet (
 static inline h5_err_t
 get_triangles_dadj_to_tet (
 	h5_file_t* const f,
-	const h5_id_t eid,
+	const h5_loc_id_t eid,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (eid);
 
-	h5_id_t i;
+	int i;
 	for (i = 0; i < 4; i++) {
 		TRY( compute_sections_of_triangle (
 			     f,
-			     h5tpriv_build_edge_id ( i, eid ),
+			     h5tpriv_build_edge_id ( i, elem_idx ),
 			     children) );
 	}
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t* did = children->items;
+	h5_loc_id_t* did = children->items;
 	for (i = 0; i < children->num_items; i++, did++) {
 		TRY( h5priv_search_idlist (f, *list, *did) );
 	}
@@ -745,7 +742,7 @@ dim_error(
 static inline h5_err_t
 get_adjacencies_to_vertex (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -764,7 +761,7 @@ get_adjacencies_to_vertex (
 static inline h5_err_t
 get_adjacencies_to_edge (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -783,7 +780,7 @@ get_adjacencies_to_edge (
 static inline h5_err_t
 get_adjacencies_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -802,7 +799,7 @@ get_adjacencies_to_triangle (
 static inline h5_err_t
 get_adjacencies_to_tet (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -821,11 +818,11 @@ get_adjacencies_to_tet (
 static h5_err_t
 get_adjacencies (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
-	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
+	h5_loc_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);

src/h5core/h5t_adjacencies_trim.c

@@ -19,20 +19,14 @@
 
 static inline h5_err_t
 alloc_tv (
-	h5_file_t* const f,
-	const h5_loc_idx_t level_idx
-
+	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
-	h5_loc_idx_t idx = (level_idx <= 0) ? 0 : t->num_vertices[level_idx-1];
-	h5_loc_idx_t last = t->num_vertices[t->num_levels-1];
+	h5_loc_idx_t num_vertices = t->num_vertices[t->num_levels-1];
 
 	h5t_adjacencies_t* adj = &t->adjacencies;
-	adj->tv.size = last;
-	size_t size = last * sizeof(adj->tv.v[0]);
-	TRY( adj->tv.v = h5priv_alloc (f, adj->tv.v, size) );
-	size = (last-idx) * sizeof(adj->tv.v[0]);
-	memset (&adj->tv.v[idx], 0, size);
+	// allocate one ID list per vertex
+	TRY( adj->tv.v = h5priv_calloc (f, num_vertices, sizeof(*adj->tv.v)) );
 
 	return H5_SUCCESS;
 }
@@ -63,19 +57,20 @@ compute_elems_of_vertices (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
 	) {
+	h5_debug (f, "%s (%lld)", __func__, from_lvl);
 	/* expand structure */
-	TRY( alloc_tv (f, from_lvl) );
+	TRY( alloc_tv (f) );
 
 	/* loop over all elements in current level */
 	h5t_fdata_t *t = f->t;
 	h5_loc_idx_t idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
 	h5_loc_idx_t last = t->num_elems[t->num_levels-1];
-	h5_triangle_t *el = &t->loc_elems.tris[idx];
+	h5_loc_triangle_t *el = &t->loc_elems.tris[idx];
 	for (;idx < last; idx++, el++) {
 		int face_idx;
 		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];
+			h5_loc_idx_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
 				     f,
 				     &t->adjacencies.tv.v[vidx],
@@ -83,6 +78,7 @@ compute_elems_of_vertices (
 					     face_idx, idx)) );
 		}
 	}
+	h5_debug (f, "%s (%lld): done", __func__, from_lvl);
 	return H5_SUCCESS;
 }
 
@@ -103,26 +99,28 @@ compute_elems_of_edges (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
 	) {
+	h5_debug (f, "%s (%lld)", __func__, from_lvl);
 	h5t_fdata_t *t = f->t;
-	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_loc_idx_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_loc_idx_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)) );
 	for (;elem_idx < num_elems; elem_idx++) {
-		int face_idx;
-		int num_faces = h5tpriv_ref_elem_get_num_edges (t);
+		h5_loc_idx_t face_idx;
+		h5_loc_idx_t  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 ) );
 		}
 	}
+	h5_debug (f, "%s (%lld): done", __func__, from_lvl);
 	return H5_SUCCESS;
 }
 
 static inline h5_err_t
 compute_children_of_edge (
 	h5_file_t * const f,
-	h5_id_t kid,
+	h5_loc_id_t kid,
 	h5_idlist_t *children
 	) {
 	h5t_fdata_t *t = f->t;
@@ -134,18 +132,18 @@ compute_children_of_edge (
 		      h5tpriv_get_elem_idx ( kid ),
 		      &te ) 
 		);
-	h5_id_t *edge = te->items;
-	h5_id_t *end = te->items+te->num_items;
+	h5_loc_id_t *edge = te->items;
+	h5_loc_id_t *end = te->items+te->num_items;
 	for ( ; edge < end; edge++ ) {
-		h5_id_t elem_idx = h5tpriv_get_elem_idx ( *edge );
-		h5_id_t face_idx =  h5tpriv_get_face_idx ( *edge );
-		h5_generic_elem_t *el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_idx];
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge );
+		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx ( *edge );
+		h5_generic_loc_elem_t *el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_OK ) {
 			TRY ( h5priv_append_to_idlist (
 				      f, children, *edge )
 				);
 		} else {
-			h5_id_t kids[2];
+			h5_loc_id_t kids[2];
 			TRY ( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
@@ -166,7 +164,7 @@ compute_children_of_edge (
 static inline h5_err_t
 compute_sections_of_edge (
 	h5_file_t * const f,
-	h5_id_t kid,
+	h5_loc_id_t kid,
 	h5_idlist_t *children
 	) {
 	h5t_fdata_t *t = f->t;
@@ -178,19 +176,19 @@ compute_sections_of_edge (
 		      h5tpriv_get_elem_idx ( kid ),
 		      &te )
 		);
-	h5_id_t *edge = te->items;
-	h5_id_t *end = te->items+te->num_items;
+	h5_loc_id_t *edge = te->items;
+	h5_loc_id_t *end = te->items+te->num_items;
 	int refined = 0;
 	for ( ; edge < end; edge++ ) {
-		h5_id_t eid = h5tpriv_get_elem_idx ( *edge );
-		h5_id_t face_id =  h5tpriv_get_face_idx ( *edge );
-		h5_generic_elem_t *el = (h5_generic_elem_t*)&t->loc_elems.tris[eid];
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge );
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx ( *edge );
+		h5_generic_loc_elem_t *el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
 		if ( ! h5tpriv_elem_is_on_cur_level ( f, el ) == H5_OK ) {
 			refined = 1;
-			h5_id_t kids[2];
+			h5_loc_id_t kids[2];
 			TRY ( h5tpriv_get_direct_children_of_edge (
 				      f,
-				      face_id,
+				      face_idx,
 				      el->child_idx,
 				      kids ) );
 			TRY ( compute_sections_of_edge (
@@ -214,8 +212,8 @@ static inline h5_err_t
 add_edge (
 	h5_file_t * const f,
 	h5_idlist_t *list,
-	h5_id_t face_idx,
-	h5_id_t elem_idx
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx
 	) {
 	h5_idlist_t *te;
 	TRY ( h5tpriv_find_te2 ( f, face_idx, elem_idx, &te ) );
@@ -227,7 +225,7 @@ add_edge (
 static inline h5_err_t
 get_edges_uadj_to_vertex (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t **list
 	) {
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
@@ -238,11 +236,11 @@ get_edges_uadj_to_vertex (
 	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
-	h5_id_t* vertex_idp = tv->items;
+	h5_loc_id_t* vertex_idp = tv->items;
 	for ( i = 0; i < tv->num_items; i++, vertex_idp++ ) {
-		h5_id_t elem_idx = h5tpriv_get_elem_idx ( *vertex_idp );
-		h5_id_t face_idx = h5tpriv_get_face_idx ( *vertex_idp );
-		h5_generic_elem_t* el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_idx];
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *vertex_idp );
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx ( *vertex_idp );
+		h5_generic_loc_elem_t* el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
 
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_NOK ) {
 			continue;
@@ -259,7 +257,7 @@ get_edges_uadj_to_vertex (
 static inline h5_err_t
 get_triangles_uadj_to_vertex (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t **list
 	) {
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
@@ -270,10 +268,10 @@ get_triangles_uadj_to_vertex (
 	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
-	h5_id_t *vertex_idp = tv->items;
+	h5_loc_id_t *vertex_idp = tv->items;
 	for ( i = 0; i < tv->num_items; i++, vertex_idp++ ) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *vertex_idp );
-		h5_generic_elem_t* el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_idx];
+		h5_generic_loc_elem_t* el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
 
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_NOK ) {
 			continue;
@@ -286,18 +284,18 @@ get_triangles_uadj_to_vertex (
 static inline h5_err_t
 get_triangles_uadj_to_edge (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t **list
 	) {
 	h5_idlist_t *children;
 	TRY ( h5priv_alloc_idlist ( f, &children, 8 ) );
 	TRY ( compute_children_of_edge ( f, entity_id, children ) );
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
-	h5_id_t *edge_id = children->items;
-	h5_id_t *end = children->items+children->num_items;
+	h5_loc_id_t *edge_id = children->items;
+	h5_loc_id_t *end = children->items+children->num_items;
 	for ( ; edge_id < end; edge_id++ ) {
-		h5_id_t elem_id = h5tpriv_get_elem_idx ( *edge_id );
-		TRY ( h5priv_search_idlist ( f, *list, elem_id ) );
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge_id );
+		TRY ( h5priv_search_idlist ( f, *list, elem_idx ) );
 	}
 	TRY ( h5priv_free_idlist( f, &children ) );
 
@@ -307,7 +305,7 @@ get_triangles_uadj_to_edge (
 static inline h5_err_t
 get_vertices_dadj_to_edge (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t **list
 	) {
 	h5_idlist_t *children;
@@ -315,12 +313,12 @@ get_vertices_dadj_to_edge (
 	TRY( compute_sections_of_edge ( f, entity_id, children ) );
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
 	int i;
-	h5_id_t *edge_id = children->items;
+	h5_loc_id_t *edge_id = children->items;
 	for ( i = 0; i < children->num_items; i++, edge_id++ ) {
-		h5_id_t vids[2];
-		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_id, vids ) );
-		TRY ( h5priv_search_idlist ( f, *list, vids[0] ) );
-		TRY ( h5priv_search_idlist ( f, *list, vids[1] ) );
+		h5_loc_idx_t vertex_indices[2];
+		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_id, vertex_indices ) );
+		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[0] ) );
+		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[1] ) );
 	}
 	TRY ( h5priv_free_idlist( f, &children ) );
 	return H5_SUCCESS;
@@ -332,16 +330,16 @@ get_vertices_dadj_to_edge (
 static inline h5_err_t
 get_vertices_dadj_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY ( h5priv_alloc_idlist ( f, &children, 8 ) );
 
-	h5_id_t elem_idx = h5tpriv_get_elem_idx ( entity_id );
+	h5_loc_idx_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 = h5tpriv_ref_elem_get_num_edges (f->t);
+	h5_loc_idx_t face_idx;
+	h5_loc_idx_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,
@@ -349,13 +347,13 @@ get_vertices_dadj_to_triangle (
 			     children) );
 	}
 	TRY ( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t *edge_idp = children->items;
+	h5_loc_id_t *edge_idp = children->items;
 	int i;
 	for ( i = 0; i < children->num_items; i++, edge_idp++ ) {
-		h5_id_t vids[2];
-		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_idp, vids ) );
-		TRY ( h5priv_search_idlist ( f, *list, vids[0] ) );
-		TRY ( h5priv_search_idlist ( f, *list, vids[1] ) );
+		h5_loc_idx_t vertex_indices[2];
+		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_idp, vertex_indices ) );
+		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[0] ) );
+		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[1] ) );
 	}
 	TRY ( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -364,16 +362,16 @@ get_vertices_dadj_to_triangle (
 static inline h5_err_t
 get_edges_dadj_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_idlist_t** list
 	) {
 	h5_idlist_t* children;
 	TRY ( h5priv_alloc_idlist (f, &children, 8) );
 
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_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 = h5tpriv_ref_elem_get_num_edges (f->t);
+	h5_loc_idx_t face_idx;
+	h5_loc_idx_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,
@@ -381,7 +379,7 @@ get_edges_dadj_to_triangle (
 			     children) );
 	}
 	TRY ( h5priv_alloc_idlist (f, list, 8) );
-	h5_id_t *edge_idp = children->items;
+	h5_loc_id_t *edge_idp = children->items;
 	int i;
 	for (i = 0; i < children->num_items; i++, edge_idp++) {
 		TRY ( h5priv_search_idlist (f, *list, *edge_idp) );
@@ -404,7 +402,7 @@ dim_error(
 static inline h5_err_t
 get_adjacencies_to_vertex (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -421,7 +419,7 @@ get_adjacencies_to_vertex (
 static inline h5_err_t
 get_adjacencies_to_edge (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -438,7 +436,7 @@ get_adjacencies_to_edge (
 static inline h5_err_t
 get_adjacencies_to_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
@@ -455,11 +453,11 @@ get_adjacencies_to_triangle (
 static h5_err_t
 get_adjacencies (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	) {
-	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
+	h5_loc_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);
@@ -478,6 +476,7 @@ update_internal_structs (
 	h5_file_t* const f,
 	const h5_id_t from_lvl
 	) {
+	h5_debug (f, "%s (%lld)", __func__, (long long)from_lvl);
 	clock_t t1 = clock();
 	TRY( compute_elems_of_vertices (f, from_lvl) );
 	clock_t t2 = clock();
@@ -488,7 +487,7 @@ update_internal_structs (
 	t2 = clock();
 	fprintf (stderr, "compute_elems_of_edge(): %f\n",
 		 (float)(t2-t1)/CLOCKS_PER_SEC);
-
+	h5_debug (f, "%s (%lld): done", __func__, (long long)from_lvl);
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_consts.c

@@ -19,15 +19,6 @@ h5tpriv_meshes_grpnames[] = {
 	"TetMeshes"
 };
 
-const size_t
-h5tpriv_sizeof_elem[] = {
-	0,
-	0,
-	0,
-	sizeof (h5_triangle_t),
-	sizeof (h5_tetrahedron_t)
-};
-
 const char*
 h5tpriv_map_oid2str (
 	h5_oid_t oid

src/h5core/h5t_consts_private.h

@@ -3,7 +3,6 @@
 
 extern const char * h5tpriv_oid_names[];
 extern const char * h5tpriv_meshes_grpnames[];
-extern const size_t h5tpriv_sizeof_elem[];
 
 const char *h5tpriv_map_oid2str ( h5_oid_t oid );
 

src/h5core/h5t_core_private.h

@@ -10,7 +10,6 @@
 #include "h5t_access_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_openclose_private.h"
@@ -19,4 +18,6 @@
 #include "h5t_retrieve_private.h"
 #include "h5t_store_private.h"
 
+#include "h5t_errorhandling_private.h"
+
 #endif

src/h5core/h5t_errorhandling.c

@@ -6,11 +6,12 @@
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
+#if 0
 const char* ERR_ELEM_NEXIST = "Element with local vertex IDs (%s) doesn't exist!";
 h5_err_t
 h5tpriv_error_local_elem_nexist (
 	h5_file_t* const f,
-	h5_id_t local_vertex_indices[]
+	h5_loc_idx_t local_vertex_indices[]
 	) {
 	h5t_fdata_t* t = f->t;
 	char s[1024];
@@ -30,5 +31,5 @@ h5tpriv_error_local_elem_nexist (
 	}
 
 	return h5_error (f, H5_ERR_NOENTRY, ERR_ELEM_NEXIST, s);
-}
-	
+}	
+#endif

src/h5core/h5t_errorhandling_private.h

@@ -1,11 +1,32 @@
 #ifndef __H5T_ERRORHANDLING_PRIVATE_H
 #define __H5T_ERRORHANDLING_PRIVATE_H
 
-h5_err_t
+#define ERR_ELEM_NEXIST  "Element with local vertex IDs (%s) doesn't exist!"
+
+static inline h5_err_t
 h5tpriv_error_local_elem_nexist (
 	h5_file_t * const f,
-	h5_id_t local_vertex_indices[]
-	);
+	h5_loc_idx_t vertex_indices[]
+	) {
+	h5t_fdata_t* t = f->t;
+	char s[1024];
+
+	int num_chars_printed = snprintf (s, sizeof(s), "%lld,",
+					  (long long)vertex_indices[0]);
+	int i;
+	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,
+			"%lld,", (long long)vertex_indices[i]);
+		if ((sizeof (s) - num_chars_printed) < 32) {
+			// buffer to small
+			return h5_error_internal (f, __FILE__, __func__, __LINE__);
+		}
+	}
+
+	return h5_error (f, H5_ERR_NOENTRY, ERR_ELEM_NEXIST, s);
+}
 
 #define h5tpriv_error_undef_mesh( f )		\
 	h5_error(				\

src/h5core/h5t_hsearch.c

@@ -61,8 +61,8 @@ h5tpriv_resize_te_htab (
 h5_err_t
 h5tpriv_search_te2 (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t** retval
 	) {
 	h5t_fdata_t* t = f->t;
@@ -90,7 +90,7 @@ h5tpriv_search_te2 (
 		  Thus for a tetrahedal mesh we 3 time the remaining elements!
 		  @@@
 		 */
-		h5_id_t num_elems = t->num_elems[t->num_levels-1];
+		h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 		TRY( h5priv_hresize (
 			     f,
 			     3*(num_elems - elem_idx),
@@ -150,8 +150,8 @@ h5tpriv_find_te (
 h5_err_t
 h5tpriv_find_te2 (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t** retval
 	) {
 	h5t_te_entry_t item;
@@ -221,8 +221,8 @@ h5tpriv_resize_td_htab (
 h5_err_t
 h5tpriv_search_td2 (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t** retval
 	) {
 	h5t_fdata_t* t = f->t;
@@ -238,7 +238,7 @@ h5tpriv_search_td2 (
 	  resize hash table if more than 3/4 filled
 	*/
 	if ((a->td_hash.size*6) <= (a->td_hash.filled<<3)) {
-		h5_id_t num_elems = t->num_elems[t->num_levels-1];
+		h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 		TRY( h5priv_hresize (
 			     f,
 			     3*(num_elems-elem_idx),
@@ -290,8 +290,8 @@ h5tpriv_find_td (
 h5_err_t
 h5tpriv_find_td2 (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t** retval
 	) {
 	h5t_td_entry_t item;
@@ -309,12 +309,13 @@ h5tpriv_find_td2 (
 h5_err_t
 h5tpriv_find_tv2 (
 	h5_file_t* const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t** retval
 	) {
 
-	h5_id_t idx = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx);
+	h5_loc_idx_t idx = h5tpriv_get_loc_elem_vertex_idx (
+		f, elem_idx, face_idx);
 	*retval = &f->t->adjacencies.tv.v[idx];
 
 	return H5_SUCCESS;

src/h5core/h5t_hsearch_private.h

@@ -2,15 +2,15 @@
 #define __H5T_HSEARCH_PRIVATE_H
 
 typedef struct h5t_te_entry_key {
-	h5_id_t vids[2];
+	h5_loc_idx_t vids[2];
 } h5t_te_entry_key_t;
 
 typedef struct h5t_td_entry_key {
-	h5_id_t vids[3];
+	h5_loc_idx_t vids[3];
 } h5t_td_entry_key_t;
 
 typedef struct h5t_idlisthash_key {
-	h5_id_t ids[1];
+	h5_loc_id_t ids[1];
 } h5t_idlisthash_key_t;
 
 /*
@@ -47,8 +47,8 @@ h5tpriv_resize_te_htab (
 h5_err_t
 h5tpriv_search_te2 (
 	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t **entry
 	);
 
@@ -62,8 +62,8 @@ h5tpriv_find_te (
 h5_err_t
 h5tpriv_find_te2 (
 	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t **retval
 	);
 
@@ -83,8 +83,8 @@ h5tpriv_resize_td_htab (
 h5_err_t
 h5tpriv_search_td2 (
 	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t **entry
 	);
 
@@ -98,16 +98,16 @@ h5tpriv_find_td (
 h5_err_t
 h5tpriv_find_td2 (
 	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t **rentry
 	);
 
 h5_err_t
 h5tpriv_find_tv2 (
 	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
 	h5_idlist_t **retval
 	);
 #endif

src/h5core/h5t_inquiry.c

@@ -14,14 +14,24 @@ h5t_get_num_meshes (
 	h5_file_t* const f,
 	const h5_oid_t type_id
 	) {
-	hid_t topo_gid;
-	hid_t meshes_gid;
+	hid_t topo_gid = -1;
+	hid_t meshes_gid = -1;
 
-	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]) );
+	h5_err_t exists;
+	TRY( exists = h5priv_hdf5_link_exists (f, f->root_gid, H5T_CONTAINER_GRPNAME) );
+	if (!exists) return 0;
 
-	return h5_get_num_hdf5_groups (f, meshes_gid);
+	TRY( topo_gid = h5priv_open_hdf5_group (f, f->root_gid, H5T_CONTAINER_GRPNAME) );
+
+	TRY( exists = h5priv_hdf5_link_exists (f, topo_gid, h5tpriv_meshes_grpnames[type_id]) );
+	if (!exists) return 0;
+
+	TRY( meshes_gid = h5priv_open_hdf5_group (f, topo_gid, h5tpriv_meshes_grpnames[type_id]) );
+
+	h5_size_t num_meshes = h5_get_num_hdf5_groups (f, meshes_gid);
+	TRY( h5priv_close_hdf5_group (f, meshes_gid) );
+	TRY( h5priv_close_hdf5_group (f, topo_gid) );
+	return num_meshes;
 }
 
 /*!

src/h5core/h5t_map.c

@@ -30,16 +30,16 @@ cmp_vertices (
 static int
 qsort_cmp_vertices (
 	void* _f,
-	const void* _local_vid1,
-	const void* _local_vid2
+	const void* _vertex_idx1,
+	const void* _vertex_idx2
 	) {
 	h5_file_t* f = (h5_file_t*)_f;
-	h5_id_t local_vid1 = *(h5_id_t*)_local_vid1;
-	h5_id_t local_vid2 = *(h5_id_t*)_local_vid2;
+	h5_loc_idx_t vertex_idx1 = *(h5_loc_idx_t*)_vertex_idx1;
+	h5_loc_idx_t vertex_idx2 = *(h5_loc_idx_t*)_vertex_idx2;
 
 	return cmp_vertices (
-		f->t->vertices[local_vid1].P,
-		f->t->vertices[local_vid2].P );
+		f->t->vertices[vertex_idx1].P,
+		f->t->vertices[vertex_idx2].P );
 }
 
 /*!
@@ -52,12 +52,12 @@ h5tpriv_sort_vertices (
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
 
-	h5_id_t local_vid = t->cur_level > 0 ?
+	h5_loc_idx_t vertex_idx = t->cur_level > 0 ?
 		t->num_vertices[t->cur_level-1] : 0;
 
-	h5_id_t num_vertices = t->num_vertices[t->num_levels-1];
-	for (; local_vid < num_vertices; local_vid++) {
-		t->sorted_lvertices.items[local_vid] = local_vid;
+	h5_loc_idx_t num_vertices = t->num_vertices[t->num_levels-1];
+	for (; vertex_idx < num_vertices; vertex_idx++) {
+		t->sorted_lvertices.items[vertex_idx] = vertex_idx;
 	}
 	t->sorted_lvertices.num_items = num_vertices;
 
@@ -73,24 +73,24 @@ h5tpriv_sort_vertices (
 
 
 /*!
-  Return local vertex id of a vertex given by its coordinates.
+  Return local vertex index of a vertex given by its coordinates.
 
-  \return	local vertex id if found
+  \return	local vertex idx if found
   \return	else negativ value
  */
-h5_id_t
+h5_loc_idx_t
 h5tpriv_get_local_vid (
 	h5_file_t* const f,
 	h5_float64_t P[3]
 	) {
 	h5t_fdata_t*t = f->t;
-	register h5_id_t low = 0;
-	register h5_id_t high = t->sorted_lvertices.num_items - 1;
+	register h5_loc_idx_t low = 0;
+	register h5_loc_idx_t high = t->sorted_lvertices.num_items - 1;
 	while (low <= high) {
-		register int mid = (low + high) / 2;
+		register h5_loc_idx_t mid = (low + high) / 2;
 
-		h5_id_t local_vid = t->sorted_lvertices.items[mid];
-		h5_float64_t *P1 = t->vertices[local_vid].P;
+		h5_loc_idx_t vertex_idx = t->sorted_lvertices.items[mid];
+		h5_float64_t *P1 = t->vertices[vertex_idx].P;
 	        int diff = cmp_vertices ( P, P1 );
            	if ( diff < 0 )
                		high = mid - 1;
@@ -108,13 +108,13 @@ h5tpriv_get_local_vid (
 static inline int
 cmp_elems (
 	h5_file_t* const  f,
-	const h5_id_t elem_idx1,
-	const h5_id_t elem_idx2
+	const h5_loc_idx_t elem_idx1,
+	const h5_loc_idx_t elem_idx2
 	) {
 	h5t_fdata_t* t = f->t;
 	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);
+	h5_loc_idx_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
+	h5_loc_idx_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
 
 	int i;
 	for (i = 0; i < num_vertices; i++) {
@@ -132,13 +132,13 @@ cmp_elems (
 static inline int
 cmp_elems1 (
 	h5_file_t* f,
-	h5_id_t	elem_idx1,
-	h5_id_t elem_idx2
+	h5_loc_idx_t elem_idx1,
+	h5_loc_idx_t elem_idx2
 	) {
 	h5t_fdata_t *t = f->t;
 	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);
+	h5_loc_idx_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
+	h5_loc_idx_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
 
 	int imap[] = { 1, 0, 2, 3 };
 	int i;
@@ -158,25 +158,25 @@ cmp_elems1 (
 static int
 qsort_cmp_elems0 (
 	void* _f,
-	const void* _local_eid1,
-	const void* _local_eid2
+	const void* _elem_idx1,
+	const void* _elem_idx2
 	) {
 	h5_file_t* f = (h5_file_t*)_f;
-	h5_id_t local_eid1 = *(h5_id_t*)_local_eid1;
-	h5_id_t local_eid2 = *(h5_id_t*)_local_eid2;
-	return cmp_elems (f, local_eid1, local_eid2);
+	h5_loc_idx_t elem_idx1 = *(h5_loc_idx_t*)_elem_idx1;
+	h5_loc_idx_t elem_idx2 = *(h5_loc_idx_t*)_elem_idx2;
+	return cmp_elems (f, elem_idx1, elem_idx2);
 }
 
 static int
 qsort_cmp_elems1 (
 	void* _f,
-	const void* _local_eid1,
-	const void* _local_eid2
+	const void* _elem_idx1,
+	const void* _elem_idx2
 	) {
 	h5_file_t* f = (h5_file_t*)_f;
-	h5_id_t local_eid1 = *(h5_id_t*)_local_eid1;
-	h5_id_t local_eid2 = *(h5_id_t*)_local_eid2;
-	return cmp_elems1 (f, local_eid1, local_eid2);
+	h5_loc_idx_t elem_idx1 = *(h5_loc_idx_t*)_elem_idx1;
+	h5_loc_idx_t elem_idx2 = *(h5_loc_idx_t*)_elem_idx2;
+	return cmp_elems1 (f, elem_idx1, elem_idx2);
 }
 
 /*!
@@ -189,14 +189,14 @@ h5tpriv_sort_loc_elems (
 	) {
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
-	h5_id_t local_eid = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
-	h5_size_t num_elems = t->num_elems[t->num_levels-1];
+	h5_loc_idx_t elem_idx = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
+	h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 
 	int k;
-	h5_id_t i;
+	h5_loc_idx_t i;
 	for (k = 0; k < 2; k++) {
 		TRY( h5priv_alloc_idlist_items (f, &t->sorted_elems[k], num_elems) );
-		for (i = local_eid; i < num_elems; i++) {
+		for (i = elem_idx; i < num_elems; i++) {
 			t->sorted_elems[k].items[i] = i;
 		}
 		t->sorted_elems[k].num_items = num_elems;
@@ -224,16 +224,16 @@ h5tpriv_sort_loc_elems (
 h5_err_t
 h5tpriv_sort_local_vertex_indices (
 	h5_file_t* const f,
-	h5_id_t* const indices,		/* IN/OUT: local vertex indices */	
+	h5_loc_idx_t* const indices,		/* IN/OUT: local vertex indices */	
 	const h5_size_t size		/* size of array */
 	) {
 	h5t_fdata_t* t = f->t;
 
 	h5_size_t i;
 	for (i = 1; i < size; ++i) {
-		h5_id_t idx = indices[i];
+		h5_loc_idx_t idx = indices[i];
 
-		h5_id_t j = i;
+		h5_size_t j = i;
 		while ((j >= 1 ) && cmp_vertices (
 			       t->vertices[idx].P,
 			       t->vertices[indices[j-1]].P 
@@ -249,14 +249,14 @@ h5tpriv_sort_local_vertex_indices (
 /*!
   Map a global vertex index to corresponding local index.
 */
-h5_id_t
+h5_loc_idx_t
 h5t_map_global_vertex_idx2local (
 	h5_file_t* const f,
-	const h5_id_t glb_idx
+	const h5_glb_idx_t glb_idx
 	) {
 	if (glb_idx < 0) return -1;
 	
-	h5_id_t loc_idx = h5priv_search_idmap (&f->t->map_vertex_g2l, glb_idx);
+	h5_loc_idx_t loc_idx = h5priv_search_idxmap (&f->t->map_vertex_g2l, glb_idx);
 	if (loc_idx < 0) 
 		return h5tpriv_error_global_id_nexist (f, "vertex", glb_idx);
 	return loc_idx;
@@ -265,11 +265,11 @@ h5t_map_global_vertex_idx2local (
 h5_err_t
 h5t_map_global_vertex_indices2local (
 	h5_file_t* const f,
-	const h5_id_t* const glb_indices,
-	const h5_id_t size,
-	h5_id_t* const loc_indices
+	const h5_glb_idx_t* const glb_indices,
+	const h5_size_t size,
+	h5_loc_idx_t* const loc_indices
 	) {
-	int i;
+	h5_size_t i;
 	for (i = 0; i < size; i++) {
 		TRY( (loc_indices[i] =
 		      h5t_map_global_vertex_idx2local (f, glb_indices[i])) );
@@ -285,31 +285,31 @@ h5t_map_global_vertex_indices2local (
 
   \return	Local element index or error code.
 */
-h5_id_t
-h5t_map_global_elem_idx2local (
+h5_loc_idx_t
+h5t_map_glb_elem_idx2loc (
 	h5_file_t* const f,
-	const h5_id_t glb_idx
+	const h5_glb_idx_t glb_idx
 	) {
 	if (glb_idx < 0) return -1;
 
-	h5_id_t loc_idx = h5priv_search_idmap (&f->t->map_elem_g2l, glb_idx);
+	h5_loc_idx_t loc_idx = h5priv_search_idxmap (&f->t->map_elem_g2l, glb_idx);
 	if (loc_idx < 0) 
 		return h5tpriv_error_global_id_nexist (f, "elem", glb_idx);
 	return loc_idx;
 }
 
 h5_err_t
-h5t_map_global_elem_indices2local (
+h5t_map_glb_elem_indices2loc (
 	h5_file_t* const f,
-	const h5_id_t*  glb_indices,
-	const h5_id_t size,
-	h5_id_t* loc_indices
+	const h5_glb_idx_t*  glb_indices,
+	const h5_size_t size,
+	h5_loc_idx_t* loc_indices
 	) {
-	const h5_id_t*  end = glb_indices+size;
+	const h5_glb_idx_t*  end = glb_indices+size;
 
 	while (glb_indices < end) {
 		TRY( (*loc_indices =
-		      h5t_map_global_elem_idx2local (f, *glb_indices)) );
+		      h5t_map_glb_elem_idx2loc (f, *glb_indices)) );
 		loc_indices++;
 		glb_indices++;
 	}
@@ -318,46 +318,51 @@ h5t_map_global_elem_indices2local (
 
 
 /*
-
+  rebuild mapping of global vertex indices to their local indices
  */
 h5_err_t
-h5tpriv_rebuild_global_2_local_map_of_vertices (
+h5tpriv_rebuild_vertex_indices_mapping (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s()", __func__);
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
 
 	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];
+	h5_idxmap_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;
+		item->glb_idx = t->vertices[loc_idx].idx; 
+		item->loc_idx = loc_idx;
 		t->map_vertex_g2l.num_items++;
 	}
-	h5priv_sort_idmap (&t->map_vertex_g2l);
+	h5priv_sort_idxmap (&t->map_vertex_g2l);
 
 	return H5_SUCCESS;
 }
 
+/*
+  Rebuild mapping of global element indices to their local indices.
+*/
 h5_err_t
-h5tpriv_rebuild_global_2_local_map_of_elems (
+h5tpriv_rebuild_elem_indices_mapping (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s()", __func__);
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
 
-	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];
+	h5_loc_idx_t loc_idx = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
+	h5_loc_idx_t num_loc_elems = t->num_elems[t->num_levels-1];
+	h5_idxmap_el_t *item = &t->map_elem_g2l.items[loc_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;
+		item->glb_idx = h5tpriv_get_glb_elem_idx (f, loc_idx);
+		item->loc_idx = loc_idx;
 		t->map_elem_g2l.num_items++;
 	}
-	h5priv_sort_idmap (&t->map_elem_g2l);
+	h5priv_sort_idxmap (&t->map_elem_g2l);
 
 	return H5_SUCCESS;
 }
@@ -366,8 +371,8 @@ h5tpriv_rebuild_global_2_local_map_of_elems (
 h5_err_t
 h5t_get_vertex_indices_of_entity (
 	h5_file_t* const f,		// in
-	const h5_id_t entity_id,	// in
-	h5_id_t* vertex_indices		// out
+	const h5_loc_id_t entity_id,	// in
+	h5_loc_idx_t* vertex_indices   	// out
 	) {
 	static int map_entity_type_to_dimension[] = {
 		-1,
@@ -377,11 +382,11 @@ h5t_get_vertex_indices_of_entity (
 		[H5_OID_TETRAHEDRON] = 3
 	};
 
-	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
-	h5_id_t face_idx = h5tpriv_get_face_idx (entity_id);
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_id_t entity_type = h5tpriv_get_entity_type (entity_id);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (entity_id);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	int dim =  map_entity_type_to_dimension[entity_type];
-	h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	h5_loc_idx_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
 	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
 	int num_vertices = ref_elem->num_vertices_of_face[dim][face_idx];
 	int i;
@@ -395,11 +400,11 @@ h5t_get_vertex_indices_of_entity (
 h5_err_t
 h5t_get_vertex_index_of_vertex (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_index
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_index
 	) {
-	h5_id_t face_idx = h5tpriv_get_face_idx (entity_id);
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (entity_id);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	return h5t_get_vertex_index_of_vertex2 (
 		f, face_idx, elem_idx, vertex_index);
 }
@@ -407,9 +412,9 @@ h5t_get_vertex_index_of_vertex (
 h5_err_t
 h5t_get_vertex_index_of_vertex2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,		// vertex index according ref. element
-	const h5_id_t elem_idx,		// local element index
-	h5_id_t* vertex_indices		// OUT: vertex ID's
+	const h5_loc_idx_t face_idx,	// vertex index according ref. element
+	const h5_loc_idx_t elem_idx,	// local element index
+	h5_loc_idx_t* vertex_indices	// OUT: vertex ID's
 	) {
 	vertex_indices[0] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx); 
 	return H5_SUCCESS;
@@ -421,11 +426,11 @@ h5t_get_vertex_index_of_vertex2 (
 h5_err_t
 h5t_get_vertex_indices_of_edge (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_indices
 	) {
-	h5_id_t face_idx = h5tpriv_get_face_idx (entity_id);
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (entity_id);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	return h5t_get_vertex_indices_of_edge2 (
 		f, face_idx, elem_idx, vertex_indices);
 }
@@ -440,11 +445,11 @@ h5t_get_vertex_indices_of_edge (
 h5_err_t
 h5t_get_vertex_indices_of_edge2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,		// edge index according ref. element
-	const h5_id_t elem_idx,		// local element index
-	h5_id_t* vertex_indices		// OUT: vertex ID's
+	const h5_loc_idx_t face_idx,	// edge index according ref. element
+	const h5_loc_idx_t elem_idx,	// local element index
+	h5_loc_idx_t* vertex_indices	// OUT: vertex indices
 	) {
-	const h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	const h5_loc_idx_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
 	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
 
  	vertex_indices[0] = indices[ ref_elem->map[1][face_idx][0] ];
@@ -455,11 +460,11 @@ h5t_get_vertex_indices_of_edge2 (
 h5_err_t
 h5t_get_vertex_indices_of_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_indices
 	) {
-	h5_id_t face_idx = h5tpriv_get_face_idx (entity_id);
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (entity_id);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	return h5t_get_vertex_indices_of_triangle2 (
 		f, face_idx, elem_idx, vertex_indices);
 }
@@ -467,11 +472,12 @@ h5t_get_vertex_indices_of_triangle (
 h5_err_t
 h5t_get_vertex_indices_of_triangle2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx,
-	h5_id_t* vertex_indices
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx,
+	h5_loc_idx_t* vertex_indices
 	) {
-	const h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	const h5_loc_idx_t* indices = h5tpriv_get_loc_elem_vertex_indices (
+		f, elem_idx);
 	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
 
  	vertex_indices[0] = indices[ ref_elem->map[2][face_idx][0] ];
@@ -484,11 +490,12 @@ h5t_get_vertex_indices_of_triangle2 (
 h5_err_t
 h5t_get_vertex_indices_of_tet (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_indices
 	) {
-	const h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
-	const h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	const h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	const h5_loc_idx_t* indices = h5tpriv_get_loc_elem_vertex_indices (
+		f, elem_idx);
 	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
 
  	vertex_indices[0] = indices[ ref_elem->map[3][0][0] ];

src/h5core/h5t_map_private.h

@@ -4,7 +4,7 @@
 h5_err_t
 h5tpriv_sort_local_vertex_indices (
 	h5_file_t * const f,
-	h5_id_t * const indices,
+	h5_loc_idx_t * const indices,
 	const h5_size_t size
 	);
 
@@ -13,18 +13,24 @@ h5tpriv_sort_vertices (
 	h5_file_t * const f
 	);
 
+h5_loc_idx_t
+h5tpriv_get_local_vid (
+	h5_file_t * const f,
+	h5_float64_t P[3]
+	);
+
 h5_err_t
 h5tpriv_sort_loc_elems (
 	h5_file_t * const f
 	);
 
 h5_err_t
-h5tpriv_rebuild_global_2_local_map_of_vertices (
+h5tpriv_rebuild_vertex_indices_mapping (
 	h5_file_t * const f
 	);
 
 h5_err_t
-h5tpriv_rebuild_global_2_local_map_of_elems (
+h5tpriv_rebuild_elem_indices_mapping (
 	h5_file_t * const f
 	);
 

src/h5core/h5t_openclose.c

@@ -38,7 +38,7 @@ create_array_types (
 			dims)
 		);
 	TRY( 
-		dtypes->h5_3id_t = h5priv_create_hdf5_array_type (
+		dtypes->h5_3glb_idx_t = h5priv_create_hdf5_array_type (
 			f,
 			H5_ID_T,
 			1,
@@ -46,7 +46,7 @@ create_array_types (
 		);
 	dims[0] = 4;
 	TRY(
-		dtypes->h5_4id_t = h5priv_create_hdf5_array_type (
+		dtypes->h5_4glb_idx_t = h5priv_create_hdf5_array_type (
 			f,
 			H5_ID_T,
 			1,
@@ -66,20 +66,20 @@ create_vertex_type (
 		dtypes->h5_vertex_t = h5priv_create_hdf5_type (
 			f,
 			H5_COMPOUND_T,
-			sizeof (struct h5_vertex)) );
+			sizeof (h5_glb_vertex_t)) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_vertex_t,
 			"idx",
-			HOFFSET (struct h5_vertex, idx),
+			HOFFSET (h5_glb_vertex_t, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_vertex_t,
 			"P",
-			HOFFSET (struct h5_vertex, P),
+			HOFFSET (h5_glb_vertex_t, P),
 			dtypes->h5_coord3d_t) );
 
 	return H5_SUCCESS;
@@ -95,42 +95,42 @@ create_triangle_type (
 		dtypes->h5_triangle_t = h5priv_create_hdf5_type (
 			f,
 			H5_COMPOUND_T,
-			sizeof (struct h5_triangle)) );
+			sizeof (h5_glb_triangle_t)) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
 			"idx",
-			HOFFSET (struct h5_triangle, idx),
+			HOFFSET (h5_glb_triangle_t, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
 			"parent_idx",
-			HOFFSET (struct h5_triangle, parent_idx),
+			HOFFSET (h5_glb_triangle_t, parent_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
 			"child_idx",
-			HOFFSET(struct h5_triangle, child_idx),
+			HOFFSET(h5_glb_triangle_t, child_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
 			"vertex_indices",
-			HOFFSET (struct h5_triangle, vertex_indices),
-			dtypes->h5_3id_t) );
+			HOFFSET (h5_glb_triangle_t, vertex_indices),
+			dtypes->h5_3glb_idx_t) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
 			"neighbor_indices",
-			HOFFSET(struct h5_triangle, neighbor_indices),
-			dtypes->h5_3id_t) );
+			HOFFSET(h5_glb_triangle_t, neighbor_indices),
+			dtypes->h5_3glb_idx_t) );
 
 	return H5_SUCCESS;
 }
@@ -174,62 +174,46 @@ create_tet_type (
 		dtypes->h5_tet_t = h5priv_create_hdf5_type (
 			f,
 			H5_COMPOUND_T,
-			sizeof (struct h5_tetrahedron)) );
+			sizeof (h5_glb_tetrahedron_t)) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
 			"idx",
-			HOFFSET (struct h5_tetrahedron, idx),
+			HOFFSET (h5_glb_tetrahedron_t, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
 			"parent_idx",
-			HOFFSET (struct h5_tetrahedron, parent_idx),
+			HOFFSET (h5_glb_tetrahedron_t, parent_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
 			"child_idx",
-			HOFFSET (struct h5_tetrahedron, child_idx),
+			HOFFSET (h5_glb_tetrahedron_t, child_idx),
 			H5T_NATIVE_INT32) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
 			"vertex_indices",
-			HOFFSET (struct h5_tetrahedron, vertex_indices),
-			dtypes->h5_4id_t) );
+			HOFFSET (h5_glb_tetrahedron_t, vertex_indices),
+			dtypes->h5_4glb_idx_t) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
 			"neighbor_indices",
-			HOFFSET (struct h5_tetrahedron, neighbor_indices),
-			dtypes->h5_4id_t) );
+			HOFFSET (h5_glb_tetrahedron_t, neighbor_indices),
+			dtypes->h5_4glb_idx_t) );
 
 	return H5_SUCCESS;
 }
 
-
-#if 0
-h5_err_t
-h5priv_set_dataset_properties (
-	h5_dsinfo_t* dsinfo,
-	const char* name,
-	const hid_t type,
-	const int rank,
-	const hsize_t* dims,
-	const hsize_t* maxdims,
-	const hsize_t chunk_dims
-	) {
-	return H5_SUCCESS;
-}
-#endif
-
 static h5_err_t
 init_fdata (
 	h5_file_t* const f
@@ -342,8 +326,6 @@ init_fdata (
 		     t->dsinfo_num_elems_on_level.chunk_dims) );
 	t->dsinfo_num_elems_on_level.access_prop = H5P_DEFAULT;
 
-
-
 	return H5_SUCCESS;
 }
 
@@ -362,7 +344,7 @@ h5tpriv_open_file (
 	h5_file_t* const f			/*!< IN: file handle */
 	) {
 
-	TRY( (f->t = h5priv_alloc (f, NULL, sizeof (*f->t))) );
+	TRY( (f->t = h5priv_calloc (f, 1, sizeof (*f->t))) );
 	h5t_fdata_t* t = f->t;
 
 	t->dtypes.h5_id_t = H5_INT64_T;
@@ -406,8 +388,9 @@ h5tpriv_open_topo_group (
 	h5_file_t * const f
 	) {
 	h5t_fdata_t* t = f->t;
-
-	t->topo_gid = h5priv_open_group (f, f->root_gid, H5T_CONTAINER_GRPNAME);
+	if (t->topo_gid == 0 || t->topo_gid == -1) {
+		t->topo_gid = h5priv_open_group (f, f->root_gid, H5T_CONTAINER_GRPNAME);
+	}
 	return t->topo_gid;
 }
 
@@ -464,6 +447,7 @@ h5t_open_mesh (
 	h5_id_t id,
 	const h5_oid_t type_id
 	) {
+	h5_debug (f, "%s ()", __func__);
 	h5t_fdata_t* t = f->t;
 
 	TRY( h5t_close_mesh (f) );
@@ -549,12 +533,16 @@ h5_err_t
 h5t_close_mesh (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s ()", __func__);
 	if (!(f->mode & H5_O_RDONLY)) {
 		TRY( h5tpriv_write_mesh (f) );
 	}
+	TRY( h5priv_close_hdf5_group (f, f->t->mesh_gid) );
+	TRY( h5priv_close_hdf5_group (f, f->t->meshes_gid) );
+	TRY( h5priv_close_hdf5_group (f, f->t->topo_gid) );
+
 	TRY( release_memory (f) );
 	TRY( init_fdata (f) );
-
 	return H5_SUCCESS;
 }
 
@@ -589,7 +577,7 @@ h5tpriv_alloc_num_vertices (
 
 	ssize_t size = num * sizeof (t->vertices[0]);
 	TRY( t->vertices = h5priv_alloc (f, t->vertices, size) );
-	TRY( h5priv_alloc_idmap (f, &t->map_vertex_g2l, num) );
+	TRY( h5priv_alloc_idxmap (f, &t->map_vertex_g2l, num) );
 	TRY( h5priv_alloc_idlist_items (f, &t->sorted_lvertices, num) );
 
 	return H5_SUCCESS;
@@ -609,7 +597,9 @@ h5_err_t
 h5tpriv_close_file (
 	h5_file_t* const f		/*!< IN: file handle */
 	) {
+	h5_debug (f, "%s ()", __func__);
 	TRY( h5t_close_mesh (f) );
+	TRY( h5priv_close_hdf5_group (f, f->t->meshes_gid) );
 
 	return H5_SUCCESS;
 }

src/h5core/h5t_openclose_private.h

@@ -1,21 +1,57 @@
 #ifndef __H5T_OPENCLOSE_PRIVATE_H
 #define __H5T_OPENCLOSE_PRIVATE_H
 
-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, 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 );
-h5_err_t h5tpriv_init_step ( h5_file_t * const f );
-
-h5_err_t h5tpriv_alloc_num_vertices ( h5_file_t * const f,
-				   const h5_size_t num_vertices );
-h5_err_t h5tpriv_alloc_tris ( h5_file_t * const f, const size_t cur,
-			   const size_t new_size );
-h5_err_t h5tpriv_alloc_tets ( h5_file_t * const f, const size_t cur,
-			   const size_t new_size );
+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,
+	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
+	);
+h5_err_t
+h5tpriv_init_step (
+	h5_file_t * const f
+	);
+h5_err_t
+h5tpriv_alloc_num_vertices (
+	h5_file_t * const f,
+	const h5_size_t num_vertices
+	);
+h5_err_t
+h5tpriv_alloc_tris (
+	h5_file_t * const f,
+	const size_t cur,
+	const size_t new_size
+	);
+h5_err_t
+h5tpriv_alloc_tets (
+	h5_file_t * const f,
+	const size_t cur,
+	const size_t new_size
+	);
 
 #endif

src/h5core/h5t_readwrite.c

@@ -85,6 +85,7 @@ h5_err_t
 h5tpriv_write_mesh (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s ()", __func__);
 	h5t_fdata_t* t = f->t;
 	if (t->mesh_changed) {
 		TRY( write_vertices (f) );
@@ -176,7 +177,7 @@ read_vertices (
 		     open_file_space_vertices,
 		     t->vertices) );
 	TRY( h5tpriv_sort_vertices (f) );
-	TRY( h5tpriv_rebuild_global_2_local_map_of_vertices (f) );
+	TRY( h5tpriv_rebuild_vertex_indices_mapping (f) );
 
 	return H5_SUCCESS;
 }
@@ -252,7 +253,7 @@ read_elems (
 		     t->glb_elems.data) );
 
 	TRY( h5tpriv_sort_loc_elems (f) );
-	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
+	TRY( h5tpriv_rebuild_elem_indices_mapping (f) );
 	TRY( h5tpriv_init_loc_elems_struct (f) );
 
 	return H5_SUCCESS;

src/h5core/h5t_readwrite_tetm.c

@@ -9,25 +9,25 @@ init_loc_elems_struct (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* const t = f->t;
-	h5_id_t idx = 0;
-	const h5_id_t num_elems = t->num_elems[t->num_levels-1];
+	h5_loc_idx_t elem_idx = 0;
+	const h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 	h5_id_t level_idx = 0;
 	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;
+	h5_loc_tet_t* loc_elem = t->loc_elems.tets;
+	h5_glb_tet_t* glb_elem = t->glb_elems.tets;
 
-	for (idx = 0; idx < num_elems; idx++, loc_elem++, glb_elem++) {
+	for (elem_idx = 0; elem_idx < num_elems; elem_idx++, loc_elem++, glb_elem++) {
 		// local parent index
 		TRY( loc_elem->parent_idx =
-		     h5t_map_global_elem_idx2local (f, glb_elem->parent_idx) );
+		     h5t_map_glb_elem_idx2loc (f, glb_elem->parent_idx) );
 
 		// local child index
 		TRY( loc_elem->child_idx =
-		     h5t_map_global_elem_idx2local (f, glb_elem->child_idx) );
+		     h5t_map_glb_elem_idx2loc (f, glb_elem->child_idx) );
 
 		// level idx
-		if (idx >= t->num_elems[level_idx]) {
+		if (elem_idx >= t->num_elems[level_idx]) {
 			level_idx++;
 		}
 		loc_elem->idx = level_idx;
@@ -40,7 +40,7 @@ init_loc_elems_struct (
 			     loc_elem->vertex_indices) );
 
 		// neighbor indices
-		TRY( h5t_map_global_elem_indices2local (
+		TRY( h5t_map_glb_elem_indices2loc (
 			     f,
 			     glb_elem->neighbor_indices,
 			     num_edges,

src/h5core/h5t_readwrite_trim.c

@@ -9,22 +9,22 @@ init_loc_elems_struct (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* const t = f->t;
-	h5_id_t idx = 0;
-	const h5_id_t num_elems = t->num_elems[t->num_levels-1];
+	h5_loc_idx_t idx = 0;
+	const h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 	h5_id_t level_idx = 0;
 	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;
+	h5_loc_triangle_t* loc_elem = t->loc_elems.tris;
+	h5_glb_triangle_t* glb_elem = t->glb_elems.tris;
 
 	for (idx = 0; idx < num_elems; idx++, loc_elem++, glb_elem++) {
 		// local parent index
 		TRY( loc_elem->parent_idx =
-		     h5t_map_global_elem_idx2local (f, glb_elem->parent_idx) );
+		     h5t_map_glb_elem_idx2loc (f, glb_elem->parent_idx) );
 
 		// local child index
 		TRY( loc_elem->child_idx =
-		     h5t_map_global_elem_idx2local (f, glb_elem->child_idx) );
+		     h5t_map_glb_elem_idx2loc (f, glb_elem->child_idx) );
 
 		// level idx
 		if (idx >= t->num_elems[level_idx]) {
@@ -40,7 +40,7 @@ init_loc_elems_struct (
 			     loc_elem->vertex_indices) );
 
 		// neighbor indices
-		TRY( h5t_map_global_elem_indices2local (
+		TRY( h5t_map_glb_elem_indices2loc (
 			     f,
 			     glb_elem->neighbor_indices,
 			     num_edges,

src/h5core/h5t_retrieve.c

@@ -13,7 +13,7 @@ h5tpriv_skip_to_next_elem_on_level (
 	h5_file_t* f,
 	h5t_entity_iterator_t* iter
 	) {
-	h5_generic_elem_t* el;
+	h5_generic_loc_elem_t* el;
 	do {
 		iter->elem_idx++;
 		if (iter->elem_idx >= num_elems_on_cur_level) {
@@ -33,7 +33,7 @@ h5tpriv_skip_to_next_elem_on_level (
 h5_err_t
 h5tpriv_elem_is_on_cur_level (
 	h5_file_t* const f,
-	h5_generic_elem_t *el // ptr to local element
+	h5_generic_loc_elem_t *el // ptr to local element
 	) {
 	h5t_fdata_t* t = f->t;
 	if ( (el->idx > t->cur_level) ||
@@ -74,7 +74,7 @@ h5t_begin_iterate_entities (
 /*!
   Travere entities with co-dim > 0
 */
-static h5_id_t
+static h5_loc_id_t
 iterate_faces (
 	h5_file_t* const f,
 	h5t_entity_iterator_t* iter
@@ -101,10 +101,10 @@ iterate_faces (
 		TRY( (iter->find)(f, iter->face_idx,
 				  iter->elem_idx, &entry) );
 		i = -1;
-		h5_generic_elem_t *el;
+		h5_generic_loc_elem_t *el;
 		do {
 			i++;
-			h5_id_t idx = h5tpriv_get_elem_idx (entry->items[i]);
+			h5_loc_idx_t idx = h5tpriv_get_elem_idx (entry->items[i]);
 			el = h5tpriv_get_loc_elem (f, idx);
 		} while (h5tpriv_elem_is_on_cur_level (f, el) == H5_NOK);
 	} while (iter->elem_idx != h5tpriv_get_elem_idx(entry->items[i]));
@@ -112,7 +112,7 @@ iterate_faces (
 	return entry->items[0];
 }
 
-static h5_id_t
+static h5_loc_id_t
 iterate_elems (
 	h5_file_t* const f,
 	h5t_entity_iterator_t*iter
@@ -124,7 +124,7 @@ iterate_elems (
 	return h5tpriv_build_elem_id ( iter->elem_idx );
 }
 
-h5_id_t
+h5_loc_id_t
 h5t_iterate_entities (
 	h5_file_t* const f,
 	h5t_entity_iterator_t* iter
@@ -155,10 +155,10 @@ h5t_end_iterate_entities (
 h5_err_t
 h5t_get_vertex_coords_by_index (
 	h5_file_t* const f,
-	h5_id_t vertex_index,
+	h5_loc_idx_t vertex_index,
 	h5_float64_t P[3]
 	) {
-	h5_vertex_t *vertex = &f->t->vertices[vertex_index];
+	h5_loc_vertex_t *vertex = &f->t->vertices[vertex_index];
 	memcpy ( P, &vertex->P, sizeof ( vertex->P ) );
 	return H5_SUCCESS;
 }
@@ -166,10 +166,10 @@ h5t_get_vertex_coords_by_index (
 h5_err_t
 h5t_get_vertex_coords_by_id (
 	h5_file_t* const f,
-	h5_id_t vertex_id,
+	h5_loc_id_t vertex_id,
 	h5_float64_t P[3]
 	) {
-	h5_id_t vertex_index;
+	h5_loc_idx_t vertex_index;
 	h5t_get_vertex_index_of_vertex (f, vertex_id, &vertex_index );
 	h5t_get_vertex_coords_by_index (f, vertex_index, P);
 	return H5_SUCCESS;

src/h5core/h5t_retrieve_private.h

@@ -10,7 +10,7 @@ h5tpriv_skip_to_next_elem_on_level (
 h5_err_t
 h5tpriv_elem_is_on_cur_level (
 	h5_file_t* const f,
-	h5_generic_elem_t* el
+	h5_generic_loc_elem_t* el
 	);
 
 extern struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods;

src/h5core/h5t_store.c

@@ -38,7 +38,8 @@ assign_global_vertex_indices (
 	/*
 	  simple in serial runs: global_id = local_id
 	*/
-	h5_id_t local_idx = (t->cur_level == 0) ? 0 : t->num_vertices[t->cur_level-1];
+	h5_loc_idx_t local_idx = (t->cur_level == 0) ?
+		0 : t->num_vertices[t->cur_level-1];
 	for (local_idx = 0;
 	     local_idx < t->num_vertices[t->num_levels-1];
 	     local_idx++) {
@@ -65,7 +66,7 @@ assign_glb_elem_indices (
 	h5_loc_idx_t loc_idx = (t->cur_level == 0) ? 0 : t->num_elems[t->cur_level-1];
 	
 	for (; loc_idx < t->num_elems[t->cur_level]; loc_idx++) {
-		h5_generic_elem_t *glb_elem = h5tpriv_get_glb_elem (f, loc_idx);
+		h5_generic_glb_elem_t *glb_elem = h5tpriv_get_glb_elem (f, loc_idx);
 
 		glb_elem->idx = loc_idx;
 	}
@@ -89,14 +90,14 @@ assign_glb_elem_data (
 	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);
+		h5_generic_loc_elem_t *loc_elem = h5tpriv_get_loc_elem (f, loc_idx);
+		h5_generic_glb_elem_t *glb_elem = h5tpriv_get_glb_elem (f, loc_idx);
 
 		glb_elem->parent_idx = loc_elem->parent_idx;
 		if (loc_elem->parent_idx >= 0) {
-			h5_generic_elem_t *loc_parent = h5tpriv_get_loc_elem (
+			h5_generic_loc_elem_t *loc_parent = h5tpriv_get_loc_elem (
 				f, loc_elem->parent_idx);
-			h5_generic_elem_t *glb_parent = h5tpriv_get_glb_elem (
+			h5_generic_glb_elem_t *glb_parent = h5tpriv_get_glb_elem (
 				f, glb_elem->parent_idx);
 			
 			glb_parent->child_idx = loc_parent->child_idx;
@@ -104,8 +105,8 @@ assign_glb_elem_data (
 
 		glb_elem->child_idx = loc_elem->child_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);
+		h5_glb_idx_t* glb_indices = h5tpriv_get_glb_elem_vertex_indices (f, loc_idx);
+		h5_loc_idx_t* loc_indices = h5tpriv_get_loc_elem_vertex_indices (f, loc_idx);
 
 		memcpy (glb_indices, loc_indices, num_vertices*sizeof(*glb_indices));
 
@@ -179,10 +180,10 @@ h5t_begin_store_vertices (
 	return h5tpriv_alloc_num_vertices (f, cur_num_vertices+num);
 }
 
-h5_id_t
+h5_loc_idx_t
 h5t_store_vertex (
 	h5_file_t* const f,		/*!< file handle		*/
-	const h5_id_t glb_idx,     	/*!< global vertex id or -1	*/
+	const h5_glb_idx_t glb_id,	/*!< global vertex id from mesher or -1	*/
 	const h5_float64_t P[3]		/*!< coordinates		*/
 	) {
 	h5t_fdata_t* const t = f->t;
@@ -200,9 +201,9 @@ h5t_store_vertex (
 	if (t->cur_level < 0)
 		return h5tpriv_error_undef_level(f);
 
-	h5_id_t local_idx = ++t->last_stored_vid;
-	h5_vertex_t *vertex = &t->vertices[local_idx];
-	vertex->idx = glb_idx;     /* ID from mesher, replaced later!*/
+	h5_loc_idx_t local_idx = ++t->last_stored_vid;
+	h5_loc_vertex_t *vertex = &t->vertices[local_idx];
+	vertex->idx = glb_id;     /* ID from mesher, replaced later!*/
 	memcpy (&vertex->P, P, sizeof (vertex->P));
 	return local_idx;
 }
@@ -216,7 +217,7 @@ h5t_end_store_vertices (
 	t->num_vertices[t->cur_level] = t->last_stored_vid+1;
 	TRY( assign_global_vertex_indices (f) );
 	TRY( h5tpriv_sort_vertices (f) );
-	TRY( h5tpriv_rebuild_global_2_local_map_of_vertices (f) );
+	TRY( h5tpriv_rebuild_vertex_indices_mapping (f) );
 	return H5_SUCCESS;
 }
 
@@ -259,11 +260,11 @@ h5t_begin_store_elems (
   \param[in]	vertices		Local vertex indices defining the
 					tetrahedron.
  */
-h5_id_t
+h5_loc_idx_t
 h5t_store_elem (
 	h5_file_t* const f,
-	const h5_id_t parent_idx,
-	const h5_id_t* vertex_indices
+	const h5_loc_idx_t parent_idx,
+	const h5_loc_idx_t* vertex_indices
 	) {
 	h5t_fdata_t* t = f->t;
 
@@ -288,18 +289,21 @@ h5t_store_elem (
 	}
 
 	/* store elem data (but neighbors) */
-	h5_id_t elem_idx = ++t->last_stored_eid;
+	h5_loc_idx_t elem_idx = ++t->last_stored_eid;
 	h5tpriv_set_loc_elem_parent_idx (f, elem_idx, parent_idx);
 	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_vertex_indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	// get ptr to local vertices store
+	h5_loc_idx_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);
+	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 map  edges -> elements */
-	h5_id_t face_idx;
+	h5_loc_idx_t face_idx;
 	int num_faces = h5tpriv_ref_elem_get_num_edges (t);
 	h5_idlist_t* retval;
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
@@ -317,6 +321,7 @@ h5_err_t
 h5t_end_store_elems (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s ()", __func__);
 	h5t_fdata_t* const t = f->t;
 
 	t->num_elems[t->cur_level] = t->last_stored_eid+1;
@@ -327,7 +332,7 @@ h5t_end_store_elems (
 	TRY( assign_glb_elem_indices (f) );
 
 	/* rebuild map: global index -> local_index */
-	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
+	TRY( h5tpriv_rebuild_elem_indices_mapping (f) );
 
 	/* mesh specific finalize */
 	TRY( (t->methods.store->end_store_elems)(f) );
@@ -335,6 +340,7 @@ h5t_end_store_elems (
 	/* setup global element data */
 	TRY( assign_glb_elem_data (f) );
 
+	h5_debug (f, "%s (): done", __func__);
 	return H5_SUCCESS;
 }
 
@@ -344,7 +350,7 @@ h5t_end_store_elems (
 h5_err_t
 h5t_mark_entity (
 	h5_file_t* const f,
-	const h5_id_t entity_id
+	const h5_loc_id_t entity_id
 	) {
 	h5t_fdata_t* const t = f->t;
 	return h5priv_append_to_idlist (f, &t->marked_entities, entity_id);

src/h5core/h5t_store_private.h

@@ -24,12 +24,12 @@ h5tpriv_alloc_elems (
 	return (*f->t->methods.store->alloc_elems) (f, cur, new);
 }
 
-static inline h5_id_t
+static inline h5_loc_idx_t
 h5tpriv_refine_elem (
 	h5_file_t * const f,
-	const h5_id_t local_eid
+	const h5_loc_idx_t elem_idx
 	) {
-	return (*f->t->methods.store->refine_elem)(f, local_eid);
+	return (*f->t->methods.store->refine_elem)(f, elem_idx);
 }
 
 #endif

src/h5core/h5t_store_tetm.c

@@ -32,7 +32,7 @@ alloc_tets (
 		(new-cur) * sizeof (t->loc_elems.tets[0]) );
 
 	/* alloc mem for global to local ID mapping */
-	TRY ( h5priv_alloc_idmap ( f, &t->map_elem_g2l, new ) );
+	TRY ( h5priv_alloc_idxmap ( f, &t->map_elem_g2l, new ) );
 
 	return  H5_SUCCESS;
 }
@@ -72,7 +72,7 @@ get_direct_children_of_edge (
 
   \return local index of vertex
 */
-static h5_id_t
+static h5_loc_idx_t
 bisect_edge (
 	h5_file_t* const f,
 	const h5_loc_idx_t face_idx,
@@ -89,8 +89,8 @@ bisect_edge (
 	 */
 	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);
+		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!
@@ -134,7 +134,7 @@ bisect_edge (
 
   \return Local id of first new tetrahedron or \c -1
 */
-static h5_id_t
+static h5_loc_idx_t
 refine_tet (
 	h5_file_t* const f,
 	const h5_loc_idx_t elem_idx
@@ -142,7 +142,7 @@ refine_tet (
 	h5t_fdata_t* t = f->t;
 	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];
+	h5_loc_tet_t* el = &t->loc_elems.tets[elem_idx];
 
 	if ( el->child_idx >= 0 )
 		return h5_error (
@@ -280,7 +280,7 @@ compute_neighbors_of_new_elems (
 	}
 	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];
+	h5_loc_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++) {

src/h5core/h5t_store_trim.c

@@ -32,7 +32,7 @@ alloc_triangles (
 		(new-cur) * sizeof (t->loc_elems.tris[0]) );
 
 	/* alloc mem for global to local ID mapping */
-	TRY ( h5priv_alloc_idmap ( f, &t->map_elem_g2l, new ) );
+	TRY ( h5priv_alloc_idxmap ( f, &t->map_elem_g2l, new ) );
 
 	return  H5_SUCCESS;
 }
@@ -140,7 +140,7 @@ refine_triangle (
 	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];
+	h5_loc_triangle_t* el = &t->loc_elems.tris[elem_idx];
 
 	if (el->child_idx >= 0)
 		return h5_error (
@@ -237,6 +237,7 @@ static inline h5_err_t
 compute_neighbors_of_new_elems (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s()", __func__);
 	h5t_fdata_t * const t = f->t;
 	if (t->cur_level < 0) {
 		// or should we consider this as an error?
@@ -244,7 +245,7 @@ compute_neighbors_of_new_elems (
 	}
 	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];
+	h5_loc_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++) {
@@ -262,6 +263,7 @@ static h5_err_t
 end_store_elems (
 	h5_file_t* const f
 	) {
+	h5_debug (f, "%s()", __func__);
 	h5t_fdata_t* t = f->t;
 
 	TRY( h5tpriv_update_adjacency_structs (f, t->cur_level) );

src/h5core/h5t_tags.c

@@ -351,14 +351,14 @@ static h5_err_t
 set_mtag (
 	h5_file_t *const f,
 	H5T_Tagset *tagset,
-	const h5_id_t id,
+	const h5_loc_id_t id,
 	const size_t size,
 	void *val 
 	) {
 	size_t offs[5] = { 14, 0, 4, 10, 14 };
-	h5_id_t el_idx = h5tpriv_get_elem_idx ( id );
-	h5_id_t eoe_id = h5tpriv_get_face_idx ( id );
-	h5_id_t type_id = h5tpriv_get_entity_type ( id );
+	h5_loc_idx_t el_idx = h5tpriv_get_elem_idx ( id );
+	h5_loc_idx_t eoe_id = h5tpriv_get_face_idx ( id );
+	h5_loc_idx_t type_id = h5tpriv_get_entity_type ( id );
 	if ( tagset->elems[el_idx] == NULL ) {
 		/*
 		  alloc new structure to store all tags for this element
@@ -427,7 +427,7 @@ h5_err_t
 h5t_set_mtag_by_name (
 	h5_file_t *const f,
 	char name[],
-	const h5_id_t id,
+	const h5_loc_id_t id,
 	const size_t size,
 	void *val
 	) {
@@ -440,20 +440,20 @@ static h5_err_t
 get_tag_valp (
 	h5_file_t* const f,
 	const H5T_Tagset* tagset,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	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 );
+	h5_loc_idx_t el_idx = h5tpriv_get_elem_idx ( entity_id );
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx ( entity_id );
+	h5_loc_idx_t type_id = h5tpriv_get_entity_type ( entity_id );
 
 	if ( tagset->elems[el_idx] == NULL ) {
 		return H5_NOK; /* no tags for this element */
 	}
 	h5t_tagsel_t *tagselem = tagset->elems[el_idx];
 	size_t offs[5] = { 14, 0, 4, 10, 14 };
-	size_t i = offs[type_id]+subentity_id;
+	size_t i = offs[type_id]+face_idx;
 
 	if ( tagselem->idx[i] < 0 ) {
 		return H5_NOK; /* no value set for this subentity */
@@ -479,7 +479,7 @@ h5_ssize_t
 h5t_get_tag (
 	h5_file_t *const f,
 	const H5T_Tagset *tagset,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	size_t* const dim,
 	void* const vals
 	) {
@@ -510,13 +510,13 @@ h5_ssize_t
 h5t_get_mtag_by_name (
 	h5_file_t* const f,
 	const char name[],
-	const h5_id_t id,
+	const h5_loc_id_t entity_id,
 	size_t* dim,
 	void* vals
 	) {
 	H5T_Tagset* tagset;
 	TRY ( h5t_open_mtagset ( f, name, &tagset ) );
-	return h5t_get_tag ( f, tagset, id, dim, vals );
+	return h5t_get_tag ( f, tagset, entity_id, dim, vals );
 }
 
 /*!
@@ -530,18 +530,18 @@ h5_err_t
 h5t_remove_mtag (
 	h5_file_t* const f,
 	H5T_Tagset* tagset,
-	const h5_id_t id
+	const h5_loc_id_t entity_id
 	) {
-	h5_id_t el_idx = h5tpriv_get_elem_idx ( id );
-	h5_id_t subentity_id = h5tpriv_get_face_idx ( id );
-	h5_id_t type_id = h5tpriv_get_entity_type ( id );
+	h5_loc_idx_t el_idx = h5tpriv_get_elem_idx ( entity_id );
+	h5_loc_idx_t face_idx = h5tpriv_get_face_idx ( entity_id );
+	h5_loc_idx_t type_id = h5tpriv_get_entity_type ( entity_id );
 
 	if ( tagset->elems[el_idx] == NULL ) {
 		return H5_SUCCESS; /* no tags for this element */
 	}
 	h5t_tagsel_t *tagselem = tagset->elems[el_idx];
 	size_t offs[5] = { 14, 0, 4, 10, 14 };
-	size_t i = offs[type_id]+subentity_id;
+	size_t i = offs[type_id]+face_idx;
 
 	if ( tagselem->idx[i] < 0 ) {
 		return H5_SUCCESS; /* no value set for this subentity */
@@ -577,11 +577,11 @@ h5_err_t
 h5t_remove_mtag_by_name (
 	h5_file_t *const f,
 	const char name[],
-	const h5_id_t id
+	const h5_loc_id_t entity_id
 	) {
 	H5T_Tagset *tagset;
 	TRY ( h5t_open_mtagset ( f, name, &tagset ) );
-	return h5t_remove_mtag ( f, tagset, id );
+	return h5t_remove_mtag ( f, tagset, entity_id );
 }
 
 static hid_t
@@ -609,8 +609,8 @@ write_tagset (
 	  alloc memory
 	 */
 	h5t_tag_idx_t *elems;
-	size_t el_idx;
-	size_t num_elems = t->num_elems[t->num_levels-1];
+	h5_loc_idx_t el_idx;
+	h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 	TRY ( ( elems = h5priv_calloc (
 			f, num_elems+1, sizeof(*elems) ) ) );
 
@@ -628,26 +628,26 @@ write_tagset (
 	TRY ( ( vals = h5priv_calloc (
 			f, max_vals, sizeof(*vals) ) ) );
 
-	h5_id_t tmap[15] = { H5T_ETYPE_VERTEX, H5T_ETYPE_VERTEX,
-			     H5T_ETYPE_VERTEX, H5T_ETYPE_VERTEX,
-			     H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
-			     H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
-			     H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
-			     H5T_ETYPE_TRIANGLE, H5T_ETYPE_TRIANGLE,
-			     H5T_ETYPE_TRIANGLE, H5T_ETYPE_TRIANGLE,
-			     H5T_ETYPE_TET };
+	h5_loc_id_t tmap[15] = { H5T_ETYPE_VERTEX, H5T_ETYPE_VERTEX,
+				 H5T_ETYPE_VERTEX, H5T_ETYPE_VERTEX,
+				 H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
+				 H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
+				 H5T_ETYPE_EDGE, H5T_ETYPE_EDGE,
+				 H5T_ETYPE_TRIANGLE, H5T_ETYPE_TRIANGLE,
+				 H5T_ETYPE_TRIANGLE, H5T_ETYPE_TRIANGLE,
+				 H5T_ETYPE_TET };
 	/* sub-entity indices */
-	h5_id_t smap[15] = { 0, 1, 2, 3,	/* vertices */
-			     0, 1, 2, 3, 4, 5,	/* edges */
-			     0, 1, 2, 3,	/* triangles */
-			     0 };		/* tetrahedron */
+	int smap[15] = { 0, 1, 2, 3,	/* vertices */
+			 0, 1, 2, 3, 4, 5,	/* edges */
+			 0, 1, 2, 3,	/* triangles */
+			 0 };		/* tetrahedron */
 	/*
 	  build data structures in memory
 	 */
 	for ( el_idx = 0; el_idx < num_elems; el_idx++ ) {
 		h5t_tagsel_t *tags_of_elem = tagset->elems[el_idx];
 		size_t num_subentities = 0;
-		h5_id_t start_idx_entities = ent_idx;
+		size_t start_idx_entities = ent_idx;
 		size_t i;
 		for ( i = 0; i < 15; i++ ) {
 			int k = tags_of_elem->idx[i];
@@ -678,10 +678,11 @@ write_tagset (
 						max_entities*sizeof(*entities) )
 					      ) );
 			}
-			h5_id_t type_id = tmap[i];
-			h5_id_t sentity_id = smap[i];
+			h5_glb_id_t type_id = tmap[i];
+			h5_glb_id_t face_idx = smap[i];
+			// TODO: map local elem idx to global index
 			entities[ent_idx].eid = h5tpriv_build_id (
-				type_id, sentity_id, el_idx );
+				type_id, face_idx, el_idx );
 			entities[ent_idx].idx = val_idx;
 			val_idx += valp->size;
 			ent_idx++;
@@ -916,7 +917,7 @@ static h5_ssize_t
 get_tagset_names_of_entity (
 	h5_file_t * const f,
 	h5t_tagcontainer_t *ctn,
-	h5_id_t entity_id,
+	h5_loc_id_t entity_id,
 	char *names[],
 	h5_size_t dim
 	) {
@@ -945,7 +946,7 @@ get_tagset_names_of_entity (
 h5_ssize_t
 h5t_get_mtagset_names_of_entity (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	char *names[],
 	const h5_size_t dim
 	) {

src/h5core/h5t_tags_private.h

@@ -79,8 +79,8 @@ typedef struct {
 
 
 typedef struct {
-	h5_id_t eid ;
-	h5_id_t idx;
+	h5_glb_id_t eid ;	// global entity id
+	h5_glb_idx_t idx;	// global index
 } h5t_tag_idx_t;
 
 h5_err_t h5tpriv_write_mtags ( h5_file_t *const f );

src/h5core/h5t_types_private.h

@@ -1,50 +1,88 @@
 #ifndef __H5T_TYPES_PRIVATE_H
 #define __H5T_TYPES_PRIVATE_H
 
-typedef struct h5_vertex {
-	h5_id_t		idx;
+typedef struct h5_glb_vertex {
+	h5_glb_idx_t	idx;
 	h5_coord3d_t	P;
-} h5_vertex_t;
+} h5_glb_vertex_t;
 
-typedef struct h5_triangle {
-	h5_id_t		idx;
-	h5_id_t		parent_idx;
-	h5_id_t		child_idx;
-	h5_3id_t	vertex_indices;
-	h5_3id_t	neighbor_indices;
-} h5_triangle_t;
+typedef struct h5_loc_vertex {
+	h5_loc_idx_t	idx;
+	h5_coord3d_t	P;
+} h5_loc_vertex_t;
 
-typedef struct h5_tetrahedron {
-	h5_id_t		idx;
-	h5_id_t		parent_idx;
-	h5_id_t		child_idx;
-	h5_4id_t	vertex_indices;
-	h5_4id_t	neighbor_indices;
-} h5_tetrahedron_t;
-typedef h5_tetrahedron_t	h5_tet_t;
+typedef struct h5_glb_triangle {
+	h5_glb_idx_t	idx;
+	h5_glb_idx_t	parent_idx;
+	h5_glb_idx_t	child_idx;
+	h5_glb_idx_t	vertex_indices[3];
+	h5_glb_idx_t	neighbor_indices[3];
+} h5_glb_triangle_t;
 
-typedef struct h5_generic_elem {
-	h5_id_t		idx;
-	h5_id_t		parent_idx;
-	h5_id_t		child_idx;
-	h5_id_t		indices[1];
-} h5_generic_elem_t;
+typedef struct h5_loc_triangle {
+	h5_loc_idx_t	idx;
+	h5_loc_idx_t	parent_idx;
+	h5_loc_idx_t	child_idx;
+	h5_loc_idx_t	vertex_indices[3];
+	h5_loc_idx_t	neighbor_indices[3];
+} h5_loc_triangle_t;
 
+typedef struct h5_glb_tetrahedron {
+	h5_glb_idx_t	idx;
+	h5_glb_idx_t	parent_idx;
+	h5_glb_idx_t	child_idx;
+	h5_glb_idx_t	vertex_indices[4];
+	h5_glb_idx_t	neighbor_indices[4];
+} h5_glb_tetrahedron_t;
+typedef h5_glb_tetrahedron_t	h5_glb_tet_t;
 
-typedef union h5_elems {
-	h5_tet_t	*tets;
-	h5_triangle_t	*tris;
+typedef struct h5_loc_tetrahedron {
+	h5_loc_idx_t	idx;
+	h5_loc_idx_t	parent_idx;
+	h5_loc_idx_t	child_idx;
+	h5_loc_idx_t	vertex_indices[4];
+	h5_loc_idx_t	neighbor_indices[4];
+} h5_loc_tetrahedron_t;
+typedef h5_loc_tetrahedron_t	h5_loc_tet_t;
+
+typedef struct h5_generic_glb_elem {
+	h5_glb_idx_t	idx;
+	h5_glb_idx_t	parent_idx;
+	h5_glb_idx_t	child_idx;
+	h5_glb_idx_t	indices[1];
+} h5_generic_glb_elem_t;
+
+typedef struct h5_generic_loc_elem {
+	h5_loc_idx_t	idx;
+	h5_loc_idx_t	parent_idx;
+	h5_loc_idx_t	child_idx;
+	h5_loc_idx_t	indices[1];
+} h5_generic_loc_elem_t;
+
+typedef union h5_glb_elems {
+	h5_glb_tet_t	*tets;
+	h5_glb_triangle_t *tris;
 	void		*data;
-} h5_elems_t;
+} h5_glb_elems_t;
+
+typedef union h5_loc_elems {
+	h5_loc_tet_t	*tets;
+	h5_loc_triangle_t *tris;
+	void		*data;
+} h5_loc_elems_t;
 
 /*** type ids' for compound types ***/
 typedef struct h5_dtypes {
 	hid_t		h5_id_t;		/* ID's */
+
+	hid_t		h5_glb_id_t;		/* ID's */
+	hid_t		h5_glb_idx_t;		/* ID's */
+
 	hid_t		h5_int64_t;		/* 64 bit signed integer */
 	hid_t		h5_float64_t;		/* 64 bit floating point */
 	hid_t		h5_coord3d_t;		/* 3-tuple of 64-bit float */
-	hid_t		h5_3id_t;		/* 3-tuple of ID's */
-	hid_t		h5_4id_t;		/* 4-tuple of ID's */
+	hid_t		h5_3glb_idx_t;		/* 3-tuple of indices */
+	hid_t		h5_4glb_idx_t;		/* 4-tuple of indices */
 	hid_t		h5_vertex_t;		/* vertex structure */
 	hid_t		h5_triangle_t;		/* triangle structure */
 	hid_t		h5_tet_t;		/* tetrahedron structure */
@@ -53,8 +91,8 @@ typedef struct h5_dtypes {
 
 typedef struct h5t_adjacencies {
 	struct {
-		h5_size_t size;
-		h5_idlist_t *v;
+		// h5_size_t size;
+		h5_idlist_t* v;
 	} tv;
 	h5_hashtable_t te_hash;
 	h5_hashtable_t td_hash;
@@ -62,69 +100,76 @@ typedef struct h5t_adjacencies {
 
 struct h5t_store_methods {
 	h5_err_t (*alloc_elems)(h5_file_t* const, const size_t, const size_t);
-	h5_id_t (*refine_elem)(h5_file_t* const, const h5_id_t);
+	h5_loc_idx_t (*refine_elem)(h5_file_t* const, const h5_loc_idx_t);
 	h5_err_t (*end_store_elems)(h5_file_t* const);
-	h5_id_t (*get_direct_children_of_edge)(h5_file_t* const, const h5_id_t, const h5_id_t, h5_id_t*);
+	h5_err_t (*get_direct_children_of_edge)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t,
+		h5_loc_id_t*);
 };
 
 struct h5t_retrieve_methods {
-	h5_err_t (*init_iterator)(h5_file_t* const, h5t_entity_iterator_t*, const int);
+	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);
-	h5_id_t (*get_loc_elem_parent_idx)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*set_loc_elem_parent_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*get_loc_elem_child_idx)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*set_loc_elem_child_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_generic_loc_elem_t* (*get_loc_elem)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_loc_idx_t (*get_loc_elem_parent_idx)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_loc_idx_t (*set_loc_elem_parent_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_loc_id_t (*get_loc_elem_child_idx)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_loc_id_t (*set_loc_elem_child_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
 	h5_id_t (*get_loc_elem_level_idx)(
-		h5_file_t* const, const h5_id_t);
+		h5_file_t* const, const h5_loc_idx_t);
 	h5_id_t (*set_loc_elem_level_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t* (*get_loc_elem_vertex_indices)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*get_loc_elem_vertex_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*set_loc_elem_vertex_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
-	h5_id_t* (*get_loc_elem_neighbor_indices)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*get_loc_elem_neighbor_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*set_loc_elem_neighbor_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
+		h5_file_t* const, const h5_loc_idx_t, const h5_id_t);
+	h5_loc_idx_t* (*get_loc_elem_vertex_indices)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_loc_idx_t (*get_loc_elem_vertex_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_loc_idx_t (*set_loc_elem_vertex_idx)(
+		h5_file_t* const,
+		const h5_loc_idx_t, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_loc_idx_t* (*get_loc_elem_neighbor_indices)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_loc_idx_t (*get_loc_elem_neighbor_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_loc_idx_t (*set_loc_elem_neighbor_idx)(
+		h5_file_t* const,
+		const h5_loc_idx_t, const h5_loc_idx_t, const h5_loc_idx_t);
 
-	h5_generic_elem_t* (*get_glb_elem)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*get_glb_elem_idx)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*set_glb_elem_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*get_glb_elem_parent_idx)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*set_glb_elem_parent_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*get_glb_elem_child_idx)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*set_glb_elem_child_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t* (*get_glb_elem_vertex_indices)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*get_glb_elem_vertex_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t);
-	h5_id_t (*set_glb_elem_vertex_idx)(
-		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
-	h5_id_t* (*get_glb_elem_neighbor_indices)(
-		h5_file_t* const, const h5_id_t);
-	h5_id_t (*get_glb_elem_neighbor_idx)(
-		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);
+	h5_generic_glb_elem_t* (*get_glb_elem)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_glb_id_t (*get_glb_elem_idx)(
+		h5_file_t* const, const h5_loc_id_t);
+	h5_glb_id_t (*set_glb_elem_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_glb_idx_t);
+	h5_glb_idx_t (*get_glb_elem_parent_idx)(
+		h5_file_t* const, const h5_loc_id_t);
+	h5_glb_idx_t (*set_glb_elem_parent_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_glb_idx_t);
+	h5_glb_idx_t (*get_glb_elem_child_idx)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_glb_idx_t (*set_glb_elem_child_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_glb_idx_t);
+	h5_glb_idx_t* (*get_glb_elem_vertex_indices)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_glb_idx_t (*get_glb_elem_vertex_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_glb_id_t (*set_glb_elem_vertex_idx)(
+		h5_file_t* const,
+		const h5_loc_idx_t, const h5_loc_idx_t, const h5_glb_idx_t);
+	h5_glb_idx_t* (*get_glb_elem_neighbor_indices)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5_glb_idx_t (*get_glb_elem_neighbor_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	h5_glb_idx_t (*set_glb_elem_neighbor_idx)(
+		h5_file_t* const,
+		const h5_loc_idx_t, const h5_loc_idx_t, const h5_glb_idx_t);
 };
 
 struct h5t_read_methods {
@@ -135,7 +180,8 @@ 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_adjacencies)(
-		h5_file_t * const, const h5_id_t, const h5_int32_t, h5_idlist_t**);
+		h5_file_t * const,
+		const h5_loc_id_t, const h5_int32_t, h5_idlist_t**);
 };
 
 typedef struct h5t_methods {
@@ -173,22 +219,22 @@ typedef struct h5t_fdata {
 	struct h5t_methods methods;
 
 	/*** vertices ***/
-	h5_vertex_t	*vertices;
+	h5_loc_vertex_t	*vertices;
 	h5_size_t	*num_vertices;
-	h5_idmap_t	map_vertex_g2l;	/* map global to local idx */
+	h5_idxmap_t	map_vertex_g2l;	/* map global to local idx */
 	h5_idlist_t	sorted_lvertices;
-	h5_id_t		last_stored_vid;
+	h5_loc_idx_t		last_stored_vid;
 	h5_dsinfo_t	dsinfo_vertices;
 	h5_dsinfo_t	dsinfo_num_vertices;
 	
 
 	/*** Elements ***/
-	h5_elems_t	glb_elems;
-	h5_elems_t	loc_elems;
+	h5_glb_elems_t	glb_elems;
+	h5_loc_elems_t	loc_elems;
 
 	h5_size_t	*num_elems;
 	h5_size_t	*num_elems_on_level;
-	h5_idmap_t	map_elem_g2l;	/* map global id to local id */
+	h5_idxmap_t	map_elem_g2l;	/* map global id to local id */
 
 	/*
 	  array with geometrically sorted local entitiy ids
@@ -198,7 +244,7 @@ typedef struct h5t_fdata {
 	*/
 	h5_idlist_t	sorted_elems[H5_MAX_VERTICES_PER_ELEM];
 
-	h5_id_t		last_stored_eid;
+	h5_loc_idx_t	last_stored_eid;
 	h5_dsinfo_t	dsinfo_elems;
 	h5_dsinfo_t	dsinfo_num_elems;
 	h5_dsinfo_t	dsinfo_num_elems_on_level;

src/include/H5Fed_adjacency.h

@@ -4,7 +4,7 @@
 h5_err_t
 H5FedGetAdjacencies (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t** list
 	);

src/include/H5Fed_retrieve.h

@@ -20,7 +20,7 @@ H5FedBeginTraverseEntities (
 	h5_file_t* const f,
 	int codim
 	);
-h5_id_t
+h5_loc_id_t
 H5FedTraverseEntities (
 	h5_file_t* const f,
 	h5t_entity_iterator_t* iter
@@ -33,41 +33,41 @@ H5FedEndTraverseEntities (
 h5_err_t
 H5FedGetVertexCoordsByIndex (
 	h5_file_t* const f,
-	h5_id_t vertex_index,
+	h5_loc_idx_t vertex_index,
 	h5_float64_t P[3]
 	);
 h5_err_t
 H5FedGetVertexCoordsByID (
 	h5_file_t* const f,
-	h5_id_t vertex_id,
+	h5_loc_id_t vertex_id,
 	h5_float64_t P[3]
 	);
 
 h5_err_t
 H5FedGetVertexIndicesOfEdge (
 	h5_file_t* const f,
-	h5_id_t entity_id,
-	h5_id_t* const vertex_indices
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* const vertex_indices
 	);
 
 h5_err_t
 H5FedGetVertexIndicesOfTriangle (
 	h5_file_t* const f,
-	h5_id_t entity_id,
-	h5_id_t* const vertex_indices
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* const vertex_indices
 	);
 
 h5_err_t
 H5FedGetVertexIndicesOfTet (
 	h5_file_t* const f,
-	h5_id_t entity_id,
-	h5_id_t* const vertex_indices
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* const vertex_indices
 	);
 
 h5_err_t
 H5FedGetVertexIndicesOfEntity (
 	h5_file_t* const f,
-	h5_id_t entity_id,
-	h5_id_t* const vertex_indices
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* const vertex_indices
 	);
 #endif

src/include/H5Fed_store.h

@@ -36,10 +36,10 @@ H5FedBeginStoreVertices (
 	const h5_size_t num
 	);
 
-h5_id_t
+h5_loc_idx_t
 H5FedStoreVertex (
 	h5_file_t * const f,
-	const h5_id_t id,
+	const h5_glb_idx_t id,
 	const h5_float64_t P[3]
 	);
 
@@ -55,10 +55,10 @@ H5FedBeginStoreElements (
 	);
 
 
-h5_id_t
+h5_err_t
 H5FedStoreElement (
 	h5_file_t * const f,
-	const h5_id_t local_vids[]
+	const h5_loc_idx_t vertex_indices[]
 	);
 
 h5_err_t
@@ -71,10 +71,10 @@ H5FedBeginRefineElements (
 	h5_file_t * const f
 	);
 
-h5_id_t
+h5_loc_idx_t
 H5FedRefineElement (
 	h5_file_t * const f,
-	const h5_id_t eid
+	const h5_loc_idx_t elem_idx
 	);
 
 h5_err_t
@@ -82,11 +82,4 @@ H5FedEndRefineElements (
 	h5_file_t * const f
 	);
 
-h5_err_t
-H5FedMarkRefineElement (
-	h5_file_t * const f,
-	const h5_id_t eid
-	);
-
-
 #endif

src/include/H5Fed_tags.h

@@ -1,40 +1,47 @@
 #ifndef __H5FED_TAGS_H
 #define __H5FED_TAGS_H
-h5_err_t	H5FedAddMTagset ( h5_file_t * const f,
-				  char * name,
-				  h5_id_t type );
-h5_err_t	H5FedRemoveMTagset ( h5_file_t *const f,
-				     char name[] );
-h5_size_t	H5FedGetMTagsets ( h5_file_t *const f,
-				   char **names[] );
-h5_id_t		H5FedGetTypeOfMTagset ( h5_file_t *const f,
-					char name[] );
-h5_err_t	H5FedSetMTag ( h5_file_t *const f,
-			       char name[], h5_id_t id,
-			       const size_t dims, void *val );
-h5_err_t	H5FedSetMTagToVertex ( h5_file_t *const f,
-				       char name[], h5_id_t id,
-				       const size_t dims, void *val );
-h5_err_t	H5FedSetMTagToEdge ( h5_file_t *const f,
-				     char name[], h5_id_t id,
-				     const size_t dims, void *val );
-h5_err_t	H5FedSetMTagToTriangle ( h5_file_t *const f,
-					 char name[], h5_id_t id,
-					 const size_t dims, void *val );
-h5_err_t	H5FedSetMTagToTet ( h5_file_t *const f,
-				    char name[], h5_id_t id,
-				    const size_t dims, void *val );
+h5_err_t
+H5FedAddMTagset (
+	h5_file_t* const f,
+	char* name,
+	h5_id_t type
+	);
+h5_err_t
+H5FedRemoveMTagset (
+	h5_file_t* const f,
+	char name[]
+	);
+h5_size_t
+H5FedGetMTagsets (
+	h5_file_t* const f,
+	char** names[]
+	);
+h5_id_t
+H5FedGetTypeOfMTagset (
+	h5_file_t* const f,
+	char name[]
+	);
+h5_err_t
+H5FedSetMTag (
+	h5_file_t* const f,
+	char name[],
+	h5_loc_id_t entity_id,
+	const size_t dims,
+	void* val
+	);
+h5_err_t
+H5FedGetMTag (
+	h5_file_t* const f,
+	const char name[],
+	const h5_loc_id_t id, 
+	size_t* dims,
+	void* val
+	);
+h5_err_t
+H5FedRemoveMTag (
+	h5_file_t* const f,
+	const char name[],
+	const h5_loc_id_t id
+	);
 
-h5_err_t	H5FedGetMTag ( h5_file_t *const f,
-			       const char name[], const h5_id_t id, 
-			       size_t *dims, void *val );
-h5_err_t	H5FedRemoveMTag ( h5_file_t *const f,
-				  const char name[], const h5_id_t id );
-
-/*
-  Get descriptor for a tagset
-  Get tag value by descriptor
-  get size of value
-  Get tagset names for specific entity
-*/
 #endif

src/include/h5core/h5_core.h

@@ -5,7 +5,6 @@
 #include "h5_errno.h"
 
 #include "h5_attribs.h"
-#include "h5_errorhandling.h"
 #include "h5_hdf5.h"
 #include "h5_maps.h"
 #include "h5_openclose.h"
@@ -20,4 +19,6 @@
 
 #include "h5t_core.h"
 
+#include "h5_errorhandling.h"
+
 #endif

src/include/h5core/h5_errorhandling.h

@@ -1,7 +1,8 @@
 #ifndef __H5_ERRORHANDLING_H
 #define __H5_ERRORHANDLING_H
 
-#define SET_FNAME( f, fname )	h5_set_funcname( f, fname );
+extern h5_int32_t h5priv_debug_level;
+
 #define CHECK_FILEHANDLE( f )					\
 	if ( h5_check_filehandle ( f ) != H5_SUCCESS )		\
 		return h5_get_errno( f );
@@ -88,6 +89,21 @@ h5_abort_errorhandler (
 	va_list ap
 	);
 
+void
+h5priv_vprintf (
+	FILE* f,
+	const char* prefix,
+	const char* __funcname,
+	const char* fmt,
+	va_list ap
+	);
+
+const char *
+h5_get_funcname (
+	const h5_file_t * const f
+	);
+
+
 h5_err_t
 h5_error (
 	h5_file_t * const f,
@@ -125,14 +141,12 @@ __attribute__ ((format (printf, 2, 3)))
 #endif
 ;
 
-void
-h5_vinfo (
-	const h5_file_t * const f,
-	const char *fmt,
-	va_list ap
-	);
+/*!
+  \ingroup h5_core_errorhandling
 
-void
+  Print an informational message to \c stdout.
+*/
+static inline void
 h5_info (
 	const h5_file_t * const f,
 	const char *fmt,
@@ -142,15 +156,32 @@ h5_info (
 __attribute__ ((format (printf, 2, 3)))
 #endif
 ;
+static inline void
+h5_info (
+	const h5_file_t* const f,
+	const char* fmt,
+	...
+	) {
+	if (h5priv_debug_level >= 3) {
+		va_list ap;
+		va_start (ap, fmt);
+		h5priv_vprintf (stdout, "I", h5_get_funcname(f), fmt, ap);
+		va_end (ap);
+	}
+}
 
-void
-h5_vdebug (
-	const h5_file_t * const f,
-	const char *fmt,
-	va_list ap
-	);
+/*!
+  \ingroup h5_core_errorhandling
 
-void
+  Print a debug message to \c stdout.
+*/
+#if defined(HAVE__VA_ARGS__)
+#define h5_debug(f, ...)						\
+	if (h5priv_debug_level >= 4) {					\
+		h5priv_vprintf (stdout, "D", h5_get_funcname(f), __VA_ARGS__); \
+	}
+#else
+static inline void
 h5_debug (
 	const h5_file_t * const f,
 	const char *fmt,
@@ -159,7 +190,22 @@ h5_debug (
 #ifdef __GNUC__
 __attribute__ ((format (printf, 2, 3)))
 #endif
-;
+	;
+
+static inline void
+h5_debug (
+	const h5_file_t * const f,
+	const char *fmt,
+	...
+	) {
+	if (h5priv_debug_level >= 4) {
+		va_list ap;
+		va_start (ap, fmt);
+		h5priv_vprintf (stdout, "D", h5_get_funcname(f), fmt, ap);
+		va_end (ap);
+	}
+}
+#endif
 
 void
 h5_set_funcname (
@@ -167,9 +213,13 @@ h5_set_funcname (
 	const char  * const fname
 	);
 
-const char *
-h5_get_funcname (
-	const h5_file_t * const f
-	);
+static inline void
+SET_FNAME (
+	h5_file_t* const f,
+	const char* const fname
+	) {
+	h5_set_funcname( f, fname );
+	h5_debug (f, "%s", " "); // just print the function name
+}
 
 #endif

src/include/h5core/h5_maps.h

@@ -1,103 +1,4 @@
 #ifndef __H5_MAPS_H
 #define __H5_MAPS_H
 
-h5_err_t
-h5priv_alloc_idlist (
-	h5_file_t * const f,
-	h5_idlist_t **list,
-	const h5_size_t	size
-	);
-
-h5_err_t
-h5priv_free_idlist (
-	h5_file_t * const f,
-	h5_idlist_t **list
-	);
-
-h5_err_t
-h5priv_alloc_idlist_items (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	const h5_size_t	size
-	);
-
-h5_err_t
-h5priv_free_idlist_items (
-	h5_file_t * const f,
-	h5_idlist_t *list
-	);
-
-h5_err_t
-h5priv_append_to_idlist (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	h5_id_t id
-	);
-
-int
-h5priv_cmp_ids_by_eid (
-	const void *_id1,
-	const void *_id2
-	);
-
-int
-h5priv_cmp_ids (
-	const void *_id1,
-	const void *_id2
-	);
-
-h5_err_t
-h5priv_sort_idlist_by_eid (
-	h5_file_t * const f,
-	h5_idlist_t *list
-	);
-
-h5_id_t
-h5priv_find_idlist (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	h5_id_t	item
-	);
-
-h5_id_t
-h5priv_insert_idlist (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	h5_id_t	item,
-	h5_id_t idx
-	);
-
-h5_id_t
-h5priv_search_idlist (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	h5_id_t	item
-	);
-
-h5_err_t
-h5priv_alloc_idmap (
-	h5_file_t * const f,
-	h5_idmap_t *map,
-	const h5_size_t	size
-	);
-
-h5_err_t
-h5priv_insert_idmap (
-	h5_file_t * const f,
-	h5_idmap_t *map,
-	h5_id_t global_id,
-	h5_id_t local_id
-	);
-
-h5_id_t
-h5priv_search_idmap (
-	h5_idmap_t *map,
-	h5_id_t value
-	);
-
-h5_err_t
-h5priv_sort_idmap (
-	h5_idmap_t *map
-	);
-
 #endif

src/include/h5core/h5_types.h

@@ -79,8 +79,8 @@ typedef struct h5_idlist {
 	h5_id_t		*items;
 } h5_idlist_t;
 
-struct h5_idmap;
-typedef struct h5_idmap h5_idmap_t;
+struct h5_idxmap;
+typedef struct h5_idxmap h5_idxmap_t;
 
 
 enum h5_oid {

src/include/h5core/h5t_adjacencies.h

@@ -4,7 +4,7 @@
 h5_err_t
 h5t_get_adjacencies (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_idlist_t **list
 	);

src/include/h5core/h5t_core.h

@@ -49,7 +49,7 @@
 #define H5T_ETYPE_TRIANGLE	((h5_id_t)3)
 #define H5T_ETYPE_TET		((h5_id_t)4)
 
-#define h5tpriv_set_entity_type( type, elem_idx )			\
+#define h5tpriv_set_entity_type( type, elem_idx )		\
 	(							\
 		((h5_id_t)(type) << (sizeof(h5_id_t)*8-4)) |	\
 		((h5_id_t)(elem_idx))				\
@@ -58,7 +58,6 @@
 	((entity_id & H5T_ETYPE_MASK) >> (sizeof(h5_id_t)*8-4))
 
 
-
 #define h5tpriv_build_id( type, comp_idx, elem_idx )		\
 	(							\
 		((h5_id_t)(type) << (sizeof(h5_id_t)*8-4)) |	\

src/include/h5core/h5t_map.h

@@ -4,106 +4,88 @@
 h5_id_t
 h5t_map_global_vertex_idx2local (
 	h5_file_t * const f,
-	h5_id_t global_idx
+	h5_glb_idx_t glb_idx
 	);
 
 h5_err_t
 h5t_map_global_vertex_indices2local (
 	h5_file_t* f,
-	const h5_id_t* const glb_indices,
-	const h5_id_t size,
-	h5_id_t* const loc_indices
+	const h5_glb_id_t* const glb_indices,
+	const h5_size_t size,
+	h5_loc_idx_t* const loc_indices
 	);
 
-h5_id_t
-h5t_map_local_vid2global (
-	h5_file_t *f,
-	h5_id_t local_vid
-	);
-
-h5_id_t
-h5t_map_global_elem_idx2local (
+h5_loc_idx_t
+h5t_map_glb_elem_idx2loc (
 	h5_file_t * const f,
-	const h5_id_t global_idx
+	const h5_glb_idx_t glb_idx
 	);
 
-h5_id_t
-h5t_map_global_elem_indices2local (
+h5_err_t
+h5t_map_glb_elem_indices2loc (
 	h5_file_t * const f,
-	const h5_id_t* glb_indices,
-	const h5_id_t size,
-	h5_id_t* loc_indices
-	);
-
-h5_id_t
-h5tpriv_get_local_vid (
-	h5_file_t * const f,
-	h5_float64_t P[3]
-	);
-
-h5_id_t
-h5t_get_local_eid (
-	h5_file_t *f,
-	h5_id_t * const local_vids
+	const h5_glb_idx_t* glb_indices,
+	const h5_size_t size,
+	h5_loc_idx_t* loc_indices
 	);
 
 h5_err_t
 h5t_get_vertex_index_of_vertex (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	h5_id_t* vertex_index
 	);
 
 h5_err_t
 h5t_get_vertex_index_of_vertex2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx,
-	h5_id_t* vertex_indices
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx,
+	h5_loc_idx_t* vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_edge (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t *vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t *vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_edge2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_id,
-	h5_id_t* vertex_indices
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_id,
+	h5_loc_idx_t* vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_triangle (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_triangle2 (
 	h5_file_t* const f,
-	const h5_id_t face_idx,
-	const h5_id_t elem_idx,
-	h5_id_t* vertex_indices
+	const h5_loc_idx_t face_idx,
+	const h5_loc_idx_t elem_idx,
+	h5_loc_idx_t* vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_tet (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t *vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t *vertex_indices
 	);
 
 h5_err_t
 h5t_get_vertex_indices_of_entity (
 	h5_file_t * const f,
-	const h5_id_t entity_id,
-	h5_id_t *vertex_indices
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t *vertex_indices
 	);
 
 #endif

src/include/h5core/h5t_openclose.h

@@ -1,29 +1,17 @@
 #ifndef __H5T_OPENCLOSE_H
 #define __H5T_OPENCLOSE_H
 
-
-h5_err_t h5t_open_mesh ( h5_file_t * const f, const h5_id_t id,
-			 const h5_oid_t type );
-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 );
-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_close_step ( h5_file_t * const f );
-
-h5_err_t h5tpriv_init_fdata ( h5_file_t * const f );
-h5_err_t h5tpriv_init_step ( h5_file_t * const f );
-
-h5_err_t h5tpriv_alloc_num_vertices ( h5_file_t * const f,
-				   const h5_size_t num_vertices );
-h5_err_t h5tpriv_alloc_tris ( h5_file_t * const f, const size_t cur,
-			   const size_t new_size );
-h5_err_t h5tpriv_alloc_tets ( h5_file_t * const f, const size_t cur,
-			   const size_t new_size );
+h5_err_t h5t_open_mesh (
+	h5_file_t * const f,
+	const h5_id_t id,
+	const h5_oid_t type
+	);
+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
+	);
 
 #endif
-#endif

src/include/h5core/h5t_retrieve.h

@@ -48,14 +48,14 @@ h5t_end_iterate_entities (
 h5_err_t
 h5t_get_vertex_coords_by_index (
 	h5_file_t* const f,
-	h5_id_t vertex_index,
+	h5_loc_idx_t vertex_idx,
 	h5_float64_t P[3]
 	);
 
 h5_err_t
 h5t_get_vertex_coords_by_id (
 	h5_file_t* const f,
-	h5_id_t vertex_id,
+	h5_loc_id_t vertex_id,
 	h5_float64_t P[3]
 	);
 #endif

src/include/h5core/h5t_storemesh.h

@@ -21,7 +21,7 @@ h5t_begin_store_vertices (
 h5_id_t
 h5t_store_vertex (
 	h5_file_t * const f,
-	const h5_id_t mesher_vid,
+	const h5_glb_id_t glb_id,
 	const h5_float64_t P[3]
 	);
 
@@ -36,11 +36,11 @@ h5t_begin_store_elems (
 	const h5_size_t num
 	);
 
-h5_id_t
+h5_loc_idx_t
 h5t_store_elem    (
 	h5_file_t * const f,
-	const h5_id_t local_parent_eid,
-	const h5_id_t local_vids[]
+	const h5_loc_idx_t parent_idx,
+	const h5_loc_idx_t* vertex_indices
 	);
 
 h5_err_t
@@ -66,7 +66,7 @@ h5t_end_refine_elems (
 h5_err_t
 h5t_mark_entity (
 	h5_file_t* const f,
-	const h5_id_t entity_id
+	const h5_loc_id_t entity_id
 	);
 
 h5_err_t

src/include/h5core/h5t_tags.h

@@ -3,34 +3,73 @@
 
 typedef struct h5t_tagset H5T_Tagset;
 
-h5_err_t h5t_add_mtagset ( h5_file_t* const f, char name[], h5_id_t id );
-h5_err_t h5t_remove_mtagset ( h5_file_t* const f, const char name[] );
-h5_err_t h5t_open_mtagset ( h5_file_t* const f, const char *name,
-			    H5T_Tagset** retval );
-h5_ssize_t h5t_get_num_mtagsets ( h5_file_t* const f );
-h5_ssize_t h5t_get_mtagsets ( h5_file_t* const f, char** names[] );
-h5_err_t h5t_get_mtagset_info ( h5_file_t* const f, const h5_id_t idx,
-				char** names, h5_id_t* type );
-h5_id_t h5t_get_mtagset_type_by_name ( h5_file_t* const f, char name[] );
+h5_err_t
+h5t_add_mtagset (
+	h5_file_t* const f,
+	char name[],
+	h5_id_t id
+	);
+h5_err_t
+h5t_remove_mtagset (
+	h5_file_t* const f,
+	const char name[]
+	);
+h5_err_t h5t_open_mtagset (
+	h5_file_t* const f,
+	const char *name,
+	H5T_Tagset** retval
+	);
+h5_ssize_t
+h5t_get_num_mtagsets (
+	h5_file_t* const f
+	);
+h5_ssize_t
+h5t_get_mtagsets (
+	h5_file_t* const f,
+	char** names[]
+	);
+h5_err_t
+h5t_get_mtagset_info (
+	h5_file_t* const f,
+	const h5_id_t idx,
+	char** names,
+	h5_id_t* type
+	);
+h5_id_t
+h5t_get_mtagset_type_by_name (
+	h5_file_t* const f,
+	char name[]
+	);
 
-h5_err_t h5t_set_mtag_by_name ( h5_file_t* const f, char name[], const h5_id_t id,
-				const size_t dim, void* value );
+h5_err_t
+h5t_set_mtag_by_name (
+	h5_file_t* const f,
+	char name[],
+	const h5_loc_id_t entity_id,
+	const size_t dim,
+	void* value
+	);
 
-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_get_mtag_by_name (
+	h5_file_t* const f,
+	const char name[],
+	const h5_loc_id_t entity_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
+	const h5_loc_id_t entity_id
 	);
 
 h5_ssize_t
 h5t_get_tag (
 	h5_file_t *const f,
 	const H5T_Tagset *tagset,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	size_t* const dim,
 	void* const vals
 	);
@@ -39,13 +78,13 @@ h5_err_t
 h5t_remove_mtag (
 	h5_file_t* const f,
 	H5T_Tagset* tagset,
-	const h5_id_t id
+	const h5_loc_id_t entity_id
 	);
 
 h5_ssize_t
 h5t_get_mtagset_names_of_entity (
 	h5_file_t* const f,
-	const h5_id_t entity_id,
+	const h5_loc_id_t entity_id,
 	char *names[],
 	const h5_size_t dim
 	);