- reference elements revisited (extensions, bugfixes...)

- adjacency computation reviewed, bug fixes
- some reformating and refactoring

src/h5core/h5_hdf5.c

@@ -1247,7 +1247,7 @@ _iter_op_get_obj_type (
 
 	if ( info->type == H5L_TYPE_EXTERNAL ) {
 		char *buf;
-		TRY( buf = h5_alloc(f, NULL, info->u.val_size) );
+		TRY( buf = h5_calloc(f, 1, info->u.val_size) );
 
 		herr = H5Lget_val(g_id, name, buf,
 					info->u.val_size, H5P_DEFAULT);
@@ -1271,7 +1271,7 @@ _iter_op_get_obj_type (
 			"Followed external link to file '%s' / object '%s'.",
 			filename, objname);
 
-		free(buf);
+		h5_free(f, buf);
 
 		hid_t obj_id = H5Oopen(g_id, name, H5P_DEFAULT);
 		if ( obj_id < 0 )

src/h5core/h5_lustre.c

@@ -33,7 +33,7 @@ _get_lustre_stripe_size(h5_file_t *const f,  const char *path )
 	size_t nbytes = sizeof(struct lov_user_md) +
 				INIT_ALLOC_NUM_OSTS * sizeof(struct lov_user_ost_data);
 	struct lov_user_md *lum;
-	TRY( lum = h5_alloc(f, NULL, nbytes) );
+	TRY( lum = h5_calloc(f, 1, nbytes) );
 	lum->lmm_magic = LOV_USER_MAGIC;
 
 	int fd = open64(path, O_RDONLY);
@@ -84,7 +84,7 @@ _get_lustre_stripe_size(h5_file_t *const f,  const char *path )
 		_print_stripe_info(lum);
 
 	ssize_t stripe_size = (ssize_t)lum->lmm_stripe_size;
-	free(lum);
+	h5_free(f, lum);
 
 	return stripe_size;
 }
@@ -98,7 +98,7 @@ h5_optimize_for_lustre (
 	ssize_t stripe_size;
 	if ( f->myproc == 0 )
 	{
-		char *path = malloc(strlen(filename)+4);
+		char *path = h5_calloc(f, 1, strlen(filename)+4);
 		strcpy(path, filename);
 		/* check for existing file */
 		FILE *test = fopen(path, "r");
@@ -116,7 +116,7 @@ h5_optimize_for_lustre (
 
 		stripe_size = _get_lustre_stripe_size(f, path);
 
-		free(path);
+		h5_free(f, path);
 	}
 
 	TRY( h5priv_mpi_bcast(f, &stripe_size, 1, MPI_LONG_LONG, 0, f->comm) );

src/h5core/h5_maps.c

@@ -89,7 +89,7 @@ h5_loc_id_t
 h5priv_find_idlist (
 	h5_file_t* const f,
 	h5_idlist_t* list,
-	h5_loc_id_t item
+	const h5_loc_id_t item
 	) {
 	UNUSED_ARGUMENT (f);
 	if (!list) {
@@ -97,9 +97,17 @@ h5priv_find_idlist (
 	}
 	register h5_loc_idx_t low = 0;
 	register h5_loc_idx_t high = list->num_items - 1;
+	register h5_loc_id_t diff;
+	register h5_loc_id_t mid;
+	const h5_loc_id_t face_idx =  h5tpriv_get_face_idx(item);
+	const h5_loc_id_t elem_idx =  h5tpriv_get_elem_idx(item);
 	while (low <= high) {
-		register h5_loc_idx_t mid = (low + high) / 2;
-		register h5_loc_id_t diff = list->items[mid] - item;
+		mid = (low + high) / 2;
+		diff = h5tpriv_get_elem_idx(list->items[mid]) - elem_idx;
+		// if element indices are equal, we decide on the face indices
+		if (diff == 0) {
+			diff = h5tpriv_get_face_idx(list->items[mid]) - face_idx;
+		}
            	if ( diff > 0 )
                		high = mid - 1;
            	else if ( diff < 0 )

src/h5core/h5_openclose.c

@@ -302,7 +302,7 @@ h5upriv_close_file (
 	TRY( h5priv_close_hdf5_dataspace (f, u->diskshape) );
 	TRY( h5priv_close_hdf5_dataspace (f, u->memshape) );
 	TRY( h5priv_close_hdf5_property (f, u->dcreate_prop) );
-	free (f->u);
+	h5_free (f, f->u);
 	f->u = NULL;
 
 	return f->__errno;
@@ -333,7 +333,7 @@ h5bpriv_close_file (
 #if defined(PARALLEL_IO)
 	TRY( h5priv_mpi_type_free (f, &b->partition_mpi_t) );
 #endif
-	free (f->b);
+	h5_free (f, f->b);
 	f->b = NULL;
 
 	return H5_SUCCESS;
@@ -368,9 +368,9 @@ h5_close_file (
 	TRY( h5priv_close_hdf5_property (f, f->create_prop) );
 	TRY( h5priv_close_hdf5_group (f, f->root_gid) );
 	TRY( h5priv_close_hdf5_file (f, f->file) );
-
-	free (f);
 	h5_debug (f, "%s (): done", __func__);
+
+	h5_free (f, f);
 	return H5_SUCCESS;
 }
 

src/h5core/h5b_model.c

@@ -371,7 +371,7 @@ _dissolve_ghostzones (
 		
 		_dissolve_ghostzone ( f, p_max->p, p_max->q );
 
-		free ( p_max );
+		h5_free (f, p_max);
 		p_el = p_max = p_begin->next;
 
 		while ( p_el ) {
@@ -385,13 +385,13 @@ _dissolve_ghostzones (
 					p_el->next->prev = p_el->prev;
 				p_el->prev->next = p_el->next;
 				p_save = p_el->next;
-				free ( p_el );
+				h5_free (f, p_el);
 				p_el = p_save;
 			}
 		}
 
 	}
-	free ( p_begin );
+	h5_free (f, p_begin);
 
 	return H5_SUCCESS;
 }
@@ -581,8 +581,8 @@ h5b_3d_set_view (
 
 
 
-	free(user_layout);
-	free(write_layout);
+	h5_free(f, user_layout);
+	h5_free(f, write_layout);
 
 	TRY( h5bpriv_release_hyperslab(f) );
 #endif

src/h5core/h5t_adjacencies_trim.c

@@ -43,10 +43,10 @@ release_tv (
 	h5t_adjacencies_t* adj = &t->adjacencies;
 	if (adj->tv.v == NULL) return H5_SUCCESS;
 
-	h5_loc_idx_t idx = 0;
+	h5_loc_idx_t vertex_idx = 0;
 	h5_loc_idx_t last = t->num_vertices[t->num_leaf_levels-1];
-	for (; idx < last; idx++) {
-		TRY( h5priv_free_idlist (f, &adj->tv.v[idx]) );
+	for (; vertex_idx < last; vertex_idx++) {
+		TRY( h5priv_free_idlist (f, &adj->tv.v[vertex_idx]) );
 	}
 	TRY( h5_free (f, adj->tv.v) );
 	adj->tv.v = NULL;
@@ -66,19 +66,13 @@ compute_elems_of_vertices (
 
 	/* 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_leaf_levels-1];
-	h5_loc_triangle_t *el = &t->loc_elems.tris[idx];
-	for (;idx < last; idx++, el++) {
+	h5_loc_idx_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_loc_idx_t last = (t->num_leaf_levels < 0) ? 0 : t->num_elems[t->num_leaf_levels-1];
+	for (;elem_idx < last; elem_idx++) {
 		int face_idx;
 		int num_faces = h5tpriv_ref_elem_get_num_vertices (t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
-			h5_loc_idx_t vidx = el->vertex_indices[face_idx];
-			TRY( h5priv_insert_idlist (
-				     f,
-				     &t->adjacencies.tv.v[vidx],
-				     h5tpriv_build_vertex_id (face_idx, idx),
-				     -1) );
+			TRY( h5tpriv_search_tv2 (f, face_idx, elem_idx, NULL) );
 		}
 	}
 	return H5_SUCCESS;
@@ -92,60 +86,51 @@ compute_elems_of_edges (
 	h5_file_t* const f,
 	const h5t_lvl_idx_t from_lvl
 	) {
-	h5_debug (f, "%s (%lld)", __func__, (long long)from_lvl);
 	h5t_fdata_t *t = f->t;
 	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_leaf_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++) {
 		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 ) );
+			TRY ( h5tpriv_search_te2 (f, face_idx, elem_idx, NULL ) );
 		}
 	}
-	h5_debug (f, "%s (): done", __func__);
 	return H5_SUCCESS;
 }
 
+/*
+  Compute the children o an edge
+ */
 static inline h5_err_t
 compute_children_of_edge (
-	h5_file_t * const f,
-	h5_loc_id_t kid,
-	h5_idlist_t *children
+	h5_file_t* const f,
+	h5_loc_id_t entity_id,
+	h5_idlist_t** children
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_idlist_t *te;
-
-	TRY ( h5tpriv_find_te2 (
-		      f,
-		      h5tpriv_get_face_idx ( kid ),
-		      h5tpriv_get_elem_idx ( kid ),
-		      &te ) 
-		);
-	h5_loc_id_t *edge = te->items;
-	h5_loc_id_t *end = te->items+te->num_items;
-	for ( ; edge < end; edge++ ) {
-		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_is_leaf_elem ( f, el ) == H5_OK ) {
-			TRY( h5priv_insert_idlist (f, &children, *edge, -1) );
+	h5_idlist_t* te;
+	TRY( h5tpriv_find_te (f, entity_id, &te ) );
+	h5_loc_id_t* edge_idp = te->items;
+	h5_loc_id_t* end = te->items + te->num_items;
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge_idp);
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*edge_idp);
+		h5_loc_triangle_t *elem = &f->t->loc_elems.tris[elem_idx];
+		if (h5tpriv_is_leaf_elem (f, elem)) {
+			TRY( h5priv_insert_idlist (f, children, *edge_idp, -1) );
 		} else {
-			h5_loc_id_t kids[2];
-			TRY ( h5tpriv_get_direct_children_of_edge (
+			h5_loc_id_t edge_ids[2];
+			TRY( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
-				      el->child_idx,
-				      kids ) );
-			TRY ( compute_children_of_edge (
-				      f, kids[0], children ) );
-			TRY ( compute_children_of_edge (
-				      f, kids[1], children ) );
+				      elem->child_idx,
+				      edge_ids ) );
+			TRY( compute_children_of_edge (f, edge_ids[0], children) );
+			TRY( compute_children_of_edge (f, edge_ids[1], children) );
 		}
-	}
+	} while (++edge_idp < end);
+
 	return H5_SUCCESS;
 }
 
@@ -155,192 +140,220 @@ compute_children_of_edge (
 static inline h5_err_t
 compute_sections_of_edge (
 	h5_file_t * const f,
-	h5_loc_id_t kid,
-	h5_idlist_t *children
+	h5_loc_id_t entity_id,
+	h5_idlist_t** children
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_idlist_t *te;
-
-	TRY ( h5tpriv_find_te2 (
-		      f,
-		      h5tpriv_get_face_idx ( kid ),
-		      h5tpriv_get_elem_idx ( kid ),
-		      &te )
-		);
-	h5_loc_id_t *edge = te->items;
+	h5_idlist_t* te;
+	TRY( h5tpriv_find_te (f, entity_id, &te) );
+	h5_loc_id_t* edge_idp = te->items;
 	h5_loc_id_t *end = te->items+te->num_items;
 	int refined = 0;
-	for ( ; edge < end; edge++ ) {
-		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_is_leaf_elem ( f, el ) == H5_OK ) {
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge_idp );
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx ( *edge_idp );
+		h5_loc_triangle_t* elem = &f->t->loc_elems.tris[elem_idx];
+		if (!h5tpriv_is_leaf_elem (f, elem)) {
 			refined = 1;
-			h5_loc_id_t kids[2];
-			TRY ( h5tpriv_get_direct_children_of_edge (
+			h5_loc_id_t edge_ids[2];
+			TRY( h5tpriv_get_direct_children_of_edge (
 				      f,
 				      face_idx,
-				      el->child_idx,
-				      kids ) );
-			TRY ( compute_sections_of_edge (
-				      f, kids[0], children ) );
-			TRY ( compute_sections_of_edge (
-				      f, kids[1], children ) );
+				      elem->child_idx,
+				      edge_ids) );
+			TRY( compute_sections_of_edge (f, edge_ids[0], children) );
+			TRY( compute_sections_of_edge (f, edge_ids[1], children) );
 		}
-	}
-	if ( ! refined ) {
-		TRY( h5priv_insert_idlist (f, &children, te->items[0], -1) );
+	} while (++edge_idp < end);
+	if (!refined) {
+		TRY( h5priv_insert_idlist (f, children, te->items[0], -1) );
 	}
 	return H5_SUCCESS;
 }
 
+/*
+  Add unique ID of vertex given by face and element index to list.
+*/
+static inline h5_err_t
+add_vertex2 (
+	h5_file_t* const f,	// in
+	h5_idlist_t** list,	// out
+	h5_loc_idx_t face_idx,	// in
+	h5_loc_idx_t elem_idx	// in
+	) {
+	h5_idlist_t* tv;
+	TRY( h5tpriv_find_tv2 (f, face_idx, elem_idx, &tv) );
+	TRY( h5priv_search_idlist (f, list, tv->items[0]) );
+	return H5_SUCCESS;
+}
 
 /*
-  map edge ID to unique ID
-  if unique ID not in list: add
+  Add unique ID of edge given by ID or face and element index.
 */
 static inline h5_err_t
 add_edge (
-	h5_file_t * const f,
-	h5_idlist_t *list,
+	h5_file_t* const f,	// in
+	h5_idlist_t** list,	// out
+	h5_loc_id_t entity_id	// in
+	) {
+	h5_idlist_t* te;
+	TRY( h5tpriv_find_te (f, entity_id, &te) );
+	TRY( h5priv_search_idlist (f, list, te->items[0]) );
+	return H5_SUCCESS;
+}
+
+static inline h5_err_t
+add_edge2 (
+	h5_file_t* const f,
+	h5_idlist_t** list,
 	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 ) );
-	TRY ( h5priv_search_idlist ( f, &list, te->items[0] ) );
+	TRY( h5tpriv_find_te2 (f, face_idx, elem_idx, &te) );
+	TRY( h5priv_search_idlist (f, list, te->items[0]) );
 	return H5_SUCCESS;
 }
 
+static inline h5_err_t
+add_elem2 (
+	h5_file_t* const f,	// in
+	h5_idlist_t** list,	// out
+	h5_loc_idx_t elem_idx	// in
+	) {
+	h5_loc_id_t elem_id = h5tpriv_build_triangle_id (0, elem_idx);
+	TRY( h5priv_search_idlist (f, list, elem_id) );
 
+	return H5_SUCCESS;
+}
+
+/*
+  Get upward adjacent edges to vertex given by ID
+*/
 static inline h5_err_t
 get_edges_uadj_to_vertex (
-	h5_file_t * const f,
+	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
-	h5_idlist_t **list
+	h5_idlist_t** list
 	) {
-	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
-	
-	h5t_fdata_t* t = f->t;
-	h5_loc_idx_t idx;
-	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &idx) );
-	h5_idlist_t* tv = t->adjacencies.tv.v[idx];
+	h5_loc_idx_t vertex_idx;
+	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &vertex_idx) );
+	h5_idlist_t* tv = f->t->adjacencies.tv.v[vertex_idx];
 
-	h5_size_t i;
+	TRY( h5priv_alloc_idlist (f, list, 8) );
 	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_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];
+	h5_loc_id_t* end = vertex_idp + tv->num_items;
+	do {
+		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_loc_triangle_t* elem= &f->t->loc_elems.tris[elem_idx];
 
-		if ( h5tpriv_is_leaf_elem ( f, el ) == H5_NOK ) {
+		if (!h5tpriv_is_leaf_elem (f, elem)) {
 			continue;
 		}
-		h5_loc_idx_t edge_idx;
-		edge_idx = h5tpriv_get_edge_connected_to_vertex (t->ref_elem, face_idx, 0);
-		TRY ( add_edge ( f, *list, edge_idx, elem_idx ) );
-		edge_idx = h5tpriv_get_edge_connected_to_vertex (t->ref_elem, face_idx, 1);
-		TRY ( add_edge ( f, *list, edge_idx, elem_idx ) );
-	}
+		TRY( add_edge2 (f, list,
+			       h5tpriv_ref_elem_get_edge_idx (
+				       f->t, 0, face_idx, 0),
+				elem_idx) );
+		TRY( add_edge2 (f, list,
+			       h5tpriv_ref_elem_get_edge_idx (
+				       f->t, 0, face_idx, 1),
+			       elem_idx) );
+	} while (++vertex_idp < end);
 	return H5_SUCCESS;
 }
 
 static inline h5_err_t
 get_triangles_uadj_to_vertex (
-	h5_file_t * const f,
+	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
-	h5_idlist_t **list
+	h5_idlist_t** list
 	) {
+	h5_loc_idx_t vertex_idx;
+	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &vertex_idx) );
+	h5_idlist_t* tv = f->t->adjacencies.tv.v[vertex_idx];
+
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
-	
-	h5t_fdata_t *t = f->t;
-	h5_loc_idx_t idx;
-	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &idx) );
-	h5_idlist_t* tv = t->adjacencies.tv.v[idx];
-
-	h5_size_t i;
 	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_loc_elem_t* el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
+	h5_loc_id_t* end = vertex_idp + tv->num_items;
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vertex_idp);
+		h5_loc_triangle_t* elem = &f->t->loc_elems.tris[elem_idx];
 
-		if ( h5tpriv_is_leaf_elem ( f, el ) == H5_NOK ) {
+		if (!h5tpriv_is_leaf_elem (f, elem)) {
 			continue;
 		}
-		TRY( h5priv_search_idlist (f, list,
-					   h5tpriv_build_entity_id (
-						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
-	}
+		TRY( add_elem2 (f, list, elem_idx) );
+	} while (++vertex_idp < end);
 	return H5_SUCCESS;
 }
 
 static inline h5_err_t
 get_triangles_uadj_to_edge (
-	h5_file_t * const f,
+	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
-	h5_idlist_t **list
+	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_loc_id_t *edge_id = children->items;
+	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_loc_id_t *edge_idp = children->items;
 	h5_loc_id_t *end = children->items+children->num_items;
-	for ( ; edge_id < end; edge_id++ ) {
-		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge_id );
-		TRY( h5priv_search_idlist (f, list,
-					   h5tpriv_build_entity_id(
-						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
-	}
-	TRY ( h5priv_free_idlist( f, &children ) );
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge_idp);
+		TRY( add_elem2 (f, list, elem_idx) );
+	} while (++edge_idp < end);
+	TRY( h5priv_free_idlist (f, &children) );
 
 	return H5_SUCCESS;
 }
 
 static inline h5_err_t
 get_edges_adj_to_edge (
-	h5_file_t * const f,
+	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
-	h5_idlist_t **list
+	h5_idlist_t** list
 	) {
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_idlist_t *children;
+	h5_idlist_t* children;
 	TRY( h5priv_alloc_idlist (f, &children, 8) );
-	TRY( compute_sections_of_edge ( f, entity_id, children ) );
+	TRY( compute_sections_of_edge (f, entity_id, &children) );
 	TRY( h5priv_alloc_idlist (f, list, 8) );
-	h5_loc_id_t* edge_id = children->items;
+	h5_loc_id_t* edge_idp = children->items;
 	h5_loc_id_t* end = children->items+children->num_items;
-	h5_idlist_t* te;
-	for (; edge_id < end; edge_id++) {
-		h5_loc_idx_t face_idx = h5tpriv_get_face_idx(*edge_id);
-		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx(*edge_id);
-		TRY( h5tpriv_find_te2 (f, face_idx, elem_idx, &te) );
-		TRY( h5priv_search_idlist (f, list, te->items[0]) );
-	}
-	
+	do {
+		TRY( add_edge (f, list, *edge_idp) );
+	} while (++edge_idp < end);
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
 }
 
 static inline h5_err_t
 get_vertices_dadj_to_edge (
-	h5_file_t * const f,
+	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
-	h5_idlist_t **list
+	h5_idlist_t** list
 	) {
-	h5_idlist_t *children;
-	TRY ( h5priv_alloc_idlist ( f, &children, 8 ) );
-	TRY( compute_sections_of_edge ( f, entity_id, children ) );
-	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
-	int i;
-	h5_loc_id_t *edge_id = children->items;
-	for ( i = 0; i < children->num_items; i++, edge_id++ ) {
-		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 ) );
+	h5_idlist_t* children;
+	TRY( h5priv_alloc_idlist (f, &children, 8) );
+	TRY( compute_sections_of_edge (f, entity_id, &children) );
+	TRY( h5priv_alloc_idlist (f, list, 8) );
+	h5_loc_id_t* edge_idp = children->items;
+	h5_loc_id_t* end = edge_idp + children->num_items;
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge_idp);
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*edge_idp);
+
+		TRY( add_vertex2 (f, list,
+				 h5tpriv_ref_elem_get_vertex_idx (
+					 f->t, 1, face_idx, 0),
+				 elem_idx) );
+		TRY( add_vertex2 (f, list,
+				 h5tpriv_ref_elem_get_vertex_idx (
+					 f->t, 1, face_idx, 1),
+				 elem_idx) );
+	} while (++edge_idp < end);
+	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
 }
 
@@ -364,17 +377,24 @@ get_vertices_dadj_to_triangle (
 		TRY( compute_sections_of_edge (
 			     f,
 			     h5tpriv_build_edge_id (face_idx, elem_idx),
-			     children) );
+			     &children) );
 	}
 	TRY ( h5priv_alloc_idlist (f, list, 8) );
 	h5_loc_id_t *edge_idp = children->items;
-	int i;
-	for ( i = 0; i < children->num_items; i++, edge_idp++ ) {
-		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] ) );
-	}
+	h5_loc_id_t *end = edge_idp + children->num_items;
+	do {
+		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*edge_idp);
+		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*edge_idp);
+
+		TRY( add_vertex2 (f, list,
+				 h5tpriv_ref_elem_get_vertex_idx (
+					 f->t, 1, face_idx, 0),
+				 elem_idx) );
+		TRY( add_vertex2 (f, list,
+				 h5tpriv_ref_elem_get_vertex_idx (
+					 f->t, 1, face_idx, 1),
+				 elem_idx) );
+	} while (++edge_idp < end);
 	TRY ( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
 }
@@ -387,23 +407,21 @@ get_edges_dadj_to_triangle (
 	) {
 	h5_idlist_t* children;
 	TRY ( h5priv_alloc_idlist (f, &children, 8) );
-
 	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	// loop over all edges of triangle
-	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++ ) {
+	h5_loc_idx_t edge_idx = h5tpriv_ref_elem_get_num_edges (f->t);
+	while (--edge_idx >= 0) {
 		TRY( compute_sections_of_edge (
 			     f,
-			     h5tpriv_build_edge_id (face_idx, elem_idx),
-			     children) );
+			     h5tpriv_build_edge_id (edge_idx, elem_idx),
+			     &children) );
 	}
 	TRY ( h5priv_alloc_idlist (f, list, 8) );
-	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) );
-	}
+	h5_loc_id_t* edge_idp = children->items;
+	h5_loc_id_t* end = edge_idp + children->num_items;
+	do {
+		TRY( add_edge (f, list, *edge_idp) );
+	} while (++edge_idp < end);
 	TRY ( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
 }

src/h5core/h5t_core_private.h

@@ -88,6 +88,8 @@
 #define h5tpriv_build_triangle_id( face_idx, elem_idx )	 \
 	( h5tpriv_build_entity_id ( H5T_TYPE_TRIANGLE, face_idx, elem_idx ) )
 
+#define h5tpriv_build_tet_id( face_idx, elem_idx )	 \
+	( h5tpriv_build_entity_id ( H5T_TYPE_TET, face_idx, elem_idx ) )
 
 
 #define h5tpriv_get_face_idx( entity_id )				\

src/h5core/h5t_hsearch.c

@@ -3,6 +3,32 @@
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
+
+h5_err_t
+h5tpriv_search_tv2 (
+	h5_file_t* const f,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
+	h5_idlist_t** idlist
+	) {
+	H5_CORE_API_ENTER;
+	h5_err_t ret_value = H5_SUCCESS;
+	h5t_fdata_t* t = f->t;
+
+	h5_loc_idx_t vertex_idx;
+	TRY2( ret_value = h5t_get_vertex_index_of_vertex2 (
+		      f,
+		      face_idx, elem_idx,
+		      &vertex_idx) );
+
+	TRY2( ret_value = h5priv_search_idlist (
+		      f,
+		      &t->adjacencies.tv.v[vertex_idx],
+		      h5tpriv_build_vertex_id (face_idx, elem_idx)) );
+
+	H5_CORE_API_RETURN (ret_value);
+}
+
 static int
 cmp_te_entries (
 	const void* __a,
@@ -18,14 +44,15 @@ compute_te_hashval (
 	const void* __item
 	) {
 	h5t_te_entry_t* item = (h5t_te_entry_t*)__item;
-	char* key = (char*)item->key.vids;
-	unsigned int count = 2 * sizeof (item->key.vids[0]);
+	uint16_t* key =  (uint16_t*)item->key.vids;
+	unsigned int count = 2*sizeof (item->key.vids[0]) / sizeof (uint16_t); 
 	unsigned int hval = count;
-	while (count-- > 0) {
-		if (key[count]) {
-			hval <<= 4;
-			hval += key[count];
+	while (count--) {
+		if (*key) {
+			hval <<= 6;
+			hval += *key;
 		}
+		key++;
 	}
 	return hval;
 }
@@ -123,8 +150,8 @@ h5tpriv_search_te2 (
 
   Passing item with type entry type.
 */
-h5_err_t
-h5tpriv_find_te (
+static inline h5_err_t
+find_te (
 	h5_file_t* const f,
 	h5t_te_entry_t* item,	// in: item to find
 	h5_idlist_t** idlist	// out: 
@@ -151,6 +178,20 @@ h5tpriv_find_te (
 
   Passing item with face and local element ID.
 */
+h5_err_t
+h5tpriv_find_te (
+	h5_file_t* const f,
+	h5_loc_idx_t edge_id,	// in
+	h5_idlist_t** idlist	// out
+	) {
+	h5t_te_entry_t item;
+	TRY( h5t_get_vertex_indices_of_edge (
+		     f,
+		     edge_id,
+		     item.key.vids) );
+	return find_te (f, &item, idlist);
+}
+
 h5_err_t
 h5tpriv_find_te2 (
 	h5_file_t* const f,
@@ -164,7 +205,7 @@ h5tpriv_find_te2 (
 		     face_idx,
 		     elem_idx,
 		     item.key.vids) );
-	return h5tpriv_find_te (f, &item, idlist);
+	return find_te (f, &item, idlist);
 }
 
 static int
@@ -177,12 +218,13 @@ cmp_td_entries (
 	return memcmp (a->key.vids, b->key.vids, sizeof(a->key.vids));
 }
 
+#if 0
 static unsigned int
 compute_td_hashval (
 	const void* __item
 	) {
 	h5t_te_entry_t* item = (h5t_te_entry_t*)__item;
-	char* key = (char*)item->key.vids;
+	unsigned char* key = (unsigned char*)item->key.vids;
 	unsigned int count = sizeof (h5_3id_t);
 	unsigned int hval = count;
 	while (count-- > 0) {
@@ -193,6 +235,25 @@ compute_td_hashval (
 	}
 	return hval;
 }
+#endif
+
+static unsigned int
+compute_td_hashval (
+	const void* __item
+	) {
+	h5t_td_entry_t* item = (h5t_td_entry_t*)__item;
+	uint16_t* key =  (uint16_t*)item->key.vids;
+	unsigned int count = 3 * sizeof (item->key.vids[0]) / sizeof (uint16_t); 
+	unsigned int hval = count;
+	while (count--) {
+		if (*key) {
+			hval <<= 6;
+			hval += *key;
+		}
+		key++;
+	}
+	return hval;
+}
 
 static h5_err_t
 release_td_entry (
@@ -276,8 +337,8 @@ h5tpriv_search_td2 (
 	return H5_SUCCESS;
 }
 
-h5_err_t
-h5tpriv_find_td (
+static inline h5_err_t
+find_td (
 	h5_file_t* const f,
 	h5t_td_entry_t* item,
 	h5_idlist_t** idlist	// out
@@ -297,6 +358,20 @@ h5tpriv_find_td (
 	return H5_SUCCESS;
 }
 
+h5_err_t
+h5tpriv_find_td (
+	h5_file_t* const f,
+	h5_loc_idx_t triangle_id,
+	h5_idlist_t** idlist
+	) {
+	h5t_td_entry_t item;
+	TRY( h5t_get_vertex_indices_of_triangle (
+		     f,
+		     triangle_id,
+		     item.key.vids) );
+	return find_td (f, &item, idlist);
+}
+
 h5_err_t
 h5tpriv_find_td2 (
 	h5_file_t* const f,
@@ -310,7 +385,7 @@ h5tpriv_find_td2 (
 		     face_idx,
 		     elem_idx,
 		     item.key.vids) );
-	return h5tpriv_find_td (f, &item, idlist);
+	return find_td (f, &item, idlist);
 }
 
 /*

src/h5core/h5t_hsearch_private.h

@@ -9,28 +9,19 @@ typedef struct h5t_td_entry_key {
 	h5_loc_idx_t vids[3];
 } h5t_td_entry_key_t;
 
-typedef struct h5t_idlisthash_key {
-	h5_loc_id_t ids[1];
-} h5t_idlisthash_key_t;
-
 /*
   List of all upward adjacent elements of same coarsness of a specific face.
   The face is specified by its local vertex IDs.
  */
 typedef struct h5_te_entry {
-	h5_idlist_t* value;
 	h5t_te_entry_key_t key;
+	h5_idlist_t* value;
 } h5t_te_entry_t;
 
 typedef struct h5_td_entry {
-	h5_idlist_t* value;
 	h5t_td_entry_key_t key;
-} h5t_td_entry_t;
-
-typedef struct h5t_idlisthash_entry {
 	h5_idlist_t* value;
-	h5t_idlisthash_key_t key;
-} h5t_idlisthash_entry_t;
+} h5t_td_entry_t;
 
 h5_err_t
 h5tpriv_resize_te_htab (
@@ -38,6 +29,14 @@ h5tpriv_resize_te_htab (
 	size_t nel
 	);
 
+h5_err_t
+h5tpriv_search_tv2 (
+	h5_file_t * const f,
+	h5_loc_idx_t face_idx,
+	h5_loc_idx_t elem_idx,
+	h5_idlist_t **entry
+	);
+
 h5_err_t
 h5tpriv_search_te2 (
 	h5_file_t * const f,
@@ -49,7 +48,7 @@ h5tpriv_search_te2 (
 h5_err_t
 h5tpriv_find_te (
 	h5_file_t * const f,
-	h5t_te_entry_t *item,
+	h5_loc_idx_t edge_id,
 	h5_idlist_t **retval
 	);
 
@@ -78,7 +77,7 @@ h5tpriv_search_td2 (
 h5_err_t
 h5tpriv_find_td (
 	h5_file_t * const f,
-	h5t_td_entry_t *item,
+	h5_loc_idx_t triangle_id,
 	h5_idlist_t **retval
 	);
 

src/h5core/h5t_map.c

@@ -176,7 +176,9 @@ h5tpriv_rebuild_elem_indices_mapping (
 	return H5_SUCCESS;
 }
 
-
+/*
+  Get local vertex indices of entity given by it's local ID.
+ */
 h5_err_t
 h5t_get_vertex_indices_of_entity (
 	h5_file_t* const f,		// in
@@ -195,10 +197,13 @@ h5t_get_vertex_indices_of_entity (
 	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];
-
+	assert (dim >= 0);
 	return h5t_get_vertex_indices_of_entity2 (f, dim, face_idx, elem_idx, vertex_indices);
 }
 
+/*
+  Get local vertex indices of entity given by it's face and local element index.
+ */
 h5_err_t
 h5t_get_vertex_indices_of_entity2 (
 	h5_file_t* const f,		// [in]
@@ -212,7 +217,7 @@ h5t_get_vertex_indices_of_entity2 (
 	int num_vertices = ref_elem->num_vertices_of_face[dim][face_idx];
 	int i;
 	for (i = 0; i < num_vertices; i++) {
-		int idx = ref_elem->map[dim][face_idx][i];
+		int idx = h5tpriv_ref_elem_get_vertex_idx(f->t, dim, face_idx, i);
 		vertex_indices[i] = indices[idx];
 	}
 	return H5_SUCCESS;
@@ -271,10 +276,12 @@ h5t_get_vertex_indices_of_edge2 (
 	h5_loc_idx_t* vertex_indices	// OUT: vertex indices
 	) {
 	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] ];
-	vertex_indices[1] = indices[ ref_elem->map[1][face_idx][1] ];
+	h5_loc_idx_t idx;
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 1, face_idx, 0); 
+ 	vertex_indices[0] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 1, face_idx, 1);
+	vertex_indices[1] = indices[idx];
 	return H5_SUCCESS;
 }
 
@@ -297,13 +304,15 @@ h5t_get_vertex_indices_of_triangle2 (
 	const h5_loc_idx_t elem_idx,
 	h5_loc_idx_t* vertex_indices
 	) {
-	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;
+	const h5_loc_idx_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
 
- 	vertex_indices[0] = indices[ ref_elem->map[2][face_idx][0] ];
-	vertex_indices[1] = indices[ ref_elem->map[2][face_idx][1] ];
-	vertex_indices[2] = indices[ ref_elem->map[2][face_idx][2] ];
+	h5_loc_idx_t idx;
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 2, face_idx, 0); 
+ 	vertex_indices[0] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 2, face_idx, 1);
+	vertex_indices[1] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 2, face_idx, 2);
+	vertex_indices[2] = indices[idx];
 
 	return H5_SUCCESS;
 }
@@ -317,12 +326,16 @@ h5t_get_vertex_indices_of_tet (
 	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] ];
-	vertex_indices[1] = indices[ ref_elem->map[3][0][1] ];
-	vertex_indices[2] = indices[ ref_elem->map[3][0][2] ];
-	vertex_indices[3] = indices[ ref_elem->map[3][0][3] ];
+	h5_loc_idx_t idx;
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 3, 0, 0); 
+ 	vertex_indices[0] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 3, 0, 1);
+	vertex_indices[1] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 3, 0, 2);
+	vertex_indices[2] = indices[idx];
+	idx = h5tpriv_ref_elem_get_vertex_idx (f->t, 3, 0, 3);
+	vertex_indices[3] = indices[idx];
 
 	return H5_SUCCESS;
 }

src/h5core/h5t_readwrite_tetm.c

@@ -14,7 +14,7 @@ init_loc_elems_struct (
 	const h5_loc_idx_t num_elems = t->num_elems[t->num_leaf_levels-1];
 	h5t_lvl_idx_t level_idx = 0;
 	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
-	int num_facets = h5tpriv_ref_elem_get_num_faces (t, 2);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (t);
 	h5_loc_tet_t* loc_elem = t->loc_elems.tets;
 	h5_glb_tet_t* glb_elem = t->glb_elems.tets;
 
@@ -69,7 +69,7 @@ init_geom_boundary_info (
 	h5t_fdata_t* const t = f->t;
 	h5_loc_idx_t elem_idx = 0;
 	const h5_loc_idx_t num_elems = t->num_elems[t->num_leaf_levels-1];
-	int num_facets = h5tpriv_ref_elem_get_num_faces (t, 2);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (t);
 	h5_loc_tet_t* loc_elem = t->loc_elems.tets;
 	h5_glb_tet_t* glb_elem = t->glb_elems.tets;
 
@@ -86,52 +86,6 @@ init_geom_boundary_info (
 		if (i == num_facets) {
 			continue; // no facet on boundary
 		}
-
-#if 0
-		// mark elements which are edge- or vertex- adjacent to the boundary
-		// are there more facets on the boundary?
-		int j;
-		for (j = i+1; j < num_facets; j++) {
-			if (loc_elem->neighbor_indices[j] == -1) {
-				break; // found another boundary facet
-			}
-		}
-		// get vertex ID's of vertices on boundary
-		h5_loc_idx_t vertex_indices[4];
-		if (j < num_facets) {
-			// all vertices on boundary
-			vertex_indices[0] = h5tpriv_build_vertex_id (0, elem_idx);
-			vertex_indices[1] = h5tpriv_build_vertex_id (1, elem_idx);
-			vertex_indices[2] = h5tpriv_build_vertex_id (2, elem_idx);
-			vertex_indices[3] = h5tpriv_build_vertex_id (3, elem_idx);
-			num_vertices = 4;
-		} else {
-			// three vertices on boundary
-			// get vertices of edge i
-			h5_loc_idx_t face_idx;
-			face_idx = t->ref_elem->map[2][i][0];
-			vertex_indices[0] = h5tpriv_get_loc_elem_vertex_idx (
-				f, elem_idx, face_idx);
-			face_idx = t->ref_elem->map[2][i][1];
-			vertex_indices[1] = h5tpriv_get_loc_elem_vertex_idx (
-				f, elem_idx, face_idx);
-			face_idx = t->ref_elem->map[2][i][2];
-			vertex_indices[2] = h5tpriv_get_loc_elem_vertex_idx (
-				f, elem_idx, face_idx);
-			num_vertices = 3;
-		}
-		// mark elements
-
-		for (i = 0; i < num_vertices; i++) {
-			const h5_loc_idx_t vertex_idx = vertex_indices[i];
-			h5_idlist_t* list = &t->adjacencies.tv.v[vertex_idx];
-			// set flag
-			for (j=0; j < list->num_items; j++) {
-				h5_loc_idx_t idx = h5tpriv_get_elem_idx (list->items[j]);
-				t->loc_elems.tris[idx].flags |= H5T_BOUNDARY_ELEM_FLAG;
-			}
-		}
-#endif
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_readwrite_trim.c

@@ -14,7 +14,7 @@ init_loc_elems_struct (
 	const h5_loc_idx_t num_elems = t->num_elems[t->num_leaf_levels-1];
 	h5t_lvl_idx_t level_idx = 0;
 	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
-	int num_facets = h5tpriv_ref_elem_get_num_faces (t,1);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (t);
 	h5_loc_triangle_t* loc_elem = t->loc_elems.tris;
 	h5_glb_triangle_t* glb_elem = t->glb_elems.tris;
 
@@ -70,7 +70,7 @@ init_geom_boundary_info (
 	h5t_fdata_t* const t = f->t;
 	h5_loc_idx_t elem_idx = 0;
 	const h5_loc_idx_t num_elems = t->num_elems[t->num_leaf_levels-1];
-	int num_facets = h5tpriv_ref_elem_get_num_faces (t, 1);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (t);
 	h5_loc_triangle_t* loc_elem = t->loc_elems.tris;
 	h5_glb_triangle_t* glb_elem = t->glb_elems.tris;
 
@@ -87,46 +87,6 @@ init_geom_boundary_info (
 		if (i == num_facets) {
 			continue; // no facet on boundary
 		}
-
-#if 0
-		// mark elements which are edge- or vertex- adjacent to the boundary
-		// are there more facets on the boundary?
-		int j;
-		for (j = i+1; j < num_facets; j++) {
-			if (loc_elem->neighbor_indices[j] == -1) {
-				break; // found another boundary facet
-			}
-		}
-		// get vertex ID's of vertices on boundary
-		h5_loc_idx_t vertex_indices[4];
-		if (j < num_facets) {
-			// all vertices on boundary
-			vertex_indices[0] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, 0);
-			vertex_indices[1] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, 1);
-			vertex_indices[2] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, 2);
-			num_vertices = 3;
-		} else {
-			// two vertices on boundary
-			// get vertices of edge i
-			h5_loc_idx_t face_idx;
-			face_idx = t->ref_elem->map[1][i][0];
-			vertex_indices[0] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx);
-			face_idx = t->ref_elem->map[1][i][1];
-			vertex_indices[1] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx);
-			num_vertices = 2;
-		}
-		// mark elements
-		for (i = 0; i < num_vertices; i++) {
-			// get upward adjacent elements
-			const h5_loc_idx_t vertex_idx = vertex_indices[i];
-			h5_idlist_t* list = &t->adjacencies.tv.v[vertex_idx];
-			// set flag
-			for (j=0; j < list->num_items; j++) {
-				h5_loc_idx_t idx = h5tpriv_get_elem_idx (list->items[j]);
-				t->loc_elems.tris[idx].flags |= H5T_BOUNDARY_ELEM_FLAG;
-			}
-		}
-#endif
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_ref_elements.c

@@ -2,6 +2,40 @@
 #include "h5_core_private.h"
 
 /*
+  information we can retrieve from the reference element:
+  - number of vertices per sub-entity (1)
+  - vertex indices of all sub-elements
+  - upward connectivity
+    - which co-dim 1 entities are connected to a given vertex
+    - which co-dim 2 entities are connected to a given vertex
+    - which co-dim 1 entities are connected to a given co-dim 2 entity
+  - downward connectivity
+  - vertex coordinates
+  
+get_conn(face, dim, dim) -> list
+
+for dim 3 reference elements:
+get_conn(0, 3, 0) -> 0, 1, 2, 3 (all vertices)
+get_conn(0, 3, 1) -> 0, 1, 2, 3, 4, 5 (all edges)
+get_conn(0, 3, 2) -> 0, 1, 2, 3 (all facets)
+get_conn(0, 3, 3) -> 0
+get_conn(i, 2, 0) -> vertices  of facet i
+get_conn(i, 2, 1) -> edges of facet i
+get_conn(i, 2, 2) -> facets connected to facet i 
+get_conn(i, 2, 3) -> 0 
+get_conn(i, 1, 0) -> vertices of edge i
+get_conn(i, 1, 1) -> edges connected to edge i
+get_conn(i, 1, 2) -> facets connected to edge i
+get_conn(i, 1, 3) -> 0
+get_conn(i, 0, 0) -> i
+get_conn(i, 0, 1) -> edges connected to vertex i
+get_conn(i, 0, 2) -> facets connected to vertex i
+get_conn(i, 0, 3) -> 0
+
+(1) For triangle and tetrahedral meshes the number of vertices is 
+identical for all sub-entities within the same dimension. This is not 
+true for other grids (like prismen)
+
   
   face: All kinds of sub-elements: vertices, edges, triangles ...
   facet: co-dim 1 face
@@ -46,20 +80,21 @@ const h5t_ref_elem_t h5t_tri_ref_elem = {
 		[1] = {2, 2, 2},		// #vertices of edges
 		[2] = {3}			// #vertices of trinagles
 	},
-	{	// map sub-elements to vertices
-		[0] = {{0}, {1}, {2}},		// 3 vertices
-		[1] = {{0,1}, {0,2}, {1,2}},	// 3 edges
-		[2] = {{0,1,2}}			// 1 triangles
-	},
-	{	// edges connected to vertex
-		[0] = {0,1},
-		[1] = {0,2},
-		[2] = {1,2}
-	},
-	{	// triangles connected to vertex
-		[0] = {0},
-		[1] = {0},
-		[2] = {0}
+	{	// connectivity
+		// vertices to vertices
+		[0][0] = {{0},     {1},     {2}},
+		// vertices to edges
+		[0][1] = {{0,1},   {0,2},   {1,2}},
+		// vertices to triangles
+		[0][2] = {{0},     {0},     {0}},
+		// edges to vertices
+		[1][0] = {{0,1},   {0,2},   {1,2}},
+		// edges to edges
+		[1][1] = {{0,1,2}, {0,1,2}, {0,1,2}},
+		// edges to triangle
+		[1][2] = {{0},     {0},     {0}},
+		// triangle to vertices
+		[2][0] = {{0,1,2}}
 	},
 	{	// coordinates
 		{0.0, 0.0},
@@ -68,7 +103,6 @@ const h5t_ref_elem_t h5t_tri_ref_elem = {
 	}
 };
 
-
 /*
  3
  **
@@ -111,23 +145,40 @@ const h5t_ref_elem_t h5t_tet_ref_elem = {
 		[2] = {3,3,3,3},	       	// #vertices of trinagles
 		[3] = {4}			// #vertices of tets
 	},
-	{	// map faces to vertices
-		[0] = {{0}, {1}, {2}, {3}},		 	  // 4 vertices
-		[1] = {{0,1}, {0,2}, {1,2}, {0,3}, {1,3}, {2,3}}, // 6 edges
-		[2] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,2,3}},	  // 4 triangles
-		[3] = {{0,1,2,3}}      				  // 1 tets
-	},
-	{	// edges connected to vertex
-		[0] = {0,1,3},
-		[1] = {0,2,4},
-		[2] = {1,2,5},
-		[3] = {3,4,5}
-	},
-	{	// triangles connected to vertex
-		[0] = {0,1,2},
-		[1] = {0,1,3},
-		[2] = {0,2,3},
-		[3] = {1,2,3}
+	{	// connectivity
+		// vertex to vertices
+		[0][0] = {{0},     {1},     {2},   {3}},
+		// vertex to edges
+		[0][1] = {{0,1,3}, {0,2,4}, {1,2,5}, {3,4,5}},
+		// vertex to triangles
+		[0][2] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,2,3}},
+		// vertex to tetrahedron
+		[0][3] = {{0},     {0},     {0},     {0}},
+		// edge to vertices
+		[1][0] = {{0,1},   {0,2},   {1,2},   {0,3},   {1,3},   {2,3}}, 
+		// edge to edges
+		[1][1] = {{0,1,2,3,4}, {0,1,2,3,5}, {0,1,2,4,5},
+			  {0,1,3,4,5}, {0,2,3,4,5}, {1,2,3,4,5}},
+		// edge to triangle
+		[1][2] = {{0,1},   {0,2},   {0,3},   {1,2},   {1,3},   {2,3}},
+		// edge to tetrahedra
+		[1][3] = {{0},     {0},     {0},     {0},     {0},     {0}},
+		// triangle to vertices
+		[2][0] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,2,3}},
+		// triangle to edges
+		[2][1] = {{0,1,2}, {0,3,4}, {1,3,5}, {2,4,5}},
+		// triangle to triangle
+		[2][2] = {{0,1,2,3}, {0,1,2,3}, {0,1,2,3}, {0,1,2,3}},
+		// tetrahedron to tetrahedron
+		[2][3] = {{0}},
+		// tetrahedron to vertices
+		[3][0] = {{0,1,2,3}},
+		// tetrahedron to edges
+		[3][1] = {{0,1,2,3,4,5}},
+		// tetrahedron to triangles
+		[3][2] = {{0,1,2,3}},
+		// tetrahedron to tetrahedron
+		[3][2] = {{0}}
 	},
 	{	// coordinates
 		{0.0, 0.0, 0.0},

src/h5core/h5t_ref_elements_private.h

@@ -2,22 +2,26 @@
 #define __H5T_REF_ELEMENTS_PRIVATE_H
 
 #define h5tpriv_ref_elem_get_num_vertices(this) (this->ref_elem->num_faces[0])
+
 #define h5tpriv_ref_elem_get_num_edges(this) (this->ref_elem->num_faces[1])
 
-#define h5tpriv_ref_elem_get_num_facets(this) \
+#define h5tpriv_ref_elem_get_num_facets(this)			\
 	(this->ref_elem->num_faces[this->ref_elem->dim - 1])
 
 #define h5tpriv_ref_elem_get_num_faces(this, dim) (this->ref_elem->num_faces[dim])
 
 #define h5tpriv_ref_elem_get_dim(this) (this->ref_elem->dim)
 
-#define h5tpriv_get_edge_connected_to_vertex(this,face_idx, i) \
-	(this->edges_connected_to_vertex[face_idx][i])
+#define h5tpriv_ref_elem_get_entity_type(this,dim)	\
+	(this->ref_elem->entity_types[dim])
 
-#define h5tpriv_get_triangles_connected_to_vertex(this,face_idx, i) \
-	(this->triangles_connected_to_vertex[face_idx][i])
+#define h5tpriv_ref_elem_get_vertex_idx(this, dim, face_idx, i)	\
+	 (this->ref_elem->connect[dim][0][face_idx][i])
 
-#define h5tpriv_ref_elem_get_entity_type(this,dim) \
-	(this->entity_types[dim])
+#define h5tpriv_ref_elem_get_edge_idx(this, dim, face_idx, i)	\
+	 (this->ref_elem->connect[dim][1][face_idx][i])
+
+#define h5tpriv_ref_elem_get_triangle_idx(this, dim, face_idx, i)	\
+	 (this->ref_elem->connect[dim][2][face_idx][i])
 
 #endif

src/h5core/h5t_retrieve.c

@@ -15,10 +15,10 @@ iter_leaf_elem_idx (
 	do {
 		iter->elem_idx++;
 		if (iter->elem_idx >= f->t->num_elems[iter->leaf_level]) {
-			return H5_NOK;
+			return H5_NOK; // done
 		}
 		el = h5tpriv_get_loc_elem (f, iter->elem_idx);
-	} while (h5tpriv_elem_is_on_level (f, el, iter->leaf_level) == H5_NOK);
+	} while (!h5tpriv_is_leaf_elem (f, el));
 	return H5_SUCCESS;
 }
 
@@ -32,8 +32,8 @@ iterate_leaf_elems (
 		h5_debug ( f, "Traversing done!" );
 		return H5_NOK;
 	}
-	int dim = it->ref_elem->dim;
-	h5_loc_id_t type_id = it->ref_elem->entity_types[dim];
+	int dim = h5tpriv_ref_elem_get_dim (it);
+	h5_loc_id_t type_id = h5tpriv_ref_elem_get_entity_type (it, dim);
 	return h5tpriv_build_entity_id (type_id, 0, it->elem_idx );
 }
 
@@ -49,8 +49,8 @@ iterate_boundary_elems (
 			return H5_NOK;
 		}
 	} while (!h5tpriv_is_boundary_elem (f, it->elem_idx));
-	int dim = it->ref_elem->dim;
-	h5_loc_id_t type_id = it->ref_elem->entity_types[dim];
+	int dim = h5tpriv_ref_elem_get_dim (it);
+	h5_loc_id_t type_id = h5tpriv_ref_elem_get_entity_type (it, dim);
 	return h5tpriv_build_entity_id (type_id, 0, it->elem_idx );
 }
 
@@ -80,7 +80,7 @@ iterate_boundary_facets (
 			it->face_idx++;
 		}
 	} while (! h5tpriv_is_boundary_facet (f, it->elem_idx, it->face_idx));
-	int type = h5tpriv_ref_elem_get_entity_type (it->ref_elem, dim);
+	int type = h5tpriv_ref_elem_get_entity_type (it, dim);
 	return h5tpriv_build_entity_id (type, it->face_idx, it->elem_idx );
 }
 
@@ -120,7 +120,7 @@ iterate_leaf_faces (
 			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_level (f, el, it->leaf_level) == H5_NOK);
+		} while (!h5tpriv_is_leaf_elem (f, el));
 
 		// 3. Face already visited if 
 	} while (it->elem_idx > h5tpriv_get_elem_idx(entry->items[i]));
@@ -130,7 +130,7 @@ iterate_leaf_faces (
 	  current level and the element index of entry->items[i] is the smallest
 	  element index with the given face on the current level.
 	*/
-	return entry->items[0];
+	return entry->items[i];
 }
 
 /*

src/h5core/h5t_retrieve_private.h

@@ -16,32 +16,9 @@ extern struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods;
   - the level_id of the element is <= the current level
   - and, if any, the direct children is on a level > the current level
 */
-static inline h5_err_t
-h5tpriv_is_leaf_elem (
-	h5_file_t* const f,
-	h5_generic_loc_elem_t *el // ptr to local element
-	) {
-	h5t_fdata_t* t = f->t;
-	if ( (el->level_idx > t->leaf_level) ||
-	     (el->child_idx >= 0 && el->child_idx < f->t->num_elems[f->t->leaf_level]) ) {
-		return H5_NOK;
-	}
-	return H5_SUCCESS;
-}
-
-static inline h5_err_t
-h5tpriv_elem_is_on_level (
-	h5_file_t* const f,
-	h5_generic_loc_elem_t *el, // ptr to local element
-	const h5t_lvl_idx_t level_idx
-	) {
-	assert ( level_idx < f->t->num_leaf_levels );
-	if ( (el->level_idx > level_idx) ||
-	     (el->child_idx >= 0 && el->child_idx < f->t->num_elems[level_idx]) ) {
-		return H5_NOK;
-	}
-	return H5_SUCCESS;
-}
+#define h5tpriv_is_leaf_elem(f, el)					\
+	( (el->level_idx <= f->t->leaf_level) &&			\
+	  (el->child_idx < 0 || el->child_idx >= f->t->num_elems[f->t->leaf_level]) )
 
 static inline h5_err_t
 h5tpriv_init_entity_iterator (

src/h5core/h5t_store_tetm.c

@@ -37,7 +37,12 @@ alloc_tets (
 	return  H5_SUCCESS;
 }
 
-
+/*
+  Return the two direct children of the edge given by face and
+  element index of first child.
+  Note: the semantic of elem_idx is a bit confusing.
+  
+ */
 static h5_err_t
 get_direct_children_of_edge (
 	h5_file_t* const f,

src/include/h5core/h5t_ref_elements.h

@@ -10,12 +10,11 @@ typedef struct {
 	int entity_types[H5T_MAX_DIM+1];
 	int num_faces[H5T_MAX_DIM+1];
 	int num_vertices_of_face[H5T_MAX_DIM+1][H5T_MAX_FACES];
-	int map[H5T_MAX_DIM+1][H5T_MAX_FACES][H5T_MAX_VERTICES];
-	int edges_connected_to_vertex[H5T_MAX_VERTICES][H5T_MAX_FACES];
-	int triangles_connected_to_vertex[H5T_MAX_VERTICES][H5T_MAX_FACES];
+	int connect[H5T_MAX_DIM+1][H5T_MAX_DIM+1][H5T_MAX_FACES][H5T_MAX_FACES];
 	h5_float64_t coords[H5T_MAX_VERTICES][H5T_MAX_DIM];
 } h5t_ref_elem_t;
 
+
 extern const h5t_ref_elem_t h5t_tet_ref_elem;
 extern const h5t_ref_elem_t h5t_tri_ref_elem;