- boundary mesh iterators implemented

- #pragma replaced with macro
- several minor changes

src/C/H5Fed.c

@@ -47,6 +47,6 @@ H5FedLinkMeshToStep (
 	h5_file_t* const f,
 	const h5_id_t mesh_id
 	) {
-#pragma unused mesh_id
+	UNUSED_ARGUMENT (mesh_id);
 	return h5_error_not_implemented (f, __FILE__, __func__, __LINE__);
 }

src/C/H5Fed_retrieve.c

@@ -31,27 +31,27 @@
   \return	H5_SUCCESS or error code
 */
 
-h5t_entity_iterator_t*
+h5t_iterator_t*
 H5FedBeginTraverseEntities (
 	h5_file_t* const f,
 	const int codim
 	) {
-	h5t_entity_iterator_t* iter;
+	h5t_iterator_t* iter;
 	H5_ENTER_API (f, __func__);
-	if (h5t_alloc_entity_iterator (f, &iter, codim) < 0) {
+	if (h5t_create_mesh_iterator (f, &iter, codim) < 0) {
 		return (void*)H5_ERR;
 	}
 	return iter;
 }
 
-h5t_entity_iterator_t*
+h5t_iterator_t*
 H5FedBeginTraverseBoundaryFaces (
 	h5_file_t* const f,
 	const int codim
 	) {
-	h5t_entity_iterator_t* iter;
+	h5t_iterator_t* iter;
 	H5_ENTER_API (f, __func__);
-	if (h5t_alloc_boundary_face_iterator (f, &iter, codim) < 0) {
+	if (h5t_create_boundary_face_iterator (f, &iter, codim) < 0) {
 		return (void*)H5_ERR;
 	}
 	return iter;
@@ -70,7 +70,7 @@ H5FedBeginTraverseBoundaryFaces (
 h5_id_t
 H5FedTraverseEntities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	) {
 	H5_ENTER_API (f, __func__);
 	return h5t_iterate_entities (f, iter);
@@ -87,7 +87,7 @@ H5FedTraverseEntities (
 h5_err_t
 H5FedEndTraverseEntities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	) {
 	H5_ENTER_API (f, __func__);
 	return h5t_release_entity_iterator (f, iter);
@@ -143,6 +143,16 @@ H5FedGetVertexIndicesOfTriangle (
 	return h5t_get_vertex_indices_of_triangle (f, entity_id, vertex_indices);
 }
 
+h5_err_t
+H5FedGetVertexIndicesOfTriangleCClockwise (
+	h5_file_t* const f,
+	h5_id_t entity_id,
+	h5_id_t* vertex_indices
+	) {
+	H5_ENTER_API (f, __func__);
+	return h5t_get_vertex_indices_of_triangle_cclockwise (f, entity_id, vertex_indices);
+}
+
 h5_err_t
 H5FedGetVertexIndicesOfTet (
 	h5_file_t* const f,

src/h5core/h5_core_private.h

@@ -42,6 +42,8 @@
 	if ((int64_t)(ptrdiff_t)(func) <= (int64_t)H5_ERR)	\
 		return H5_ERR;
 
+#define UNUSED_ARGUMENT(x) (void)x
+
 #ifdef IPL_XT3
 # define SEEK_END 2 
 #endif

src/h5core/h5_hdf5.c

@@ -620,7 +620,7 @@ get_class_type_name (
 	h5_file_t* const f,
 	hid_t base_type_id
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT(f);
 	if (base_type_id == H5_COMPOUND_T)	return "H5_COMPOUND_T";
 
 	return "[unknown]";

src/h5core/h5_hsearch.c

@@ -175,7 +175,7 @@ h5priv_hsearch (
 	unsigned int hval;
 	unsigned int idx;
 
-	/* Compute an value for the given string. Perhaps use a better method. */
+	/* Compute an value for the given key. Perhaps use a better method. */
 	hval = (*htab->compute_hash)(item);
 
 	/* First hash function: simply take the modul but prevent zero. */
@@ -186,8 +186,10 @@ h5priv_hsearch (
 		   value. */
 		if (htab->table[idx].used == hval
 		    && ((*htab->compare) (item, htab->table[idx].entry) == 0) ) {
-			    *retval = htab->table[idx].entry;
-			    return H5_SUCCESS;
+			if (retval && *retval) {
+				*retval = htab->table[idx].entry;
+			}
+			return H5_SUCCESS;
 		}
 
 		/* Second hash function, as suggested in [Knuth] */
@@ -211,7 +213,9 @@ h5priv_hsearch (
 			if (htab->table[idx].used == hval
 			    && ((*htab->compare) (
 					item, htab->table[idx].entry) == 0) ) {
-				*retval = htab->table[idx].entry;
+				if (retval && *retval) {
+					*retval = htab->table[idx].entry;
+				}
 				return H5_SUCCESS;
 			}
 		} while (htab->table[idx].used);
@@ -223,7 +227,9 @@ h5priv_hsearch (
 		   with error.  */
 		if (htab->filled == htab->size)	{
 			h5_error_internal (f, __FILE__, __func__, __LINE__);
-			*retval = NULL;
+			if (retval) {
+				*retval = NULL;
+			}
 			return H5_ERR;
 		}
 
@@ -232,7 +238,9 @@ h5priv_hsearch (
 		
 		++htab->filled;
 
-		*retval = htab->table[idx].entry;
+		if (retval && *retval) {
+			*retval = htab->table[idx].entry;
+		}
 		return H5_SUCCESS;
 	} else if (action == H5_REMOVE) {
 		htab->table[idx].used = 0;		/* mark as unused, but */
@@ -240,8 +248,8 @@ h5priv_hsearch (
 		return H5_SUCCESS;
 	}
 	*retval = NULL;
-	h5_error (f, H5_ERR_INVAL, "Key not found in hash table.");
-	return H5_ERR;
+	h5_debug (f, "Key not found in hash table.");
+	return H5_NOK;
 }
 
 h5_err_t

src/h5core/h5_maps.c

@@ -23,7 +23,7 @@ h5priv_free_idlist_items (
 	h5_file_t* const f,
 	h5_idlist_t* list
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	if (list->items != NULL) free (list->items);
 	list->items = NULL;
 	list->size = 0;
@@ -107,7 +107,7 @@ h5priv_sort_idlist_by_eid (
 	h5_file_t* const f,
 	h5_idlist_t* list
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	qsort (
 		list->items,
 		list->num_items,
@@ -126,7 +126,7 @@ h5priv_find_idlist (
 	h5_idlist_t* list,
 	h5_loc_id_t item
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	register h5_loc_idx_t low = 0;
 	register h5_loc_idx_t high = list->num_items - 1;
 	while (low <= high) {

src/h5core/h5_openclose.c

@@ -45,7 +45,7 @@ h5priv_error_handler (
 	hid_t estack_id,
 	void* __f
 	) {
-#pragma unused __f
+	UNUSED_ARGUMENT (__f);
 	if (h5_get_debuglevel() >= 5) {
 		H5Eprint (estack_id, stderr);
 	}
@@ -145,7 +145,7 @@ open_file (
 	) {
 
 #if !defined(PARALLEL_IO)
-#pragma unused comm
+	UNUSED_ARGUMENT (f);
 #endif
 
 	h5_info (f, "Opening file %s.", filename);
@@ -415,10 +415,10 @@ h5_get_stepname_fmt (
 	int l_name,			/*!< length of buffer name	*/
 	int* width			/*!< OUT: Width of the number	*/
 	) {
-#pragma unused f
-#pragma unused name
-#pragma unused l_name
-#pragma unused width
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (name);
+	UNUSED_ARGUMENT (l_name);
+	UNUSED_ARGUMENT (width);
 	return h5_error_not_implemented (f, __FILE__, __func__, __LINE__);
 }
 

src/h5core/h5_syscall.c

@@ -1,5 +1,6 @@
 #include <stdlib.h>
 #include <search.h>
+#include <strings.h>
 
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
@@ -36,6 +37,19 @@ h5priv_calloc (
 	return ptr;
 }
 
+char*
+h5priv_strdup (
+	h5_file_t* const f,
+	const char* s1
+	) {
+	char* s2 = strdup (s1);
+	if (s2 == NULL) {
+		h5_error (f, H5_ERR_NOMEM, "Out of memory.");
+		return (void*)(H5_ERR);
+	}
+	return s2;
+}
+
 h5_err_t
 h5priv_free (
 	h5_file_t* const f,
@@ -70,7 +84,7 @@ h5priv_tfind (
 	void* const* rootp,
 	int (*compar) (const void* key1, const void* key2) 
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	void* ptr = tfind (key, rootp, compar);
 	if (ptr == NULL) {
 		return (void*)(H5_ERR);

src/h5core/h5_syscall_private.h

@@ -21,6 +21,11 @@ h5priv_free (
 	void* ptr
 	);
 
+char*
+h5priv_strdup (
+	h5_file_t* const f,
+	const char* s1
+	);
 void*
 h5priv_tsearch (
 	h5_file_t* const f,

src/h5core/h5t_access_private.h

@@ -1,6 +1,73 @@
 #ifndef __H5T_ACCESS_PRIVATE_H
 #define __H5T_ACCESS_PRIVATE_H
 
+struct h5t_access_methods {
+	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);
+	h5t_lvl_idx_t (*get_loc_elem_level_idx)(
+		h5_file_t* const, const h5_loc_idx_t);
+	h5t_lvl_idx_t (*set_loc_elem_level_idx)(
+		h5_file_t* const, const h5_loc_idx_t, const h5t_lvl_idx_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_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);
+	h5_err_t (*set_boundary_elem_flag)(h5_file_t* const, const h5_loc_idx_t);
+	h5_err_t (*clear_boundary_elem_flag)(h5_file_t* const, const h5_loc_idx_t);
+	h5_err_t (*set_boundary_facet_flag)(h5_file_t* const, const h5_loc_idx_t);
+	h5_err_t (*clear_boundary_facet_flag)(h5_file_t* const, const h5_loc_idx_t);
+	int (*is_boundary_elem)(h5_file_t* const, const h5_loc_idx_t);
+	int (*is_boundary_facet)(h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
+	int (*is_boundary_face)(h5_file_t* const, const int, const h5_loc_idx_t, const h5_loc_idx_t);
+};
+
 extern struct h5t_access_methods h5tpriv_access_trim_methods;
 extern struct h5t_access_methods h5tpriv_access_tetm_methods;
 

src/h5core/h5t_access_tetm.c

@@ -249,6 +249,15 @@ set_boundary_elem_flag (
 	return H5_SUCCESS;
 }
 
+static h5_err_t
+set_boundary_facet_flag (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	f->t->loc_elems.tets[elem_idx].flags |= H5T_BOUNDARY_FACET_FLAG;
+	return H5_SUCCESS;
+}
+
 static h5_err_t
 clear_boundary_elem_flag (
 	h5_file_t* const f,
@@ -258,6 +267,14 @@ clear_boundary_elem_flag (
 	return H5_SUCCESS;
 }
 
+static h5_err_t
+clear_boundary_facet_flag (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	f->t->loc_elems.tets[elem_idx].flags &= ~H5T_BOUNDARY_FACET_FLAG;
+	return H5_SUCCESS;
+}
 
 static int
 is_boundary_elem  (
@@ -283,10 +300,11 @@ is_boundary_face (
 	const h5_loc_idx_t elem_idx,
 	const h5_loc_idx_t facet_idx
 	) {
-#pragma unused f
-#pragma unused dim
-#pragma unused elem_idx
-#pragma unused facet_idx
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dim);
+	UNUSED_ARGUMENT (elem_idx);
+	UNUSED_ARGUMENT (facet_idx);
+
 	return h5_error_internal (f, __FILE__, __func__, __LINE__);
 }
 
@@ -319,6 +337,8 @@ struct h5t_access_methods h5tpriv_access_tetm_methods = {
 	set_glb_elem_neighbor_idx,
 	set_boundary_elem_flag,
 	clear_boundary_elem_flag,
+	set_boundary_facet_flag,
+	clear_boundary_facet_flag,
 	is_boundary_elem,
 	is_boundary_facet,
 	is_boundary_face,

src/h5core/h5t_access_trim.c

@@ -240,7 +240,6 @@ set_glb_elem_neighbor_idx (
 	return neighbor_idx;
 }
 
-
 static h5_err_t
 set_boundary_elem_flag (
 	h5_file_t* const f,
@@ -250,6 +249,15 @@ set_boundary_elem_flag (
 	return H5_SUCCESS;
 }
 
+static h5_err_t
+set_boundary_facet_flag (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	f->t->loc_elems.tris[elem_idx].flags |= H5T_BOUNDARY_FACET_FLAG;
+	return H5_SUCCESS;
+}
+
 static h5_err_t
 clear_boundary_elem_flag (
 	h5_file_t* const f,
@@ -259,6 +267,14 @@ clear_boundary_elem_flag (
 	return H5_SUCCESS;
 }
 
+static h5_err_t
+clear_boundary_facet_flag (
+	h5_file_t* const f,
+	h5_loc_idx_t elem_idx
+	) {
+	f->t->loc_elems.tris[elem_idx].flags &= ~H5T_BOUNDARY_FACET_FLAG;
+	return H5_SUCCESS;
+}
 
 static int
 is_boundary_elem  (
@@ -284,10 +300,10 @@ is_boundary_face (
 	const h5_loc_idx_t elem_idx,
 	const h5_loc_idx_t facet_idx
 	) {
-#pragma unused f
-#pragma unused dim
-#pragma unused elem_idx
-#pragma unused facet_idx
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dim);
+	UNUSED_ARGUMENT (elem_idx);
+	UNUSED_ARGUMENT (facet_idx);
 	return h5_error_internal (f, __FILE__, __func__, __LINE__);
 }
 
@@ -320,6 +336,8 @@ struct h5t_access_methods h5tpriv_access_trim_methods = {
 	set_glb_elem_neighbor_idx,
 	set_boundary_elem_flag,
 	clear_boundary_elem_flag,
+	set_boundary_facet_flag,
+	clear_boundary_facet_flag,
 	is_boundary_elem,
 	is_boundary_facet,
 	is_boundary_face,

src/h5core/h5t_adjacencies_private.h

@@ -1,6 +1,14 @@
 #ifndef __H5T_ADJACENCIES_PRIVATE_H
 #define __H5T_ADJACENCIES_PRIVATE_H
 
+struct h5t_adjacency_methods {
+	h5_err_t (*update_internal_structs)(h5_file_t* const, h5t_lvl_idx_t);
+	h5_err_t (*release_internal_structs)(h5_file_t* const);
+	h5_err_t (*get_adjacencies)(
+		h5_file_t * const,
+		const h5_loc_id_t, const h5_int32_t, h5_idlist_t**);
+};
+
 extern struct h5t_adjacency_methods h5tpriv_trim_adjacency_methods;
 extern struct h5t_adjacency_methods h5tpriv_tetm_adjacency_methods;
 

src/h5core/h5t_adjacencies_tetm.c

@@ -84,7 +84,7 @@ static inline h5_err_t
 release_te (
 	h5_file_t* const f
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	// @@@ TBD @@@
 	return H5_SUCCESS;
 }
@@ -117,7 +117,7 @@ static inline h5_err_t
 release_td (
 	h5_file_t* const f
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	// @@@ TBD @@@
 	return H5_SUCCESS;
 }
@@ -824,13 +824,13 @@ get_adjacencies (
 	) {
 	h5_loc_id_t entity_type = h5tpriv_get_entity_type (entity_id);
 	switch (entity_type) {
-	case H5T_ETYPE_VERTEX:
+	case H5T_TYPE_VERTEX:
 		return get_adjacencies_to_vertex (f, entity_id, dim, list);
-	case H5T_ETYPE_EDGE:
+	case H5T_TYPE_EDGE:
 		return get_adjacencies_to_edge (f, entity_id, dim, list);
-	case H5T_ETYPE_TRIANGLE:
+	case H5T_TYPE_TRIANGLE:
 		return get_adjacencies_to_triangle (f, entity_id, dim, list);
-	case H5T_ETYPE_TET:
+	case H5T_TYPE_TET:
 		return get_adjacencies_to_tet (f, entity_id, dim, list);
 	default:
 		break;

src/h5core/h5t_adjacencies_trim.c

@@ -86,7 +86,7 @@ static inline h5_err_t
 release_te (
 	h5_file_t* const f
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	// @@@ TBD @@@
 	return H5_SUCCESS;
 }
@@ -276,7 +276,9 @@ get_triangles_uadj_to_vertex (
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_NOK ) {
 			continue;
 		}
-		TRY ( h5priv_search_idlist ( f, *list, elem_idx ) );
+		TRY( h5priv_search_idlist (f, *list,
+					   h5tpriv_build_entity_id (
+						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
 	}
 	return H5_SUCCESS;
 }
@@ -295,13 +297,40 @@ get_triangles_uadj_to_edge (
 	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, elem_idx ) );
+		TRY( h5priv_search_idlist (f, *list,
+					   h5tpriv_build_entity_id(
+						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
 	}
 	TRY ( h5priv_free_idlist( f, &children ) );
 
 	return H5_SUCCESS;
 }
 
+static inline h5_err_t
+get_edges_adj_to_edge (
+	h5_file_t * const f,
+	const h5_loc_id_t entity_id,
+	h5_idlist_t **list
+	) {
+	TRY( h5priv_alloc_idlist (f, list, 8) );
+	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_id = 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]) );
+	}
+	
+	TRY( h5priv_free_idlist(f, &children) );
+	return H5_SUCCESS;
+}
+
 static inline h5_err_t
 get_vertices_dadj_to_edge (
 	h5_file_t * const f,
@@ -426,6 +455,8 @@ get_adjacencies_to_edge (
 	switch (dim) {
 	case 0:
 		return get_vertices_dadj_to_edge(f, entity_id, list);
+	case 1:
+		return get_edges_adj_to_edge(f, entity_id, list);
 	case 2:
 		return get_triangles_uadj_to_edge(f, entity_id, list);
 	default:
@@ -459,11 +490,11 @@ get_adjacencies (
 	) {
 	h5_loc_id_t entity_type = h5tpriv_get_entity_type (entity_id);
 	switch (entity_type) {
-	case H5T_ETYPE_VERTEX:
+	case H5T_TYPE_VERTEX:
 		return get_adjacencies_to_vertex (f, entity_id, dim, list);
-	case H5T_ETYPE_EDGE:
+	case H5T_TYPE_EDGE:
 		return get_adjacencies_to_edge (f, entity_id, dim, list);
-	case H5T_ETYPE_TRIANGLE:
+	case H5T_TYPE_TRIANGLE:
 		return get_adjacencies_to_triangle (f, entity_id, dim, list);
 	default:
 		break;

src/h5core/h5t_core_private.h

@@ -46,14 +46,13 @@
 
 */
 #define H5T_ELEM_MASK		( (h5_id_t) (ULLONG_MAX >> 8) )
-#define H5T_ETYPE_MASK		( 7ull << (sizeof(h5_id_t)*8-4) )
-#define H5T_COMPONENT_MASK	(~H5T_ELEM_MASK)
-#define H5T_COMPONENT_ID_MASK	(15ull << (sizeof(h5_id_t)*7) )
+#define H5T_TYPE_MASK		( 7ull << (sizeof(h5_id_t)*7+4) )
+#define H5T_FACE_MASK		(15ull << (sizeof(h5_id_t)*7) )
 
-#define H5T_ETYPE_VERTEX	(1)
-#define H5T_ETYPE_EDGE		(2)
-#define H5T_ETYPE_TRIANGLE	(3)
-#define H5T_ETYPE_TET		(4)
+#define H5T_TYPE_VERTEX		(1)
+#define H5T_TYPE_EDGE		(2)
+#define H5T_TYPE_TRIANGLE	(3)
+#define H5T_TYPE_TET		(4)
 
 #define h5tpriv_set_entity_type( type, elem_idx )		\
 	(							\
@@ -61,35 +60,48 @@
 		((h5_id_t)(elem_idx))				\
 		)
 #define h5tpriv_get_entity_type( entity_id )			\
-	((entity_id & H5T_ETYPE_MASK) >> (sizeof(h5_id_t)*8-4))
+	((entity_id & H5T_TYPE_MASK) >> (sizeof(h5_id_t)*8-4))
 
 
-#define h5tpriv_build_id( type, face_idx, elem_idx )		\
+#define h5tpriv_build_entity_id( type, face_idx, elem_idx )		\
 	(							\
 		((h5_id_t)(type) << (sizeof(h5_id_t)*8-4)) |	\
 		((h5_id_t)(face_idx) << (sizeof(h5_id_t)*7)) |	\
 		((h5_id_t)(elem_idx) & H5T_ELEM_MASK)		\
 		)
 
+#define h5tpriv_build_entity_id2( face_id, elem_idx )			\
+	(							\
+		((h5_id_t)(face_id) << (sizeof(h5_id_t)*7)) |	\
+		((h5_id_t)(elem_idx) & H5T_ELEM_MASK)		\
+		)
+
+#define h5tpriv_build_face_id( type_id, face_idx )	\
+	(type_id << 4 | face_idx)
+
 #define h5tpriv_build_vertex_id( face_idx, elem_idx )			\
-	( h5tpriv_build_id ( H5T_ETYPE_VERTEX, face_idx, elem_idx ) )
+	( h5tpriv_build_entity_id ( H5T_TYPE_VERTEX, face_idx, elem_idx ) )
 
 #define h5tpriv_build_edge_id( face_idx, elem_idx )			\
-	( h5tpriv_build_id ( H5T_ETYPE_EDGE, face_idx, elem_idx ) )
+	( h5tpriv_build_entity_id ( H5T_TYPE_EDGE, face_idx, elem_idx ) )
 
 #define h5tpriv_build_triangle_id( face_idx, elem_idx )	 \
-	( h5tpriv_build_id ( H5T_ETYPE_TRIANGLE, face_idx, elem_idx ) )
+	( h5tpriv_build_entity_id ( H5T_TYPE_TRIANGLE, face_idx, elem_idx ) )
 
 #define h5tpriv_build_elem_id( elem_idx )				\
-	( h5tpriv_build_id ( f->t->mesh_type, 0, elem_idx ) )
+	( h5tpriv_build_entity_id ( f->t->mesh_type, 0, elem_idx ) )
 
 #define h5tpriv_get_face_idx( entity_id )				\
-	( (entity_id & H5T_COMPONENT_ID_MASK) >> (sizeof(h5_id_t)*7) )
+	( (entity_id & H5T_FACE_MASK) >> (sizeof(h5_id_t)*7) )
 
-#define h5tpriv_get_elem_idx( entity_id )		\
+#define h5tpriv_get_face_id( entity_id )				\
+	( (entity_id & (H5T_TYPE_MASK|H5T_FACE_MASK)) >> (sizeof(h5_id_t)*7) )
+
+#define h5tpriv_get_elem_idx( entity_id )	\
 	( entity_id & H5T_ELEM_MASK )
 
-
 #define H5T_BOUNDARY_ELEM_FLAG 1
+#define H5T_BOUNDARY_FACET_FLAG 2
+
 
 #endif

src/h5core/h5t_errorhandling_private.h

@@ -28,6 +28,19 @@ h5tpriv_error_local_elem_nexist (
 	return h5_error (f, H5_ERR_NOENTRY, ERR_ELEM_NEXIST, s);
 }
 
+static inline h5_err_t
+h5tpriv_inval_codim (
+	h5_file_t * const f,
+	int codim,
+	int min_codim,
+	int max_codim
+	) {
+	return h5_error (f, H5_ERR_INVAL,
+			 "Co-dimension %d requested, "
+			 "but must be between %d and %d",
+			 codim, min_codim, max_codim);
+}
+
 #define h5tpriv_error_undef_mesh( f )		\
 	h5_error(				\
 		f,				\

src/h5core/h5t_inquiry.c

@@ -85,7 +85,7 @@ h5t_get_num_elems (
 	h5_file_t* const f,
 	const h5_id_t cnode
 	) {
-#pragma unused cnode
+	UNUSED_ARGUMENT (cnode);
 	h5t_fdata_t* t = f->t;
 
 	if (t->cur_mesh < 0) {
@@ -115,7 +115,7 @@ h5t_get_num_vertices (
 	h5_file_t* const f,
 	h5_id_t cnode
 	) {
-#pragma unused cnode
+	UNUSED_ARGUMENT (cnode);
 	h5t_fdata_t* t = f->t;
 
 	if (t->cur_mesh < 0) {

src/h5core/h5t_map.c

@@ -290,6 +290,22 @@ h5t_get_vertex_indices_of_triangle (
 		f, face_idx, elem_idx, vertex_indices);
 }
 
+h5_err_t
+h5t_get_vertex_indices_of_triangle_cclockwise (
+	h5_file_t* const f,
+	const h5_loc_id_t entity_id,
+	h5_loc_idx_t* vertex_indices
+	) {
+	TRY( h5t_get_vertex_indices_of_triangle (f, entity_id, vertex_indices) );
+	h5_float64_t P0[3];
+	h5_float64_t P1[3];
+	h5_float64_t P2[3];
+	TRY( h5t_get_vertex_coords_by_index (f, vertex_indices[0], P0) );
+	TRY( h5t_get_vertex_coords_by_index (f, vertex_indices[1], P1) );
+	TRY( h5t_get_vertex_coords_by_index (f, vertex_indices[2], P2) );
+
+}
+
 h5_err_t
 h5t_get_vertex_indices_of_triangle2 (
 	h5_file_t* const f,

src/h5core/h5t_openclose.c

@@ -365,7 +365,7 @@ h5_err_t
 h5tpriv_init_step (
 	h5_file_t* const f
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	return H5_SUCCESS;
 }
 
@@ -378,7 +378,7 @@ h5_err_t
 h5tpriv_close_step (
 	h5_file_t* const f
 	) {
-#pragma unused f
+	UNUSED_ARGUMENT (f);
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_readwrite.c

@@ -6,8 +6,8 @@ open_space_all (
 	h5_file_t* const f,
 	const hid_t dataset_id
 	) {
-#pragma unused f
-#pragma unused dataset_id
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dataset_id);
 	return H5S_ALL;
 }
 
@@ -125,8 +125,8 @@ open_mem_space_vertices (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
-#pragma unused f
-#pragma unused dataset_id
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dataset_id);
 	return H5S_ALL;
 }
 
@@ -135,8 +135,8 @@ open_file_space_vertices (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
-#pragma unused f
-#pragma unused dataset_id
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dataset_id);
 	return H5S_ALL;
 }
 
@@ -218,8 +218,8 @@ open_mem_space_elems (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
-#pragma unused f
-#pragma unused dataset_id
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dataset_id);
 	return H5S_ALL;
 }
 
@@ -228,8 +228,8 @@ open_file_space_elems (
 	h5_file_t* const f,
 	hid_t dataset_id
 	) {
-#pragma unused f
-#pragma unused dataset_id
+	UNUSED_ARGUMENT (f);
+	UNUSED_ARGUMENT (dataset_id);
 	return H5S_ALL;
 }
 
@@ -281,7 +281,7 @@ h5tpriv_read_mesh (
 
 	TRY( read_elems (f) );
 	TRY( h5tpriv_rebuild_elem_indices_mapping (f) );
-	TRY( h5tpriv_init_loc_elems_struct (f) );
+	TRY( h5tpriv_init_loc_elems_struct (f, 0) );
 	TRY( h5tpriv_update_adjacency_structs (f, 0) );
 	TRY( h5tpriv_init_geom_boundary_info (f, 0) );
 

src/h5core/h5t_readwrite_private.h

@@ -1,6 +1,14 @@
 #ifndef __H5T_READWRITE_PRIVATE_H
 #define __H5T_READWRITE_PRIVATE_H
 
+struct h5t_read_methods {
+	h5_err_t (*init_loc_elems_struct)(h5_file_t* const, h5t_lvl_idx_t);
+	h5_err_t (*init_geom_boundary_info)(h5_file_t* const, h5t_lvl_idx_t);
+};
+
+extern struct h5t_read_methods h5tpriv_read_trim_methods;
+extern struct h5t_read_methods h5tpriv_read_tetm_methods;
+
 h5_err_t
 h5tpriv_write_obj (
 	h5_file_t * f,
@@ -22,14 +30,13 @@ h5tpriv_write_mesh (
 	h5_file_t * const f
 	);
 
-extern struct h5t_read_methods h5tpriv_read_trim_methods;
-extern struct h5t_read_methods h5tpriv_read_tetm_methods;
 
 static inline h5_err_t
 h5tpriv_init_loc_elems_struct (
-	h5_file_t* const f
+	h5_file_t* const f,
+	const h5t_lvl_idx_t from_lvl
 	) {
-	return (*f->t->methods.read->init_loc_elems_struct) (f);
+	return (*f->t->methods.read->init_loc_elems_struct) (f, from_lvl);
 }
 
 static inline h5_err_t

src/h5core/h5t_readwrite_tetm.c

@@ -6,7 +6,8 @@
 */
 static h5_err_t
 init_loc_elems_struct (
-	h5_file_t* const f
+	h5_file_t* const f,
+	const h5t_lvl_idx_t from_lvl
 	) {
 	h5t_fdata_t* const t = f->t;
 	h5_loc_idx_t elem_idx = 0;
@@ -17,7 +18,7 @@ init_loc_elems_struct (
 	h5_loc_tet_t* loc_elem = t->loc_elems.tets;
 	h5_glb_tet_t* glb_elem = t->glb_elems.tets;
 
-	for (elem_idx = 0;
+	for (elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
 	     elem_idx < num_elems; elem_idx++, loc_elem++, glb_elem++) {
 		// global element index
 		loc_elem->glb_idx = glb_elem->idx;
@@ -48,7 +49,9 @@ init_loc_elems_struct (
 			     glb_elem->neighbor_indices,
 			     num_facets,
 			     loc_elem->neighbor_indices) );
-		// on boundary?
+#if 0
+		// done in function below
+                // on boundary?
 		int i;
 		for (i=0; i < num_facets; i++) {
 			if (loc_elem->neighbor_indices[i] == -1) {
@@ -56,6 +59,7 @@ init_loc_elems_struct (
 				break;
 			}
 		}
+#endif
 	}
 	return H5_SUCCESS;
 }
@@ -109,11 +113,14 @@ init_geom_boundary_info (
 			// 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);
+			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);
+			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);
+			vertex_indices[2] = h5tpriv_get_loc_elem_vertex_idx (
+				f, elem_idx, face_idx);
 			num_vertices = 3;
 		}
 		// mark elements

src/h5core/h5t_readwrite_trim.c

@@ -6,10 +6,11 @@
 */
 static h5_err_t
 init_loc_elems_struct (
-	h5_file_t* const f
+	h5_file_t* const f,
+	const h5t_lvl_idx_t from_lvl
 	) {
 	h5t_fdata_t* const t = f->t;
-	h5_loc_idx_t idx = 0;
+	h5_loc_idx_t elem_idx = 0;
 	const h5_loc_idx_t num_elems = t->num_elems[t->num_levels-1];
 	h5t_lvl_idx_t level_idx = 0;
 	int num_vertices = h5tpriv_ref_elem_get_num_vertices (t);
@@ -17,7 +18,8 @@ init_loc_elems_struct (
 	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++) {
+	for (elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	     elem_idx < num_elems; elem_idx++, loc_elem++, glb_elem++) {
 		// global element index
 		loc_elem->glb_idx = glb_elem->idx;
 		// local parent index
@@ -29,7 +31,7 @@ init_loc_elems_struct (
 		     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->level_idx = level_idx;
@@ -47,6 +49,7 @@ init_loc_elems_struct (
 			     glb_elem->neighbor_indices,
 			     num_facets,
 			     loc_elem->neighbor_indices) );
+#if 0
 		// on boundary?
 		int i;
 		for (i=0; i < num_facets; i++) {
@@ -55,6 +58,7 @@ init_loc_elems_struct (
 				break;
 			}
 		}
+#endif
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_ref_elements.c

@@ -32,9 +32,9 @@
 const h5t_ref_elem_t h5t_tri_ref_elem = {
 	2,					// dimension
 	{
-		H5T_ETYPE_VERTEX,
-		H5T_ETYPE_EDGE,
-		H5T_ETYPE_TRIANGLE,
+		H5T_TYPE_VERTEX,
+		H5T_TYPE_EDGE,
+		H5T_TYPE_TRIANGLE,
 	},
 	{
 		3,				// #vertices
@@ -94,10 +94,10 @@ const h5t_ref_elem_t h5t_tri_ref_elem = {
 const h5t_ref_elem_t h5t_tet_ref_elem = {
 	3,					// dimension
 	{
-		H5T_ETYPE_VERTEX,
-		H5T_ETYPE_EDGE,
-		H5T_ETYPE_TRIANGLE,
-		H5T_ETYPE_TET,
+		H5T_TYPE_VERTEX,
+		H5T_TYPE_EDGE,
+		H5T_TYPE_TRIANGLE,
+		H5T_TYPE_TET,
 	},
 	{
 		4,				// #vertices

src/h5core/h5t_retrieve.c

@@ -3,53 +3,31 @@
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
-#define num_elems_on_cur_level	f->t->num_elems[f->t->cur_level]
-
 /*
   Skip elements which have been refined on a level <= the current one.
 */
-h5_err_t
-h5tpriv_skip_to_next_elem_on_level (
+static h5_err_t
+skip_to_next_elem_on_level (
 	h5_file_t* f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
 	h5_generic_loc_elem_t* el;
 	do {
 		iter->elem_idx++;
-		if (iter->elem_idx >= num_elems_on_cur_level) {
+		if (iter->elem_idx >= f->t->num_elems[iter->level_idx]) {
 			return H5_NOK;
 		}
 		el = h5tpriv_get_loc_elem (f, iter->elem_idx);
-	} while (h5tpriv_elem_is_on_cur_level (f, el) == H5_NOK);
+	} while (h5tpriv_elem_is_on_level (f, el, iter->level_idx) == H5_NOK);
 	return H5_SUCCESS;
 }
 
-
-/*
-  Test whether given element is on current level. This is the case, if
-  - the level_id of the element is <= the current level
-  - and, if any, the direct children is on a level > the current level
-*/
-h5_err_t
-h5tpriv_elem_is_on_cur_level (
-	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->cur_level) ||
-	     (el->child_idx >= 0 && el->child_idx < num_elems_on_cur_level) ) {
-		return H5_NOK;
-	}
-	return H5_SUCCESS;
-}
-
-
 static h5_loc_id_t
 iterate_elems (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
-	if ( h5tpriv_skip_to_next_elem_on_level (f, iter) == H5_NOK) {
+	if ( skip_to_next_elem_on_level (f, iter) == H5_NOK) {
 		h5_debug ( f, "Traversing done!" );
 		return H5_NOK;
 	}
@@ -59,10 +37,10 @@ iterate_elems (
 static h5_loc_id_t
 iterate_boundary_elems (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
 	do {
-		if ( h5tpriv_skip_to_next_elem_on_level (f, iter) == H5_NOK) {
+		if ( skip_to_next_elem_on_level (f, iter) == H5_NOK) {
 			h5_debug ( f, "Traversing done!" );
 			return H5_NOK;
 		}
@@ -78,7 +56,7 @@ iterate_boundary_elems (
 static h5_loc_id_t
 iterate_boundary_facets (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
 	int num_facets = h5tpriv_ref_elem_get_num_facets (iter) - 1;
 	int dim = h5tpriv_ref_elem_get_dim (iter) - iter->codim;
@@ -96,7 +74,7 @@ iterate_boundary_facets (
 		}
 	} while (! h5tpriv_is_boundary_facet (f, iter->elem_idx, iter->face_idx));
 	int type = h5tpriv_ref_elem_get_entity_type (iter->ref_elem, dim);
-	return h5tpriv_build_id (type, iter->face_idx, iter->elem_idx );
+	return h5tpriv_build_entity_id (type, iter->face_idx, iter->elem_idx );
 }
 
 /*!
@@ -105,7 +83,7 @@ iterate_boundary_facets (
 static h5_loc_id_t
 iterate_faces (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
 	h5_idlist_t* entry;
 	int dim = h5tpriv_ref_elem_get_dim (iter) - iter->codim;
@@ -113,7 +91,7 @@ iterate_faces (
 	int i = -1;
 	do {
 		if (iter->face_idx >= num_faces) {
-			if (h5tpriv_skip_to_next_elem_on_level (f, iter) == H5_NOK) {
+			if (skip_to_next_elem_on_level (f, iter) == H5_NOK) {
 				h5_debug (f, "Traversing done!");
 				return H5_NOK;
 			}
@@ -134,7 +112,7 @@ iterate_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_cur_level (f, el) == H5_NOK);
+		} while (h5tpriv_elem_is_on_level (f, el, iter->level_idx) == H5_NOK);
 
 		// 3. Face already visited if 
 	} while (iter->elem_idx > h5tpriv_get_elem_idx(entry->items[i]));
@@ -153,7 +131,7 @@ iterate_faces (
 static h5_loc_id_t
 iterate_boundary_faces (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_mesh_iterator_t* iter
 	) {
 	// TODO!!!
 	int dim = h5tpriv_ref_elem_get_dim (iter) - iter->codim;
@@ -173,87 +151,123 @@ iterate_boundary_faces (
 			} else {
 				iter->face_idx++;
 			}
-		} while (! h5tpriv_is_boundary_face (f, dim, iter->elem_idx, iter->face_idx));
+		} while (! h5tpriv_is_boundary_face (
+				 f, dim, iter->elem_idx, iter->face_idx));
 		// Skip already visited faces
 	} while (0);
 	return h5_error_internal (f, __FILE__, __func__, __LINE__);
 }
 
-h5_err_t
-h5t_alloc_entity_iterator (
-	h5_file_t* f,
-	h5t_entity_iterator_t** iter,
-	int codim
+static h5_loc_id_t
+iterate_tags (
+	h5_file_t* const f,
+	h5t_tag_iterator_t* iter
 	) {
-	TRY( *iter = h5priv_alloc (f, NULL, sizeof (h5t_entity_iterator_t)) );
-	return h5t_begin_iterate_entities (f, *iter, codim);
+	UNUSED_ARGUMENT (f);
+#if 0
+	h5t_tagsel_t* tags;
+	do {
+		if (iter->subentity_idx >= 14) {
+			iter->elem_idx++;
+			iter->subentity_idx = 0;
+		} else {
+			iter->subentity_idx++;
+		}
+		tags = iter->tagset->elems[iter->elem_idx];
+	} while ((tags == NULL) || (tags->idx[iter->subentity_idx]));
+#endif	
+	return 0;
 }
 
 h5_err_t
-h5t_alloc_boundary_face_iterator (
+h5t_init_mesh_iterator (
 	h5_file_t* f,
-	h5t_entity_iterator_t** iter,
+	h5t_iterator_t* iter,
 	int codim
 	) {
-	TRY( *iter = h5priv_alloc (f, NULL, sizeof (h5t_entity_iterator_t)) );
-	return h5t_begin_iterate_boundary_faces (f, *iter, codim);
+	h5t_mesh_iterator_t* it = (h5t_mesh_iterator_t*)iter;
+	it->face_idx = 999;
+	it->elem_idx = -1;
+	it->codim = codim;
+	it->level_idx = f->t->cur_level;
+	it->ref_elem = f->t->ref_elem;
+
+	if (it->codim > 0) {
+		it->iter = iterate_faces;
+	} else if (it->codim == 0) {
+		it->iter = iterate_elems;
+	}
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5t_create_mesh_iterator (
+	h5_file_t* f,
+	h5t_iterator_t** iter,
+	int codim
+	) {
+	h5t_mesh_iterator_t* it;
+	TRY( it = h5priv_calloc (f, 1, sizeof (h5t_mesh_iterator_t)) );
+	TRY( h5t_init_mesh_iterator (f, (h5t_iterator_t*)it, codim) );
+	*iter =  (h5t_iterator_t*)it;
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5t_create_boundary_face_iterator (
+	h5_file_t* f,
+	h5t_iterator_t** iter,
+	int codim
+	) {
+	h5t_mesh_iterator_t* it;
+	TRY( it = h5priv_calloc (f, 1, sizeof (h5t_mesh_iterator_t)) );
+	it->face_idx = 999; // just a high enough number
+	it->elem_idx = -1;
+	it->codim = codim;
+	it->level_idx = f->t->cur_level;
+	it->ref_elem = f->t->ref_elem;
+
+	if (it->codim <= 0 || it->codim > it->ref_elem->dim) {
+		return h5tpriv_inval_codim (f, codim, 1, it->ref_elem->dim);
+	} else if (it->codim == 1) {
+		it->iter = iterate_boundary_facets;
+	}
+	else if (it->codim > 1) {
+		it->iter = iterate_boundary_faces;
+	}
+	*iter =  (h5t_iterator_t*)it;
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5t_create_mtag_iterator (
+	h5_file_t* f,
+	h5t_iterator_t** iter,
+	const char* name
+	) {
+	h5t_tag_iterator_t* it;
+	TRY( it = h5priv_calloc (f, 1, sizeof (h5t_tag_iterator_t)) );
+	h5t_open_mtagset (f, name, &it->tagset);
+	it->elem_idx = -1;
+	it->subentity_idx = 999;
+	it->level_idx = f->t->cur_level;
+	it->iter = iterate_tags;
+	*iter =  (h5t_iterator_t*)it;
+	return H5_SUCCESS;
 }
 
 h5_err_t
 h5t_release_entity_iterator (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	) {
 	return h5priv_free (f, iter);
 }
 
-h5_err_t
-h5t_begin_iterate_entities (
-	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
-	const int codim
-	) {
-	iter->face_idx = -1;
-	iter->elem_idx = -1;
-	iter->codim = codim;
-	iter->ref_elem = f->t->ref_elem;
-
-	if (iter->codim > 0) {
-		iter->iter = iterate_faces;
-	} else if (iter->codim == 0) {
-		iter->iter = iterate_elems;
-	}
-	return h5tpriv_init_iterator (f, iter, codim);
-}
-
-h5_err_t
-h5t_begin_iterate_boundary_faces (
-	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
-	const int codim
-	) {
-	iter->face_idx = 999; // just a high enough number
-	iter->elem_idx = -1;
-	iter->codim = codim;
-	iter->ref_elem = f->t->ref_elem;
-
-	if (iter->codim <= 0 || iter->codim > iter->ref_elem->dim) {
-		return h5_error (f, H5_ERR_INVAL,
-				 "Co-dimension requested %d, but must be between %d and %d",
-				 codim, 1, iter->ref_elem->dim);
-	} else if (iter->codim == 1) {
-		iter->iter = iterate_boundary_facets;
-	}
-	else if (iter->codim > 1) {
-		iter->iter = iterate_boundary_faces;
-	}
-	return H5_SUCCESS;
-}
-
 h5_loc_id_t
 h5t_iterate_entities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	) {
 	return (iter->iter (f, iter));
 }
@@ -261,15 +275,16 @@ h5t_iterate_entities (
 h5_err_t
 h5t_end_iterate_entities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	) {
-#pragma unused f
-	iter->face_idx = -1;
-	iter->elem_idx = -1;
-	iter->codim = -1;
-	iter->ref_elem = NULL;
-	iter->find = NULL;
-	iter->iter = NULL;
+	UNUSED_ARGUMENT (f);
+	h5t_mesh_iterator_t* it = (h5t_mesh_iterator_t*)iter;
+	it->face_idx = -1;
+	it->elem_idx = -1;
+	it->codim = -1;
+	it->ref_elem = NULL;
+	it->find = NULL;
+	it->iter = NULL;
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_retrieve_private.h

@@ -1,28 +1,109 @@
 #ifndef __H5T_RETRIEVE_PRIVATE_H
 #define __H5T_RETRIEVE_PRIVATE_H
 
-h5_err_t
-h5tpriv_skip_to_next_elem_on_level (
-	h5_file_t* f,
-	h5t_entity_iterator_t* iter
-	);
+#include <assert.h>
 
+/*
+  TODO: define as union of iterator types
+ */
+struct h5t_iterator {
+	h5_loc_id_t (*iter)(
+		h5_file_t *const f,
+		struct h5t_iterator* iter);
+/*		 
+	const h5t_ref_elem_t* ref_elem; // pointer to reference element
+
+ 	h5_id_t elem_idx;	// local element id
+	h5_id_t	face_idx;	// face id according reference element
+	int codim;		// dimension of entities to traverse
+	h5_err_t (*find)(
+		h5_file_t *const f,
+		h5_id_t face_idx,
+		h5_id_t elem_idx,
+		h5_idlist_t **retval);
+
+*/};
+
+typedef struct h5t_mesh_iterator {
+	h5_loc_id_t (*iter)(
+		h5_file_t *const f,
+		struct h5t_mesh_iterator* iter);
+	h5t_lvl_idx_t level_idx;
+	const h5t_ref_elem_t* ref_elem;
+	h5_loc_idx_t elem_idx;
+	h5_loc_idx_t face_idx;	// face id according reference element
+	int codim;		// dimension of entities to traverse
+	h5_err_t (*find)(
+		h5_file_t *const f,
+		h5_id_t face_idx,
+		h5_id_t elem_idx,
+		h5_idlist_t **retval);
+} h5t_mesh_iterator_t;
+
+typedef struct h5t_tag_iterator {
+	h5_loc_id_t (*iter)(
+		h5_file_t *const f,
+		struct h5t_tag_iterator* iter);
+	h5t_lvl_idx_t level_idx;
+	h5t_tagset_t* tagset;
+	h5_loc_idx_t elem_idx;
+	int subentity_idx;
+} h5t_tag_iterator_t;
+
+/*
 h5_err_t
 h5tpriv_elem_is_on_cur_level (
 	h5_file_t* const f,
 	h5_generic_loc_elem_t* el
 	);
+*/
+struct h5t_retrieve_methods {
+	h5_err_t (*init_entity_iterator)(
+		h5_file_t* const, h5t_mesh_iterator_t*, const int);
+};
 
 extern struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods;
 extern struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods;
 
+/*
+  Test whether given element is on current level. This is the case, if
+  - 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_init_iterator (
+h5tpriv_elem_is_on_cur_level (
+	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->cur_level) ||
+	     (el->child_idx >= 0 && el->child_idx < f->t->num_elems[f->t->cur_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_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;
+}
+
+static inline h5_err_t
+h5tpriv_init_entity_iterator (
 	h5_file_t* f,
-	h5t_entity_iterator_t* const iter,
+	h5t_mesh_iterator_t* const iter,
 	const int codim
 	) {
-	return (*f->t->methods.retrieve->init_iterator) (f, iter, codim);
+	return (*f->t->methods.retrieve->init_entity_iterator) (f, iter, codim);
 }
 
 #endif

src/h5core/h5t_retrieve_tetm.c

@@ -6,25 +6,26 @@
 static h5_err_t
 begin_iterate_entities (
 	h5_file_t* f,
-	h5t_entity_iterator_t* const iter,
+	h5t_mesh_iterator_t* const iter,
 	const int codim
 	) {
 	switch (iter->ref_elem->dim - codim) {
 	case 0: // iterate vertices
 		iter->find = h5tpriv_find_tv2;
-		return h5tpriv_skip_to_next_elem_on_level (f, iter);
+		break;
 	case 1: // iterate edges
 		iter->find = h5tpriv_find_te2;
-		return h5tpriv_skip_to_next_elem_on_level (f, iter);
+		break;
 	case 2: // iterate faces
 		iter->find = h5tpriv_find_td2;
-		return h5tpriv_skip_to_next_elem_on_level (f, iter);
+		break;
 	case 3: // iterate elems
 		iter->find = NULL;
-		return H5_SUCCESS;
+		break;
 	default:
 		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
+	return H5_SUCCESS;
 }
 
 struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods = {

src/h5core/h5t_retrieve_trim.c

@@ -6,22 +6,23 @@
 static h5_err_t
 begin_iterate_entities (
 	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
+	h5t_mesh_iterator_t* iter,
 	const int codim
 	) {
 	switch (h5tpriv_ref_elem_get_dim (iter) - codim) {
 	case 0: // iterate vertices
 		iter->find = h5tpriv_find_tv2;
-		return h5tpriv_skip_to_next_elem_on_level (f, iter);
+		break;
 	case 1: // iterate edges
 		iter->find = h5tpriv_find_te2;
-		return h5tpriv_skip_to_next_elem_on_level (f, iter);
+		break;
 	case 2: // iterate elems
 		iter->find = NULL;
-		return H5_SUCCESS;
+		break;
 	default:
 		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
+	return H5_SUCCESS;
 }
 
 struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods = {

src/h5core/h5t_store.c

@@ -453,8 +453,23 @@ h5t_end_refine_elems (
 	return H5_SUCCESS;
 }
 
+h5_err_t
+h5t_create_index_set (
+	h5_file_t* const f
+	) {
+	int codim;
+	int dim = h5tpriv_ref_elem_get_dim (f->t);
+	// todo: check tagset already exist
+	TRY( h5t_add_mtagset (f, "__IndexSet__", H5_INT64_T) );
 
-
-
-
-  
+	for (codim = 0; codim <= dim; codim++) {
+		h5_glb_idx_t idx = 0;
+		h5t_mesh_iterator_t it;
+		h5_glb_id_t entity_id;
+		TRY( h5t_init_mesh_iterator (f, (h5t_iterator_t*)&it, codim) );
+		while ((entity_id = it.iter(f,&it)) >= 0) {
+			TRY( h5t_set_mtag_by_name (f, "__IndexSet__", entity_id, 1, &idx) );
+		}
+	}
+	return H5_SUCCESS;
+}

src/h5core/h5t_store_private.h

@@ -1,6 +1,15 @@
 #ifndef __H5T_STOREMESH_PRIVATE_H
 #define __H5T_STOREMESH_PRIVATE_H
 
+struct h5t_store_methods {
+	h5_err_t (*alloc_elems)(h5_file_t* const, const size_t, const size_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_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*);
+};
+
 extern struct h5t_store_methods h5tpriv_trim_store_methods;
 extern struct h5t_store_methods h5tpriv_tetm_store_methods;
 

src/h5core/h5t_tags_private.h

@@ -29,53 +29,56 @@ ToDo
 
 
 /*
-  Structure to store a tag value
+  All tags of an element are stored in an array of the below defined
+  structure
 */
 typedef struct {
-	int32_t subent_id;	/* sub-entitiy id */
-	int32_t size;
 	union {
 		h5_float64_t	f;
 		h5_int64_t	i;
-	} vals[1];
+	} item;
 } h5t_tagval_t;
 
 
 /*
-  Structure with pointers to the tag values of a given tagset of an element.
-  We use idx as an index into valp: 
-  valp[idx[0]] ... valp[idx[3]] are pointing to the tag values of vertex 0 ... 3
-  valp[idx[4]] ... valp[idx[9]] are pointing to the tag values of edge 0 ... 5
-  valp[idx[10]] ... valp[idx[13]] are pointing to the tag values of triangle 0 ... 3
-  valp[idx[14]] points to the tag value of the elements itself.
 
-  If idx[k] is equal -1, no tag has been assigned to the appropriate entity.
 */
 typedef struct {
-	signed char idx[15];
-	signed char size;	/* size of valp */
-	h5t_tagval_t *valp[1];
-} h5t_tagsel_t;
+	int16_t face_id;	// face id: type and face index
+	uint16_t val_dim;	// dim of value for this entity
+	uint32_t val_idx;	// index of first value
+} h5t_taginfo_t; 
 
+typedef struct {
+	int32_t num_tags;
+	h5t_taginfo_t ti[1];
+} h5t_tageleminfo_t;
 
 struct h5t_tagset {
-	char * name;
-	unsigned int changed;	/* flag tagset changed, ... */
-	unsigned int num_elems;
-	h5_id_t type;		/* int64 or float64 */
-	h5t_tagsel_t *elems[1];
+	char* name;		// name of tagset
+	unsigned int changed;	// flag tagset changed, ...
+	struct {
+		h5t_lvl_idx_t min_level;
+		h5t_lvl_idx_t max_level;
+	} scope;
+	h5_id_t type;		// int64 or float64
+	h5_loc_idx_t num_entities;// number of tagged entities
+	h5_loc_idx_t num_values;// number of values
+	h5_loc_idx_t num_elems; // number of elements in tagset
+	h5t_tagval_t* values;	// ptr to array of tag values
+	h5t_tageleminfo_t* elems[1]; // per element structure
 };
 
 /*
   Structure for hash table of tagsets
  */
-typedef struct {
-	unsigned int changed;		/* flag container changed */
+struct h5t_tagcontainer {
+	unsigned int changed;	// flag container changed
 	hid_t group_id;
-	hsize_t num_sets;		/* number of tagsets */
-	char **names;			/* fast access via index */
-	h5_hashtable_t	sets;
-} h5t_tagcontainer_t;
+	hsize_t num_sets;	// number of tagsets
+	char** names;		// fast access via index
+	h5_hashtable_t	sets;	// hash table
+};
 
 
 typedef struct {

src/h5core/h5t_types_private.h

@@ -24,7 +24,8 @@ typedef struct h5_loc_triangle {
 	h5_loc_idx_t	parent_idx;
 	h5_loc_idx_t	child_idx;
 	h5t_lvl_idx_t	level_idx;
-	h5t_elem_flags_t	flags;
+	h5t_lvl_idx_t	refinement_level;
+	h5t_elem_flags_t flags;
 	h5_loc_idx_t	vertex_indices[3];
 	h5_loc_idx_t	neighbor_indices[3];
 } h5_loc_triangle_t;
@@ -43,7 +44,8 @@ typedef struct h5_loc_tetrahedron {
 	h5_loc_idx_t	parent_idx;
 	h5_loc_idx_t	child_idx;
 	h5t_lvl_idx_t	level_idx;
-	h5t_elem_flags_t	flags;
+	h5t_lvl_idx_t	refinement_level;
+	h5t_elem_flags_t flags;
 	h5_loc_idx_t	vertex_indices[4];
 	h5_loc_idx_t	neighbor_indices[4];
 } h5_loc_tetrahedron_t;
@@ -61,7 +63,8 @@ typedef struct h5_generic_loc_elem {
 	h5_loc_idx_t	parent_idx;
 	h5_loc_idx_t	child_idx;
 	h5_int32_t	level_idx;
-	h5_int32_t	flags;
+	h5t_lvl_idx_t	refinement_level;
+	h5t_elem_flags_t flags;
 	h5_loc_idx_t	indices[1];
 } h5_generic_loc_elem_t;
 
@@ -101,97 +104,11 @@ typedef struct h5t_adjacencies {
 	h5_hashtable_t td_hash;
 } h5t_adjacencies_t;
 
-struct h5t_store_methods {
-	h5_err_t (*alloc_elems)(h5_file_t* const, const size_t, const size_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_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);
-};
-
-struct h5t_access_methods {
-	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);
-	h5t_lvl_idx_t (*get_loc_elem_level_idx)(
-		h5_file_t* const, const h5_loc_idx_t);
-	h5t_lvl_idx_t (*set_loc_elem_level_idx)(
-		h5_file_t* const, const h5_loc_idx_t, const h5t_lvl_idx_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_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);
-	h5_err_t (*set_boundary_elem_flag)(h5_file_t* const, const h5_loc_idx_t);
-	h5_err_t (*clear_boundary_elem_flag)(h5_file_t* const, const h5_loc_idx_t);
-	int (*is_boundary_elem)(h5_file_t* const, const h5_loc_idx_t);
-	int (*is_boundary_facet)(h5_file_t* const, const h5_loc_idx_t, const h5_loc_idx_t);
-	int (*is_boundary_face)(h5_file_t* const, const int, const h5_loc_idx_t, const h5_loc_idx_t);
-};
-
-struct h5t_read_methods {
-	h5_err_t (*init_loc_elems_struct)(h5_file_t* const);
-	h5_err_t (*init_geom_boundary_info)(h5_file_t* const, h5t_lvl_idx_t);
-};
-
-struct h5t_adjacency_methods {
-	h5_err_t (*update_internal_structs)(h5_file_t* const, h5t_lvl_idx_t);
-	h5_err_t (*release_internal_structs)(h5_file_t* const);
-	h5_err_t (*get_adjacencies)(
-		h5_file_t * const,
-		const h5_loc_id_t, const h5_int32_t, h5_idlist_t**);
-};
+struct h5t_read_methods;
+struct h5t_store_methods;
+struct h5t_retrieve_methods;
+struct h5t_access_methods;
+struct h5t_adjacency_methods;
 
 typedef struct h5t_methods {
 	struct h5t_read_methods *read;

src/h5core/h5u_model.c

@@ -115,7 +115,7 @@ h5u_set_num_particles (
 	}
 
 #ifndef PARALLEL_IO
-#pragma unused total
+        UNUSED_ARGUMENT (total);
 	count = u->nparticles;
 	TRY( u->shape = h5priv_create_hdf5_dataspace(f, 1, &count, NULL) );
 	u->viewstart = 0;

src/include/H5Fed_retrieve.h

@@ -15,12 +15,12 @@
 #ifndef __H5FED_RETRIEVE_H
 #define __H5FED_RETRIEVE_H
 
-h5t_entity_iterator_t*
+h5t_iterator_t*
 H5FedBeginTraverseEntities (
 	h5_file_t* const f,
 	int codim
 	);
-h5t_entity_iterator_t*
+h5t_iterator_t*
 H5FedBeginTraverseBoundaryFaces (
 	h5_file_t* const f,
 	int codim
@@ -28,12 +28,12 @@ H5FedBeginTraverseBoundaryFaces (
 h5_loc_id_t
 H5FedTraverseEntities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	);
 h5_err_t
 H5FedEndTraverseEntities (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
+	h5t_iterator_t* iter
 	);
 h5_err_t
 H5FedGetVertexCoordsByIndex (
@@ -62,6 +62,13 @@ H5FedGetVertexIndicesOfTriangle (
 	h5_loc_idx_t* const vertex_indices
 	);
 
+h5_err_t
+H5FedGetVertexIndicesOfTriangleCClockwise (
+	h5_file_t* const f,
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* const vertex_indices
+	);
+
 h5_err_t
 H5FedGetVertexIndicesOfTet (
 	h5_file_t* const f,

src/include/h5core/h5_types.h

@@ -39,7 +39,7 @@ typedef __int64			int64_t;
 typedef int64_t			h5_int64_t;
 typedef int32_t			h5_int32_t;
 typedef int64_t			h5_id_t;
-typedef h5_int32_t		h5t_lvl_idx_t;
+typedef int16_t			h5t_lvl_idx_t;
 typedef h5_int32_t		h5t_elem_flags_t;
 typedef int64_t			h5_glb_idx_t;	// type for a global index
 typedef int64_t			h5_loc_idx_t;	// type for a local index

src/include/h5core/h5t_map.h

@@ -66,6 +66,13 @@ h5t_get_vertex_indices_of_triangle (
 	h5_loc_idx_t* vertex_indices
 	);
 
+h5_err_t
+h5t_get_vertex_indices_of_triangle_cclockwise (
+	h5_file_t* const f,
+	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,

src/include/h5core/h5t_retrieve.h

@@ -1,65 +1,52 @@
 #ifndef __H5T_RETRIEVE_H
 #define __H5T_RETRIEVE_H
 
-typedef struct h5t_entity_iterator {
-	h5_id_t elem_idx;	// local element id
-	h5_id_t	face_idx;	// face id according reference element
-	int codim;		// dimension of entities to traverse
-	const h5t_ref_elem_t* ref_elem; // pointer to reference element
-	h5_err_t (*find)(
-		h5_file_t *const f,
-		h5_id_t face_idx,
-		h5_id_t elem_idx,
-		h5_idlist_t **retval);
-	h5_loc_id_t (*iter)(
-		h5_file_t *const f,
-		struct h5t_entity_iterator* iter);		 
-} h5t_entity_iterator_t;
+typedef struct h5t_iterator h5t_iterator_t;
 
 h5_err_t
-h5t_alloc_entity_iterator (
+h5t_init_mesh_iterator (
 	h5_file_t* f,
-	h5t_entity_iterator_t** iter,
+	h5t_iterator_t* iter,
 	const int codim
 	);
 
 h5_err_t
-h5t_alloc_boundary_face_iterator (
+h5t_create_mesh_iterator (
 	h5_file_t* f,
-	h5t_entity_iterator_t** iter,
+	h5t_iterator_t** iter,
 	const int codim
 	);
 
+h5_err_t
+h5t_create_boundary_face_iterator (
+	h5_file_t* f,
+	h5t_iterator_t** iter,
+	const int codim
+	);
+
+h5_err_t
+h5t_create_mtag_iterator (
+	h5_file_t* f,
+	h5t_iterator_t** iter,
+	const char* name
+	);
+
 h5_err_t
 h5t_release_entity_iterator (
 	h5_file_t* const f,
-	h5t_entity_iterator_t* iter
-	);
-
-h5_err_t
-h5t_begin_iterate_entities (
-	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
-	const int codim
-	);
-
-h5_err_t
-h5t_begin_iterate_boundary_faces (
-	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
-	const int codim
+	h5t_iterator_t* iter
 	);
 
 h5_id_t
 h5t_iterate_entities (
 	h5_file_t * const f,
-	h5t_entity_iterator_t *iter
+	h5t_iterator_t *iter
 	);
 
 h5_err_t
 h5t_end_iterate_entities (
 	h5_file_t * const f,
-	h5t_entity_iterator_t *iter
+	h5t_iterator_t *iter
 	);
 
 

src/include/h5core/h5t_tags.h

@@ -1,23 +1,31 @@
 #ifndef __H5T_TAGS_H 
 #define __H5T_TAGS_H
 
-typedef struct h5t_tagset H5T_Tagset;
+typedef struct h5t_tagset h5t_tagset_t;
+typedef struct h5t_tagcontainer h5t_tagcontainer_t;
 
+h5_err_t
+h5t_mtagset_exists (
+	h5_file_t* const f,
+	h5t_tagcontainer_t* ctn,
+	char* name
+	);
 h5_err_t
 h5t_add_mtagset (
 	h5_file_t* const f,
 	char name[],
-	h5_id_t id
+	h5_id_t type
 	);
 h5_err_t
 h5t_remove_mtagset (
 	h5_file_t* const f,
 	const char name[]
 	);
-h5_err_t h5t_open_mtagset (
+h5_err_t
+h5t_open_mtagset (
 	h5_file_t* const f,
 	const char *name,
-	H5T_Tagset** retval
+	h5t_tagset_t** retval
 	);
 h5_ssize_t
 h5t_get_num_mtagsets (
@@ -68,7 +76,7 @@ h5t_remove_mtag_by_name (
 h5_ssize_t
 h5t_get_tag (
 	h5_file_t *const f,
-	const H5T_Tagset *tagset,
+	const h5t_tagset_t *tagset,
 	const h5_loc_id_t entity_id,
 	size_t* const dim,
 	void* const vals
@@ -77,7 +85,7 @@ h5t_get_tag (
 h5_err_t
 h5t_remove_mtag (
 	h5_file_t* const f,
-	H5T_Tagset* tagset,
+	h5t_tagset_t* tagset,
 	const h5_loc_id_t entity_id
 	);