- neighborhood informations added to elements (to be continued)

- several name changes in struct h5t_fdata
- refactoring according changes in struct h5t_fdata

src/h5core/h5_hdf5.c

@@ -1088,7 +1088,7 @@ h5priv_write_hdf5_attribute (
 	return H5_SUCCESS;
 }
 
-ssize_t
+h5_ssize_t
 h5priv_get_hdf5_attribute_name (
 	h5_file_t * const f,
 	hid_t attr_id,
@@ -1101,7 +1101,7 @@ h5priv_get_hdf5_attribute_name (
 			f,
 			H5_ERR_HDF5,
 			"Cannot get attribute name." );
-	return size;
+	return (h5_size_t)size;
 }
 
 hid_t

src/h5core/h5t_adjacencies_tetm.c

@@ -25,19 +25,18 @@ compute_elems_of_vertices (
 	const h5_id_t from_lvl
 	) {
 	h5t_fdata_t* t = f->t;
-	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
+	h5_id_t idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
+	h5_tet_t *el = &t->loc_elems.tets[idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
-	for (;elem_idx < num_elems; elem_idx++, el++) {
+	for (;idx < num_elems; idx++, el++) {
 		int face_idx;
-		int num_faces = t->ref_element->num_faces[0];
+		int num_faces = t->ref_elem->num_faces[0];
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
-			h5_id_t vidx = el->local_vertex_indices[face_idx];
+			h5_id_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
 				     f,
 				     &t->vertices_data[vidx].tv,
-				     h5tpriv_build_vertex_id (
-					     face_idx, elem_idx)) );
+				     h5tpriv_build_vertex_id (face_idx, idx)) );
 		}
 	}
 	return H5_SUCCESS;
@@ -53,13 +52,12 @@ compute_elems_of_edges (
 	) {
 	h5t_fdata_t *t = f->t;
 	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_idlist_t *retval = NULL;
 	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
-	for (;elem_idx < num_elems; elem_idx++, el++) {
+	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_element->num_faces[1];
+		int num_faces = t->ref_elem->num_faces[1];
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY( h5tpriv_search_te2 (
 				     f, face_idx, elem_idx, &retval) );
@@ -75,13 +73,12 @@ compute_elems_of_triangles (
 	) {
 	h5t_fdata_t* t = f->t;
 	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_idlist_t *retval = NULL;
 	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
-	for (;elem_idx < num_elems; elem_idx++, el++) {
+	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_element->num_faces[1];
+		int num_faces = t->ref_elem->num_faces[1];
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY( h5tpriv_search_td2 (
 				     f, face_idx, elem_idx, &retval) );
@@ -110,15 +107,15 @@ compute_children_of_edge (
 	for (; edge < end; edge++) {
 		h5_id_t elem_idx = h5tpriv_get_elem_idx (*edge);
 		h5_id_t face_idx =  h5tpriv_get_face_idx (*edge);
-		h5_elem_ldta_t* tet = &t->elems_ldta[elem_idx];
-		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK ) {
+		h5_tet_t* tet = &t->loc_elems.tets[elem_idx];
+		if (h5tpriv_elem_is_on_cur_level (f, (h5_generic_elem_t*)tet) == H5_OK ) {
 			TRY( h5priv_append_to_idlist (f, children, *edge) );
 		} else {
 			h5_id_t kids[2];
 			TRY( t->methods.store->get_direct_children_of_edge (
 				      f,
 				      face_idx,
-				      tet->local_child_idx,
+				      tet->child_idx,
 				      kids) );
 			TRY( compute_children_of_edge (f, kids[0], children) );
 			TRY( compute_children_of_edge (f, kids[1], children) );
@@ -150,14 +147,14 @@ compute_sections_of_edge (
 	for (; edge < end; edge++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*edge);
 		h5_id_t face_id =  h5tpriv_get_face_idx (*edge);
-		h5_elem_ldta_t* tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 		if (! h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			refined = 1;
 			h5_id_t kids[2];
 			TRY( t->methods.store->get_direct_children_of_edge (
 				     f,
 				     face_id,
-				     tet->local_child_idx,
+				     tet->child_idx,
 				     kids) );
 			TRY( compute_sections_of_edge (f, kids[0], children) );
 			TRY( compute_sections_of_edge (f, kids[1], children) );
@@ -213,7 +210,7 @@ compute_direct_children_of_triangle (
 		{{2,0},{2,2},{2,3},{1,7}},
 		{{3,1},{3,2},{3,3},{3,6}}
 	};
-	int num_faces = f->t->ref_element->num_faces[2];
+	int num_faces = f->t->ref_elem->num_faces[2];
 	if ((face_idx < 0) || (face_idx >= num_faces)) {
 		return h5_error_internal (f, __FILE__, __func__, __LINE__); 
 	}
@@ -248,7 +245,7 @@ compute_children_of_triangle (
 	for (; tri < end; tri++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*tri);
 		h5_id_t face_idx =  h5tpriv_get_face_idx (*tri);
-		h5_elem_ldta_t *tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			TRY( h5priv_append_to_idlist (f, children, *tri) );
 		} else {
@@ -256,7 +253,7 @@ compute_children_of_triangle (
 			TRY( compute_direct_children_of_triangle (
 				      f,
 				      face_idx,
-				      tet->local_child_idx,
+				      tet->child_idx,
 				      dids) );
 			TRY( compute_children_of_triangle (f, dids[0], children) );
 			TRY( compute_children_of_triangle (f, dids[1], children) );
@@ -286,14 +283,14 @@ compute_sections_of_triangle (
 	for (; tri < end; tri++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*tri);
 		h5_id_t face_idx =  h5tpriv_get_face_idx (*tri);
-		h5_elem_ldta_t *tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 		if (! h5tpriv_elem_is_on_cur_level (f, tet) == H5_OK) {
 			refined = 1;
 			h5_id_t dids[4];
 			TRY( compute_direct_children_of_triangle (
 				     f,
 				     face_idx,
-				     tet->local_child_idx,
+				     tet->child_idx,
 				     dids) );
 			TRY( compute_sections_of_triangle (f, dids[0], children) );
 			TRY( compute_sections_of_triangle (f, dids[1], children) );
@@ -340,7 +337,7 @@ get_edges_upadjacent_to_vertex (
 	for (i = 0; i < tv->num_items; i++, vidp++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*vidp);
 		h5_id_t face = h5tpriv_get_face_idx (*vidp);
-		h5_elem_ldta_t* tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK ) {
 			continue;
@@ -382,7 +379,7 @@ get_triangles_upadjacent_to_vertex (
 	for (i = 0; i < tv->num_items; i++, vidp++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*vidp);
 		h5_id_t face = h5tpriv_get_face_idx (*vidp);
-		h5_elem_ldta_t* tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK) {
 			continue;
@@ -409,7 +406,7 @@ get_tets_upadjacent_to_vertex (
 	h5_id_t* vidp = tv->items;
 	for (i = 0; i < tv->num_items; i++, vidp++) {
 		h5_id_t eid = h5tpriv_get_elem_idx (*vidp);
-		h5_elem_ldta_t* tet = &t->elems_ldta[eid];
+		h5_generic_elem_t* tet = (h5_generic_elem_t*)&t->loc_elems.tets[eid];
 
 		if (h5tpriv_elem_is_on_cur_level (f, tet) == H5_NOK) {
 			continue;

src/h5core/h5t_adjacencies_trim.c

@@ -26,13 +26,13 @@ compute_elems_of_vertices (
 	) {
 	h5t_fdata_t *t = f->t;
 	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
+	h5_triangle_t *el = &t->loc_elems.tris[elem_idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	for (;elem_idx < num_elems; elem_idx++, el++) {
 		int face_idx;
-		int num_faces = t->ref_element->num_faces[0];
+		int num_faces = t->ref_elem->num_faces[0];
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
-			h5_id_t vidx = el->local_vertex_indices[face_idx];
+			h5_id_t vidx = el->vertex_indices[face_idx];
 			TRY( h5priv_append_to_idlist (
 				     f,
 				     &t->vertices_data[vidx].tv,
@@ -53,13 +53,12 @@ compute_elems_of_edges (
 	) {
 	h5t_fdata_t *t = f->t;
 	h5_id_t elem_idx = (from_lvl <= 0) ? 0 : t->num_elems[from_lvl-1];
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
 	h5_idlist_t *retval = NULL;
 	TRY( h5tpriv_resize_te_htab (f, 4*(num_elems-elem_idx)) );
-	for (;elem_idx < num_elems; elem_idx++, el++) {
+	for (;elem_idx < num_elems; elem_idx++) {
 		int face_idx;
-		int num_faces = t->ref_element->num_faces[1];
+		int num_faces = t->ref_elem->num_faces[1];
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			TRY ( h5tpriv_search_te2 (
 				      f, face_idx, elem_idx, &retval ) );
@@ -88,7 +87,7 @@ compute_children_of_edge (
 	for ( ; edge < end; edge++ ) {
 		h5_id_t elem_idx = h5tpriv_get_elem_idx ( *edge );
 		h5_id_t face_idx =  h5tpriv_get_face_idx ( *edge );
-		h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
+		h5_generic_elem_t *el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_idx];
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_OK ) {
 			TRY ( h5priv_append_to_idlist (
 				      f, children, *edge )
@@ -98,7 +97,7 @@ compute_children_of_edge (
 			TRY ( t->methods.store->get_direct_children_of_edge (
 				      f,
 				      face_idx,
-				      el->local_child_idx,
+				      el->child_idx,
 				      kids ) );
 			TRY ( compute_children_of_edge (
 				      f, kids[0], children ) );
@@ -133,14 +132,14 @@ compute_sections_of_edge (
 	for ( ; edge < end; edge++ ) {
 		h5_id_t eid = h5tpriv_get_elem_idx ( *edge );
 		h5_id_t face_id =  h5tpriv_get_face_idx ( *edge );
-		h5_elem_ldta_t *el = &t->elems_ldta[eid];
+		h5_generic_elem_t *el = (h5_generic_elem_t*)&t->loc_elems.tris[eid];
 		if ( ! h5tpriv_elem_is_on_cur_level ( f, el ) == H5_OK ) {
 			refined = 1;
 			h5_id_t kids[2];
 			TRY ( t->methods.store->get_direct_children_of_edge (
 				      f,
 				      face_id,
-				      el->local_child_idx,
+				      el->child_idx,
 				      kids ) );
 			TRY ( compute_sections_of_edge (
 				      f, kids[0], children ) );
@@ -181,15 +180,15 @@ get_edges_upadjacent_to_vertex (
 	) {
 	TRY ( h5priv_alloc_idlist ( f, list, 8 ) );
 	
-	h5t_fdata_t *t = f->t;
-	h5_idlist_t *tv = &t->vertices_data[entity_id].tv;
+	h5t_fdata_t* t = f->t;
+	h5_idlist_t* tv = &t->vertices_data[entity_id].tv;
 	h5_size_t i;
 
-	h5_id_t *vertex_idp = tv->items;
+	h5_id_t* vertex_idp = tv->items;
 	for ( i = 0; i < tv->num_items; i++, vertex_idp++ ) {
 		h5_id_t elem_idx = h5tpriv_get_elem_idx ( *vertex_idp );
 		h5_id_t face_idx = h5tpriv_get_face_idx ( *vertex_idp );
-		h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
+		h5_generic_elem_t* el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_idx];
 
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_NOK ) {
 			continue;
@@ -221,7 +220,7 @@ get_triangles_upadjacent_to_vertex (
 	h5_id_t *vertex_id = tv->items;
 	for ( i = 0; i < tv->num_items; i++, vertex_id++ ) {
 		h5_id_t elem_id = h5tpriv_get_elem_idx ( *vertex_id );
-		h5_elem_ldta_t *el = &t->elems_ldta[elem_id];
+		h5_generic_elem_t* el = (h5_generic_elem_t*)&t->loc_elems.tris[elem_id];
 
 		if ( h5tpriv_elem_is_on_cur_level ( f, el ) == H5_NOK ) {
 			continue;
@@ -289,7 +288,7 @@ get_vertices_downadjacent_to_triangle (
 	h5_id_t elem_idx = h5tpriv_get_elem_idx ( entity_id );
 	// loop over all edges of triangle
 	h5_id_t face_idx;
-	h5_id_t num_faces = f->t->ref_element->num_faces[1];
+	h5_id_t num_faces = f->t->ref_elem->num_faces[1];
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
 		TRY( compute_sections_of_edge (
 			     f,
@@ -321,7 +320,7 @@ get_edges_downadjacent_to_triangle (
 	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	// loop over all edges of triangle
 	h5_id_t face_idx;
-	h5_id_t num_faces = f->t->ref_element->num_faces[1];
+	h5_id_t num_faces = f->t->ref_elem->num_faces[1];
 	for ( face_idx = 0; face_idx < num_faces; face_idx++ ) {
 		TRY( compute_sections_of_edge (
 			     f,

src/h5core/h5t_core_private.h

@@ -3,25 +3,20 @@
 
 #define H5T_CONTAINER_GRPNAME	"Topo"
 
-#include "h5t_openclose_private.h"
-#include "h5t_adjacencies_tetm_private.h"
-#include "h5t_adjacencies_trim_private.h"
 
+#include "h5t_openclose_private.h"
+#include "h5t_adjacencies_private.h"
 #include "h5t_consts_private.h"
 #include "h5t_errorhandling_private.h"
 #include "h5t_hsearch_private.h"
 #include "h5t_map_private.h"
 #include "h5t_readwrite_private.h"
-#include "h5t_retrieve_tetm_private.h"
-#include "h5t_retrieve_trim_private.h"
 #include "h5t_store_private.h"
-#include "h5t_store_tetm_private.h"
-#include "h5t_store_trim_private.h"
 #include "h5t_tags_private.h"
 
 #include "h5t_types_private.h"
 
+#include "h5t_access_private.h"
 #include "h5t_retrieve_private.h"
 
-
 #endif

src/h5core/h5t_errorhandling.c

@@ -1,6 +1,8 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>	/* va_arg - System dependent ?! */
 #include <string.h>
 #include <errno.h>
-
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
@@ -16,7 +18,7 @@ h5tpriv_error_local_elem_nexist (
 	int num_chars_printed = snprintf (s, sizeof(s), "%lld,",
 					  (long long)local_vertex_indices[0]);
 	int i;
-	int num_vertices = t->ref_element->num_faces[0];
+	int num_vertices = t->ref_elem->num_faces[0];
 	for (i = 1; i < num_vertices; i++) {
 		num_chars_printed += snprintf (
 			s + num_chars_printed, sizeof (s) - num_chars_printed,
@@ -29,4 +31,4 @@ h5tpriv_error_local_elem_nexist (
 
 	return h5_error (f, H5_ERR_NOENTRY, ERR_ELEM_NEXIST, s);
 }
-
+	

src/h5core/h5t_hsearch.c

@@ -299,6 +299,9 @@ h5tpriv_find_td2 (
 	return h5tpriv_find_td (f, &item, retval);
 }
 
+/*
+  Return list of elements sharing the same vertex.
+ */
 h5_err_t
 h5tpriv_find_tv2 (
 	h5_file_t* const f,
@@ -306,11 +309,11 @@ h5tpriv_find_tv2 (
 	h5_id_t elem_idx,
 	h5_idlist_t** retval
 	) {
-	/*
-	  map (cid,el_idx) to local index of vertex
-	*/
-	h5_id_t vertex_idx = f->t->elems_ldta[elem_idx].local_vertex_indices[face_idx];
-	*retval = &f->t->vertices_data[vertex_idx].tv;
+
+	h5_id_t idx = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx);
+	*retval = &f->t->vertices_data[idx].tv;
 
 	return H5_SUCCESS;
 }
+
+

src/h5core/h5t_map.c

@@ -102,60 +102,29 @@ h5tpriv_get_local_vid (
        	return -(low+1);  // not found
 }
 
-/*!
-  Return the coordinates of the i-th vertex of the element given by its local 
-  element id. For triangles \c i is in \c [0,1,2], for tetraheda \c i is in
-  \c [0,1,2,3].
-
-
-*/
-#define get_vertex_of_elem( f, i, eid ) \
-	(f->t->vertices[ f->t->elems_ldta[eid].local_vertex_indices[i] ].P)
-
-
-
-/*!
-  Compare two elems given by their local vertex ids
-*/
-static int
-vcmp_elems (
-	h5_file_t* const f,
-	const h5_id_t* e1,
-	const h5_id_t* e2
-	) {
-	h5t_fdata_t* t = f->t;
-	int i;
-
-	int num_vertices = t->ref_element->num_faces[0];
-
-	for (i = 0; i < num_vertices; i++) {
-		int r = cmp_vertices (
-			t->vertices[e1[i]].P,
-			t->vertices[e2[i]].P );
-		if (r < 0)		return -1;
-		else if (r > 0) 	return 1;
-	}
-	return 0;
-}
-
 /*!
   compare two elems given by their local id
 */
 static int
 cmp_elems (
 	h5_file_t* const  f,
-	const h5_id_t local_eid1,
-	const h5_id_t local_eid2
+	const h5_id_t elem_idx1,
+	const h5_id_t elem_idx2
 	) {
 	h5t_fdata_t* t = f->t;
-	int num_vertices = t->ref_element->num_faces[0];
+	int num_vertices = t->ref_elem->num_faces[0];
+	h5_id_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
+	h5_id_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
+
 	int i;
 	for (i = 0; i < num_vertices; i++) {
-		int r = cmp_vertices (
-			get_vertex_of_elem (f, i, local_eid1),
-			get_vertex_of_elem (f, i, local_eid2));
-		if (r < 0)		return -1;
-		else if (r > 0) 	return 1;
+		h5_float64_t* v1 = t->vertices[indices1[i]].P;
+		h5_float64_t* v2 = t->vertices[indices2[i]].P;
+		int r = cmp_vertices (v1, v2);
+		if (r < 0)
+			return -1;
+		else if (r > 0)
+			return 1;
 	}
 	return 0;
 }
@@ -163,19 +132,24 @@ cmp_elems (
 static int
 cmp_elems1 (
 	h5_file_t* f,
-	h5_id_t	local_eid1,
-	h5_id_t local_eid2
+	h5_id_t	elem_idx1,
+	h5_id_t elem_idx2
 	) {
-	struct h5t_fdata *t = f->t;
-	int num_vertices = t->ref_element->num_faces[0];
+	h5t_fdata_t *t = f->t;
+	int num_vertices = t->ref_elem->num_faces[0];
+	h5_id_t* indices1 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx1);
+	h5_id_t* indices2 = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx2);
+
 	int imap[] = { 1, 0, 2, 3 };
 	int i;
 	for ( i = 0; i < num_vertices; i++ ) {
-		int r = cmp_vertices (
-			get_vertex_of_elem ( f, imap[i], local_eid1 ),
-			get_vertex_of_elem ( f, imap[i], local_eid2 ) );
-		if ( r < 0 )		return -1;
-		else if ( r > 0 ) 	return 1;
+		h5_float64_t* v1 = t->vertices[ indices1[imap[i]] ].P;
+		h5_float64_t* v2 = t->vertices[ indices2[imap[i]] ].P;
+		int r = cmp_vertices (v1, v2);
+		if (r < 0)
+			return -1;
+		else if (r > 0)
+			return 1;
 	}
 	return 0;
 }
@@ -272,39 +246,6 @@ h5tpriv_sort_local_vertex_indices (
 	return H5_SUCCESS;
 }
 
-/*!
-  Binary search an element given by its local vertex ids.
-
-  \result	index in t->map_elem_s2l[0].items
- */
-static h5_id_t
-search_elem (
-	h5_file_t* const f,
-	h5_id_t* const vertex_indices	/* local vertex ids */
-	) {
-	h5t_fdata_t* t = f->t;
-	int num_vertices = t->ref_element->num_faces[0];
-	h5tpriv_sort_local_vertex_indices ( f, vertex_indices, num_vertices );
-
-	register h5_id_t low = 0;
-	register h5_id_t high = t->sorted_elems[0].num_items - 1;
-	register h5_id_t *elem1 = vertex_indices;
-	while (low <= high) {
-		register int mid = (low + high) / 2;
-
-		h5_id_t local_eid = t->sorted_elems[0].items[mid];
-		h5_id_t *elem2 = t->elems_ldta[local_eid].local_vertex_indices;
-		int diff = vcmp_elems ( f, elem1, elem2 );
-           	if (diff < 0)
-               		high = mid - 1;
-           	else if (diff > 0)
-               		low = mid + 1;
-           	else
-               		return mid; // found
-       	}
-	return h5tpriv_error_local_elem_nexist (f, vertex_indices);
-}
-
 /*!
   Map a global vertex index to corresponding local index.
 */
@@ -381,20 +322,14 @@ h5tpriv_rebuild_global_2_local_map_of_elems (
 	) {
 	h5t_fdata_t* t = f->t;
 	if (t->num_levels <= 0) return H5_SUCCESS;
-	h5_id_t local_eid = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
+
+	h5_id_t idx = t->cur_level > 0 ? t->num_elems[t->cur_level-1] : 0;
 	h5_id_t num_elems = t->num_elems[t->num_levels-1];
-	h5_idmap_el_t *item = &t->map_elem_g2l.items[local_eid];
-	size_t offset = h5tpriv_sizeof_elem[t->mesh_type];
-	void *elemp = t->elems.data + local_eid*offset;
-	for (;
-	     local_eid < num_elems;
-	     local_eid++,
-		     item++,
-		     elemp+=offset) {
-		h5_elem_t* elem = (h5_elem_t*)elemp;
-		
-		item->global_id = elem->global_idx; 
-		item->local_id = local_eid;
+	h5_idmap_el_t *item = &t->map_elem_g2l.items[idx];
+
+	for (; idx < num_elems; idx++, item++) {
+		item->global_id = h5tpriv_get_glb_elem_idx (f, idx);
+		item->local_id = idx;
 		t->map_elem_g2l.num_items++;
 	}
 	h5priv_sort_idmap (&t->map_elem_g2l);
@@ -402,31 +337,32 @@ h5tpriv_rebuild_global_2_local_map_of_elems (
 	return H5_SUCCESS;
 }
 
-static int
-map_entity_type_to_dimension[] = { -1,
-				   [H5_OID_VERTEX] = 0,
-				   [H5_OID_EDGE] = 1,
-				   [H5_OID_TRIANGLE] = 2,
-				   [H5_OID_TETRAHEDRON] = 3
-};
 
 h5_err_t
 h5t_get_vertex_indices_of_entity (
-	h5_file_t* const f,
-	const h5_id_t entity_id,
-	h5_id_t* vertex_indices
+	h5_file_t* const f,		// in
+	const h5_id_t entity_id,	// in
+	h5_id_t* vertex_indices		// out
 	) {
+	static int map_entity_type_to_dimension[] = {
+		-1,
+		[H5_OID_VERTEX] = 0,
+		[H5_OID_EDGE] = 1,
+		[H5_OID_TRIANGLE] = 2,
+		[H5_OID_TETRAHEDRON] = 3
+	};
+
 	h5_id_t entity_type = h5tpriv_get_entity_type (entity_id);
 	h5_id_t face_idx = h5tpriv_get_face_idx (entity_id);
 	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
 	int dim =  map_entity_type_to_dimension[entity_type];
-	h5_elem_ldta_t *el = &f->t->elems_ldta[elem_idx];
-	const h5t_ref_element_t* ref_element = f->t->ref_element;
-	int num_vertices = ref_element->num_vertices_of_face[dim][face_idx];
+	h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
+	int num_vertices = ref_elem->num_vertices_of_face[dim][face_idx];
 	int i;
 	for (i = 0; i < num_vertices; i++) {
-		int idx = ref_element->map[dim][face_idx][i];
-		vertex_indices[i] = el->local_vertex_indices[idx];
+		int idx = ref_elem->map[dim][face_idx][i];
+		vertex_indices[i] = indices[idx];
 	}
 	return H5_SUCCESS;
 }
@@ -450,10 +386,7 @@ h5t_get_vertex_index_of_vertex2 (
 	const h5_id_t elem_idx,		// local element index
 	h5_id_t* vertex_indices		// OUT: vertex ID's
 	) {
-	const h5t_ref_element_t* ref_element = f->t->ref_element;
-	h5_elem_ldta_t *el = &f->t->elems_ldta[elem_idx];
-
- 	vertex_indices[0] = el->local_vertex_indices[ref_element->map[0][face_idx][0]];
+	vertex_indices[0] = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx); 
 	return H5_SUCCESS;
 }
 
@@ -486,11 +419,11 @@ h5t_get_vertex_indices_of_edge2 (
 	const h5_id_t elem_idx,		// local element index
 	h5_id_t* vertex_indices		// OUT: vertex ID's
 	) {
-	const h5t_ref_element_t* ref_element = f->t->ref_element;
-	h5_elem_ldta_t* el = &f->t->elems_ldta[elem_idx];
+	const h5_id_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] = el->local_vertex_indices[ref_element->map[1][face_idx][0]];
-	vertex_indices[1] = el->local_vertex_indices[ref_element->map[1][face_idx][1]];
+ 	vertex_indices[0] = indices[ ref_elem->map[1][face_idx][0] ];
+	vertex_indices[1] = indices[ ref_elem->map[1][face_idx][1] ];
 	return H5_SUCCESS;
 }
 
@@ -513,12 +446,12 @@ h5t_get_vertex_indices_of_triangle2 (
 	const h5_id_t elem_idx,
 	h5_id_t* vertex_indices
 	) {
-	const h5t_ref_element_t* ref_element = f->t->ref_element;
-	h5_elem_ldta_t* el = &f->t->elems_ldta[elem_idx];
+	const h5_id_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] = el->local_vertex_indices[ref_element->map[2][face_idx][0]];
-	vertex_indices[1] = el->local_vertex_indices[ref_element->map[2][face_idx][1]];
-	vertex_indices[2] = el->local_vertex_indices[ref_element->map[2][face_idx][2]];
+ 	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] ];
 
 	return H5_SUCCESS;
 }
@@ -529,14 +462,14 @@ h5t_get_vertex_indices_of_tet (
 	const h5_id_t entity_id,
 	h5_id_t* vertex_indices
 	) {
-	h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
-	const h5t_ref_element_t* ref_element = f->t->ref_element;
-	h5_elem_ldta_t* el = &f->t->elems_ldta[elem_idx];
+	const h5_id_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	const h5_id_t* indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	const h5t_ref_elem_t* ref_elem = f->t->ref_elem;
 
- 	vertex_indices[0] = el->local_vertex_indices[ref_element->map[3][0][0]];
-	vertex_indices[1] = el->local_vertex_indices[ref_element->map[3][0][1]];
-	vertex_indices[2] = el->local_vertex_indices[ref_element->map[3][0][2]];
-	vertex_indices[3] = el->local_vertex_indices[ref_element->map[3][0][3]];
+ 	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] ];
 
 	return H5_SUCCESS;
 }

src/h5core/h5t_openclose.c

@@ -4,14 +4,18 @@
 #include "h5_core_private.h"
 
 static struct h5t_methods tet_funcs = {
+	&h5tpriv_read_tetm_methods,
 	&h5tpriv_tetm_store_methods,
 	&h5tpriv_tetm_retrieve_methods,
+	&h5tpriv_access_tetm_methods,
 	&h5tpriv_tetm_adjacency_methods
 };
 
 static struct h5t_methods tri_funcs = {
+	&h5tpriv_read_trim_methods,
 	&h5tpriv_trim_store_methods,
 	&h5tpriv_trim_retrieve_methods,
+	&h5tpriv_access_trim_methods,
 	&h5tpriv_trim_adjacency_methods
 };
 
@@ -96,29 +100,36 @@ create_triangle_type (
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
-			"global_idx",
-			HOFFSET (struct h5_triangle, global_idx),
+			"idx",
+			HOFFSET (struct h5_triangle, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
-			"global_parent_idx",
-			HOFFSET (struct h5_triangle, global_parent_idx),
+			"parent_idx",
+			HOFFSET (struct h5_triangle, parent_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
-			"global_child_idx",
-			HOFFSET(struct h5_triangle, global_child_idx),
+			"child_idx",
+			HOFFSET(struct h5_triangle, child_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_triangle_t,
-			"global_vertex_indices",
-			HOFFSET (struct h5_triangle, global_vertex_indices),
+			"vertex_indices",
+			HOFFSET (struct h5_triangle, vertex_indices),
+			dtypes->h5_3id_t) );
+	TRY(
+		h5priv_insert_hdf5_type (
+			f,
+			dtypes->h5_triangle_t,
+			"neighbor_indices",
+			HOFFSET(struct h5_triangle, neighbor_indices),
 			dtypes->h5_3id_t) );
 
 	return H5_SUCCESS;
@@ -168,29 +179,36 @@ create_tet_type (
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
-			"global_idx",
-			HOFFSET (struct h5_tetrahedron, global_idx),
+			"idx",
+			HOFFSET (struct h5_tetrahedron, idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
-			"global_parent_idx",
-			HOFFSET (struct h5_tetrahedron, global_parent_idx),
+			"parent_idx",
+			HOFFSET (struct h5_tetrahedron, parent_idx),
 			H5_ID_T) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
-			"global_child_idx",
-			HOFFSET (struct h5_tetrahedron, global_child_idx),
+			"child_idx",
+			HOFFSET (struct h5_tetrahedron, child_idx),
 			H5T_NATIVE_INT32) );
 	TRY(
 		h5priv_insert_hdf5_type (
 			f,
 			dtypes->h5_tet_t,
-			"global_vertex_indices",
-			HOFFSET (struct h5_tetrahedron, global_vertex_indices),
+			"vertex_indices",
+			HOFFSET (struct h5_tetrahedron, vertex_indices),
+			dtypes->h5_4id_t) );
+	TRY(
+		h5priv_insert_hdf5_type (
+			f,
+			dtypes->h5_triangle_t,
+			"neighbor_indices",
+			HOFFSET(struct h5_triangle, neighbor_indices),
 			dtypes->h5_4id_t) );
 
 	return H5_SUCCESS;
@@ -229,6 +247,18 @@ init_fdata (
 	t->meshes_gid = -1;
 	t->mesh_gid = -1;
 
+	/* initialize pointers */
+	t->glb_elems.data =		NULL;
+	t->loc_elems.data =		NULL;
+	t->num_elems =			NULL;
+	t->num_elems_on_level =		NULL;
+	t->map_elem_g2l.items =		NULL;
+	t->vertices =			NULL; 
+	t->vertices_data =		NULL;
+	t->num_vertices =		NULL;
+	t->map_vertex_g2l.items =	NULL;
+	t->mtags.names =		NULL;
+
 	/* vertices */
 	strcpy (t->dsinfo_vertices.name, "Vertices");
 	t->dsinfo_vertices.rank = 1;
@@ -313,17 +343,7 @@ init_fdata (
 		     t->dsinfo_num_elems_on_level.chunk_dims) );
 	t->dsinfo_num_elems_on_level.access_prop = H5P_DEFAULT;
 
-	/* initialize pointers */
-	t->elems.data =			NULL;
-	t->num_elems =			NULL;
-	t->elems_ldta =			NULL;
-	t->num_elems_on_level =		NULL;
-	t->map_elem_g2l.items =		NULL;
-	t->vertices =			NULL; 
-	t->vertices_data =		NULL;
-	t->num_vertices =		NULL;
-	t->map_vertex_g2l.items =	NULL;
-	t->mtags.names =		NULL;
+
 
 	return H5_SUCCESS;
 }
@@ -454,12 +474,12 @@ h5t_open_mesh (
 	case H5_OID_TETRAHEDRON:
 		t->dsinfo_elems.type_id = t->dtypes.h5_tet_t;
 		t->methods = tet_funcs;
-		t->ref_element = &h5t_tet_ref_element;
+		t->ref_elem = &h5t_tet_ref_elem;
 		break;
 	case H5_OID_TRIANGLE:
 		t->dsinfo_elems.type_id = t->dtypes.h5_triangle_t;
 		t->methods = tri_funcs;
-		t->ref_element = &h5t_tri_ref_element;
+		t->ref_elem = &h5t_tri_ref_elem;
 		break;
 	default:
 		return h5_error_internal (f, __FILE__, __func__, __LINE__);
@@ -486,9 +506,9 @@ release_elems (
 	h5_file_t* const f
 	) {
 	h5t_fdata_t* t = f->t;
-	TRY( h5priv_free (f, t->elems.data) );
+	TRY( h5priv_free (f, t->glb_elems.data) );
+	TRY( h5priv_free (f, t->loc_elems.data) );
 	TRY( h5priv_free (f, t->num_elems) );
-	TRY( h5priv_free (f, t->elems_ldta) );
 	TRY( h5priv_free (f, t->num_elems_on_level) );
 	TRY( h5priv_free (f, t->map_elem_g2l.items) );
 
@@ -590,5 +610,3 @@ h5tpriv_close_file (
 
 	return H5_SUCCESS;
 }
-
-

src/h5core/h5t_readwrite.c

@@ -65,7 +65,7 @@ write_elems (
 		     &t->dsinfo_elems,
 		     open_space_all,
 		     open_space_all,
-		     t->elems.data) );
+		     t->glb_elems.data) );
 
 	TRY( h5priv_write_dataset_by_name (
 		     f,
@@ -231,52 +231,7 @@ open_file_space_elems (
 	return H5S_ALL;
 }
 
-/*
-  setup structure "elems_data" with local ids for each element:
-  - translate the global vertex id's of each element to their
-    local id's
-  - translate the global parent id of each element to the
-    corresponding local id.
-*/
-static h5_err_t
-build_elems_ldta (
-	h5_file_t* const f
-	) {
-	h5t_fdata_t* t = f->t;
-	h5_id_t local_eid = 0;
-	h5_id_t num_elems = t->num_elems[t->num_levels-1];
-	h5_id_t level_id = 0;
 
-	void* elp = t->elems.data;
-	h5_elem_t* el;
-	h5_elem_ldta_t* el_data = t->elems_ldta;
-	int num_vertices = t->ref_element->num_faces[0];
-	for (local_eid=0;
-	     local_eid < num_elems;
-	     local_eid++, elp+=h5tpriv_sizeof_elem[t->mesh_type], el_data++) {
-		el = (h5_elem_t*)elp;
-		TRY( h5t_map_global_vertex_indices2local (
-			     f,
-			     el->global_vertex_indices,
-			     num_vertices,
-			     el_data->local_vertex_indices) );
-		if (el->global_parent_idx >= 0)
-			TRY( el_data->local_parent_idx =
-			     h5t_map_global_elem_idx2local (
-				     f, el->global_parent_idx) );
-		
-		if (el->global_child_idx >= 0)
-			TRY( el_data->local_child_idx =
-			     h5t_map_global_elem_idx2local (
-				     f, el->global_child_idx) );
-		
-		if (local_eid >= t->num_elems[level_id]) {
-			level_id++;
-		}
-		el_data->level_id = level_id;
-	}
-	return H5_SUCCESS;
-}
 
 static h5_err_t
 read_elems (
@@ -292,11 +247,11 @@ read_elems (
 		     &t->dsinfo_elems,
 		     open_mem_space_elems,
 		     open_file_space_elems,
-		     t->elems.data) );
+		     t->glb_elems.data) );
 
 	TRY( h5tpriv_sort_elems (f) );
 	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
-	TRY( build_elems_ldta (f) );
+	TRY( (*f->t->methods.read->init_loc_elems_struct) (f) );
 
 	return H5_SUCCESS;
 }

src/h5core/h5t_readwrite_private.h

@@ -22,4 +22,7 @@ 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;
+
 #endif

src/h5core/h5t_ref_elements.c

@@ -1,6 +1,6 @@
 #include "h5core/h5_core.h"
 
-const h5t_ref_element_t h5t_tri_ref_element = {
+const h5t_ref_elem_t h5t_tri_ref_elem = {
 	2,
 	{3, 3, 1}, // #vertices, #edges, #triangles
 	{
@@ -16,7 +16,7 @@ const h5t_ref_element_t h5t_tri_ref_element = {
 	{{0.0, 0.0}, {1.0, 0.0}, {0.0, 1.0}},
 };
 
-const h5t_ref_element_t h5t_tet_ref_element = {
+const h5t_ref_elem_t h5t_tet_ref_elem = {
 	3,
 	{4, 6, 4, 1}, // #vertices, #edges, #triangles, #tetrahedra
 	{

src/h5core/h5t_retrieve.c

@@ -3,6 +3,8 @@
 #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.
 */
@@ -11,19 +13,18 @@ h5tpriv_skip_to_next_elem_on_level (
 	h5_file_t* f,
 	h5t_entity_iterator_t* iter
 	) {
-	h5t_fdata_t* t = f->t;
-	h5_elem_ldta_t* el_dta;
-	int num_elems = t->num_elems[t->cur_level];
+	h5_generic_elem_t* el;
 	do {
 		iter->elem_idx++;
-		if (iter->elem_idx >= num_elems) {
+		if (iter->elem_idx >= num_elems_on_cur_level) {
 			return H5_NOK;
 		}
-		el_dta = &t->elems_ldta[iter->elem_idx];
-	} while (h5tpriv_elem_is_on_cur_level (f, el_dta) == H5_NOK);
+		el = h5tpriv_get_loc_elem (f, iter->elem_idx);
+	} while (h5tpriv_elem_is_on_cur_level (f, el) == 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
@@ -32,12 +33,11 @@ h5tpriv_skip_to_next_elem_on_level (
 h5_err_t
 h5tpriv_elem_is_on_cur_level (
 	h5_file_t* const f,
-	h5_elem_ldta_t *el_dta 
+	h5_generic_elem_t *el 
 	) {
 	h5t_fdata_t* t = f->t;
-	if ( (el_dta->level_id > t->cur_level) ||
-	     ( (el_dta->local_child_idx >= 0) &&
-	       (el_dta->local_child_idx < t->num_elems[t->cur_level]) ) ) {
+	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;
@@ -79,11 +79,10 @@ iterate_faces (
 	h5_file_t* const f,
 	h5t_entity_iterator_t* iter
 	) {
-	h5t_fdata_t* t = f->t;
 	h5_idlist_t* entry;
 	h5_size_t i;
-	int dim = iter->ref_element->dim - iter->codim;
-	int num_faces = iter->ref_element->num_faces[dim] - 1;
+	int dim = iter->ref_elem->dim - iter->codim;
+	int num_faces = iter->ref_elem->num_faces[dim] - 1;
 	do {
 		if (iter->face_idx >= num_faces) {
 			if (h5tpriv_skip_to_next_elem_on_level (f, iter) == H5_NOK) {
@@ -102,12 +101,12 @@ iterate_faces (
 		TRY( (iter->find)(f, iter->face_idx,
 				  iter->elem_idx, &entry) );
 		i = -1;
-		h5_elem_ldta_t *el_dta;
+		h5_generic_elem_t *el;
 		do {
 			i++;
-			h5_id_t eid = h5tpriv_get_elem_idx (entry->items[i]);
-			el_dta = &t->elems_ldta[eid];
-		} while (h5tpriv_elem_is_on_cur_level (f, el_dta) == H5_NOK);
+			h5_id_t idx = h5tpriv_get_elem_idx (entry->items[i]);
+			el = h5tpriv_get_loc_elem (f, idx);
+		} while (h5tpriv_elem_is_on_cur_level (f, el) == H5_NOK);
 	} while (iter->elem_idx != h5tpriv_get_elem_idx(entry->items[i]));
 	
 	return entry->items[0];
@@ -147,7 +146,7 @@ h5t_end_iterate_entities (
 	iter->face_idx = -1;
 	iter->elem_idx = -1;
 	iter->codim = -1;
-	iter->ref_element = NULL;
+	iter->ref_elem = NULL;
 	iter->find = NULL;
 	return H5_SUCCESS;
 }
@@ -164,7 +163,7 @@ h5t_get_vertex_coords_by_index (
 }
 
 h5_err_t
-h5t_get_vertrex_coords_by_id (
+h5t_get_vertex_coords_by_id (
 	h5_file_t* const f,
 	h5_id_t vertex_id,
 	h5_float64_t P[3]

src/h5core/h5t_retrieve_private.h

@@ -9,8 +9,11 @@ h5tpriv_skip_to_next_elem_on_level (
 
 h5_err_t
 h5tpriv_elem_is_on_cur_level (
-	h5_file_t * const f,
-	h5_elem_ldta_t *el_dta 
+	h5_file_t* const f,
+	h5_generic_elem_t* el
 	);
 
+extern struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods;
+extern struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods;
+
 #endif

src/h5core/h5t_retrieve_tetm.c

@@ -6,14 +6,14 @@
 static h5_err_t
 begin_iterate_entities (
 	h5_file_t* f,
-	h5t_entity_iterator_t* iter,
+	h5t_entity_iterator_t* const iter,
 	const int codim
 	) {
 	iter->face_idx = -1;
 	iter->elem_idx = -1;
 	iter->codim = codim;
-	iter->ref_element = f->t->ref_element;
-	switch (iter->ref_element->dim - codim) {
+	iter->ref_elem = f->t->ref_elem;
+	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);
@@ -31,7 +31,7 @@ begin_iterate_entities (
 	}
 }
 
-struct h5t_retrieve_methods h5tpriv_tetm_retrieve_methods = {
-	begin_iterate_entities
+struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods = {
+	begin_iterate_entities,
 };
 	

src/h5core/h5t_retrieve_trim.c

@@ -12,8 +12,8 @@ begin_iterate_entities (
 	iter->face_idx = -1;
 	iter->elem_idx = -1;
 	iter->codim = codim;
-	iter->ref_element = f->t->ref_element;
-	switch (iter->ref_element->dim - codim) {
+	iter->ref_elem = f->t->ref_elem;
+	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);
@@ -29,5 +29,5 @@ begin_iterate_entities (
 }
 
 struct h5t_retrieve_methods h5tpriv_trim_retrieve_methods = {
-	begin_iterate_entities
+	begin_iterate_entities,
 };

src/h5core/h5t_store.c

@@ -63,28 +63,26 @@ assign_global_elem_indices (
 	  simple in serial runs: global index = local index
 	*/
 	h5_id_t local_idx = (t->cur_level == 0) ? 0 : t->num_elems[t->cur_level-1];
-
+	int num_vertices = t->ref_elem->num_faces[0];
+	
 	for (; local_idx < t->num_elems[t->cur_level]; local_idx++) {
-		h5_elem_t *elem;
-		h5_elem_ldta_t *elem_ldta = &t->elems_ldta[local_idx];
-		switch ( t->mesh_type ) {
-		case H5_OID_TETRAHEDRON:
-			elem = (h5_elem_t*)&t->elems.tets[local_idx];
-			break;
-		case H5_OID_TRIANGLE:
-			elem = (h5_elem_t*)&t->elems.tris[local_idx];
-			break;
-		default:
-			return h5_error_internal (f,__FILE__,__func__,__LINE__);
-		}
-		elem->global_idx = local_idx;
-		elem->global_parent_idx = elem_ldta->local_parent_idx;
-		elem->global_child_idx = elem_ldta->local_child_idx;
-		int i;
-		int num_vertices = t->ref_element->num_faces[0];
-		for (i = 0; i < num_vertices; i++) {
-			elem->global_vertex_indices[i] = elem_ldta->local_vertex_indices[i];
-		}
+		h5_generic_elem_t *loc_elem = h5tpriv_get_loc_elem (f, local_idx);
+		h5_generic_elem_t *glb_elem = h5tpriv_get_glb_elem (f, local_idx);
+
+		glb_elem->idx = local_idx;
+		glb_elem->parent_idx = loc_elem->parent_idx;
+		glb_elem->child_idx = loc_elem->child_idx;
+
+		h5_id_t* glb_indices = h5tpriv_get_glb_elem_vertex_indices (f, local_idx);
+		h5_id_t* loc_indices = h5tpriv_get_loc_elem_vertex_indices (f, local_idx);
+
+		memcpy (glb_indices, loc_indices, num_vertices*sizeof(*glb_indices));
+
+		glb_indices = h5tpriv_get_glb_elem_neighbor_indices (f, local_idx);
+		loc_indices = h5tpriv_get_loc_elem_neighbor_indices (f, local_idx);
+
+		memcpy (glb_indices, loc_indices, num_vertices*sizeof(*glb_indices));
+
 	}
 
 	return H5_SUCCESS;
@@ -232,8 +230,8 @@ h5t_begin_store_elems (
 h5_id_t
 h5t_store_elem (
 	h5_file_t* const f,
-	const h5_id_t elem_idx_of_parent,
-	const h5_id_t* vertices
+	const h5_id_t parent_idx,
+	const h5_id_t* vertex_indices
 	) {
 	h5t_fdata_t* t = f->t;
 
@@ -248,29 +246,30 @@ h5t_store_elem (
 			t->num_elems[t->cur_level] );
 
 	/* check parent id */
-	if ((t->cur_level == 0 && elem_idx_of_parent != -1) ||
-	    (t->cur_level >  0 && elem_idx_of_parent < 0) ||
+	if ((t->cur_level == 0 && parent_idx != -1) ||
+	    (t->cur_level >  0 && parent_idx < 0) ||
 	    (t->cur_level >  0
-	     && elem_idx_of_parent >= t->num_elems[t->cur_level-1])
+	     && parent_idx >= t->num_elems[t->cur_level-1])
 		) {
 		return HANDLE_H5_PARENT_ID_ERR (
-			f,
-			h5tpriv_map_oid2str (t->mesh_type),
-			elem_idx_of_parent);
+			f, h5tpriv_map_oid2str (t->mesh_type), parent_idx);
 	}
-	h5_id_t elem_idx = ++t->last_stored_eid;
-	h5_elem_ldta_t* elem_ldta = &t->elems_ldta[elem_idx];
 
-	elem_ldta->local_parent_idx = elem_idx_of_parent;
-	elem_ldta->local_child_idx = -1;
-	elem_ldta->level_id = t->cur_level;
-	int num_vertices = t->ref_element->num_faces[0];
-	memcpy (elem_ldta->local_vertex_indices, vertices,
-		 sizeof (*vertices) * num_vertices);
-	h5tpriv_sort_local_vertex_indices (f, elem_ldta->local_vertex_indices,
-					   num_vertices);
+	/* store elem data (but neighbors) */
+	h5_id_t elem_idx = ++t->last_stored_eid;
+	h5tpriv_set_loc_elem_idx (f, elem_idx, elem_idx);
+	h5tpriv_set_loc_elem_parent_idx (f, elem_idx, parent_idx);
+	h5tpriv_set_loc_elem_child_idx (f, elem_idx, -1);
+	h5tpriv_set_loc_elem_level_idx (f, elem_idx, t->cur_level);
+
+	h5_id_t* loc_elem_vertex_indices = h5tpriv_get_loc_elem_vertex_indices (f, elem_idx);
+	int num_vertices = t->ref_elem->num_faces[0];
+	memcpy (loc_elem_vertex_indices, vertex_indices, sizeof (*vertex_indices) * num_vertices);
+	h5tpriv_sort_local_vertex_indices (f, loc_elem_vertex_indices, num_vertices);
+
+	/* add edges to directory which maps edges to elements */
 	h5_id_t face_idx;
-	int num_faces = t->ref_element->num_faces[1];
+	int num_faces = t->ref_elem->num_faces[1];
 	h5_idlist_t* retval;
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
 		// add edges to neighbour struct
@@ -294,7 +293,8 @@ h5t_end_store_elems (
 
 	TRY( h5tpriv_sort_elems (f) );
 	TRY( h5tpriv_rebuild_global_2_local_map_of_elems (f) );
-	TRY( (t->methods.adjacency->update_internal_structs)(f, t->cur_level) );
+
+	TRY( (t->methods.store->end_store_elems)(f) );
 
 	return H5_SUCCESS;
 }

src/h5core/h5t_store_private.h

@@ -1,4 +1,7 @@
 #ifndef __H5T_STOREMESH_PRIVATE_H
 #define __H5T_STOREMESH_PRIVATE_H
 
+extern struct h5t_store_methods h5tpriv_trim_store_methods;
+extern struct h5t_store_methods h5tpriv_tetm_store_methods;
+
 #endif

src/h5core/h5t_store_tetm.c

@@ -10,44 +10,26 @@ alloc_tets (
 	const size_t new
 	) {
 	h5t_fdata_t *t = f->t;
-	const size_t nvertices = 4;
 
 	/* alloc mem for elements */
-	TRY ( t->elems.tets = h5priv_alloc (
+	TRY ( t->glb_elems.tets = h5priv_alloc (
 		      f,
-		      t->elems.tets,
-		      new * sizeof(t->elems.tets[0]) ) );
+		      t->glb_elems.tets,
+		      new * sizeof(t->glb_elems.tets[0]) ) );
 	memset (
-		t->elems.tets + cur,
+		t->glb_elems.tets + cur,
 		-1,
-		(new-cur) * sizeof(t->elems.tets[0]) );
+		(new-cur) * sizeof(t->glb_elems.tets[0]) );
 
 	/* alloc mem for local data of elements */
-	TRY ( t->elems_ldta = h5priv_alloc (
+	TRY ( t->loc_elems.tets = h5priv_alloc (
 		      f,
-		      t->elems_ldta,
-		      new * sizeof (t->elems_ldta[0]) ) );
+		      t->loc_elems.tets,
+		      new * sizeof (t->loc_elems.tets[0]) ) );
 	memset (
-		t->elems_ldta + cur,
+		t->loc_elems.tets + cur,
 		-1,
-		(new-cur) * sizeof (t->elems_ldta[0]) );
-
-	/* alloc mem for local vertex IDs of elements */
-	TRY ( t->elems_lvids = h5priv_alloc (
-		      f,
-		      t->elems_lvids,
-		      new * sizeof(t->elems_lvids[0]) * nvertices ) );
-	memset (
-		t->elems_lvids + cur * nvertices,
-		-1,
-		(new-cur) * sizeof(t->elems_lvids[0]) * nvertices );
-
-	/* re-init pointer to local vertex id in local data structure */
-	h5_id_t *p = t->elems_lvids;
-	h5_id_t id;
-	for ( id = 0; id < new; id++, p+=nvertices ) {
-		t->elems_ldta[id].local_vertex_indices = p;
-	}
+		(new-cur) * sizeof (t->loc_elems.tets[0]) );
 
 	/* alloc mem for global to local ID mapping */
 	TRY ( h5priv_alloc_idmap ( f, &t->map_elem_g2l, new ) );
@@ -74,7 +56,7 @@ get_direct_children_of_edge (
 			   {1,3}, // edge 4
 			   {2,3}  // edge 5
 	};
-	int num_faces = f->t->ref_element->num_faces[1];
+	int num_faces = f->t->ref_elem->num_faces[1];
 	if ((face_idx < 0) || ( face_idx >= num_faces)) {
 		return h5_error_internal (f, __FILE__, __func__, __LINE__); 
 	}
@@ -93,24 +75,23 @@ get_direct_children_of_edge (
 static h5_id_t
 bisect_edge (
 	h5_file_t* const f,
-	h5_id_t face_id,
-	h5_id_t elem_id
+	const h5_id_t face_idx,
+	const h5_id_t elem_idx
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_id_t vids[2];
-	h5_idlist_t *retval;
+	h5t_fdata_t* t = f->t;
+	h5_idlist_t* retval;
 	/*
 	  get all elements sharing the given edge
 	 */
-	TRY( h5tpriv_find_te2 (f, face_id, elem_id, &retval) );
+	TRY( h5tpriv_find_te2 (f, face_idx, elem_idx, &retval) );
 	/*
 	  check wether one of the found elements has been refined
 	 */
 	size_t i;
 	for ( i = 0; i < retval->num_items; i++ ) {
-		h5_id_t local_id = h5tpriv_get_elem_idx ( retval->items[i] );
-		h5_elem_ldta_t *tet = &t->elems_ldta[local_id];
-		if ( tet->local_child_idx >= 0 ) {
+		h5_id_t idx = h5tpriv_get_elem_idx ( retval->items[i] );
+		h5_id_t child_idx = h5tpriv_get_loc_elem_child_idx (f, idx);
+		if ( child_idx >= 0 ) {
 			/*
 			  this element has been refined!
 			  return bisecting point
@@ -121,7 +102,7 @@ bisect_edge (
 			TRY( get_direct_children_of_edge (
 				     f,
 				     face_id,
-				     tet->local_child_idx,
+				     child_idx,
 				     kids) );
 			TRY( h5t_get_vertex_indices_of_edge (f, kids[0], edge0) );
 			TRY( h5t_get_vertex_indices_of_edge (f, kids[1], edge1) );
@@ -134,8 +115,10 @@ bisect_edge (
 	/*
 	  None of the elements has been refined -> add new vertex.
 	 */
-	h5_float64_t *P0 = t->vertices[vids[0]].P;
-	h5_float64_t *P1 = t->vertices[vids[1]].P;
+	h5_id_t indices[2];
+	TRY( h5t_get_vertex_indices_of_edge2 (f, face_idx, elem_idx, indices) );
+	h5_float64_t *P0 = t->vertices[indices[0]].P;
+	h5_float64_t *P1 = t->vertices[indices[1]].P;
 	h5_float64_t P[3];
 
 	P[0] = ( P0[0] + P1[0] ) / 2.0;
@@ -158,18 +141,18 @@ refine_tet (
 	h5t_fdata_t* t = f->t;
 	h5_id_t vertices[10];
 	h5_id_t elem_idx_of_first_child;
-	h5_elem_ldta_t *tet = &t->elems_ldta[elem_idx];
+	h5_tet_t* el = &t->loc_elems.tets[elem_idx];
 
-	if ( tet->local_child_idx >= 0 )
+	if ( el->child_idx >= 0 )
 		return h5_error (
 			f,
 			H5_ERR_INVAL,
 			"Tetrahedron %lld already refined.",
 			(long long)elem_idx );
-	vertices[0] = tet->local_vertex_indices[0];
-	vertices[1] = tet->local_vertex_indices[1];
-	vertices[2] = tet->local_vertex_indices[2];
-	vertices[3] = tet->local_vertex_indices[3];
+	vertices[0] = el->vertex_indices[0];
+	vertices[1] = el->vertex_indices[1];
+	vertices[2] = el->vertex_indices[2];
+	vertices[3] = el->vertex_indices[3];
 
 	vertices[4] = bisect_edge (f, 0, elem_idx);
 	vertices[5] = bisect_edge (f, 1, elem_idx);
@@ -231,15 +214,23 @@ refine_tet (
 	new_elem[3] = vertices[9];
 	TRY( h5t_store_elem (f, elem_idx, new_elem) );
 
-	t->elems.tets[elem_idx].global_child_idx = elem_idx_of_first_child;
-	t->elems_ldta[elem_idx].local_child_idx = elem_idx_of_first_child;
+	t->glb_elems.tets[elem_idx].child_idx = elem_idx_of_first_child;
+	t->loc_elems.tets[elem_idx].child_idx = elem_idx_of_first_child;
 	t->num_elems_on_level[t->cur_level]--;
 
 	return elem_idx_of_first_child;
 }
 
+h5_err_t
+end_store_elems (
+	h5_file_t* f
+	) {
+	return H5_SUCCESS;
+}
+
 struct h5t_store_methods h5tpriv_tetm_store_methods = {
 	alloc_tets,
 	refine_tet,
+	end_store_elems,
 	get_direct_children_of_edge
 };

src/h5core/h5t_store_trim.c

@@ -10,44 +10,26 @@ alloc_triangles (
 	const size_t new
 	) {
 	h5t_fdata_t *t = f->t;
-	const size_t nvertices = 3;
 
 	/* alloc mem for elements */
-	TRY ( t->elems.tris = h5priv_alloc (
+	TRY ( t->glb_elems.tris = h5priv_alloc (
 		      f,
-		      t->elems.tris,
-		      new * sizeof(t->elems.tris[0]) ) );
+		      t->glb_elems.tris,
+		      new * sizeof(t->glb_elems.tris[0]) ) );
 	memset (
-		t->elems.tris + cur,
+		t->glb_elems.tris + cur,
 		-1,
-		(new-cur) * sizeof(t->elems.tris[0]) );
+		(new-cur) * sizeof(t->glb_elems.tris[0]) );
 
 	/* alloc mem for local data of elements */
-	TRY ( t->elems_ldta = h5priv_alloc (
+	TRY ( t->loc_elems.tris = h5priv_alloc (
 		      f,
-		      t->elems_ldta,
-		      new * sizeof (t->elems_ldta[0]) ) );
+		      t->loc_elems.tris,
+		      new * sizeof (t->loc_elems.tris[0]) ) );
 	memset (
-		t->elems_ldta + cur,
+		t->glb_elems.tris + cur,
 		-1,
-		(new-cur) * sizeof (t->elems_ldta[0]) );
-
-	/* alloc mem for local vertex IDs of elements */
-	TRY ( t->elems_lvids = h5priv_alloc (
-		      f,
-		      t->elems_lvids,
-		      new * sizeof(t->elems_lvids[0]) * nvertices ) );
-	memset (
-		t->elems_lvids + cur * sizeof(t->elems_lvids[0]) * nvertices,
-		-1,
-		(new-cur) * sizeof(t->elems_lvids[0]) * nvertices );
-
-	/* re-init pointer to local vertex id in local data structure */
-	h5_id_t *p = t->elems_lvids;
-	h5_id_t id;
-	for ( id = 0; id < new; id++, p+=nvertices ) {
-		t->elems_ldta[id].local_vertex_indices = p;
-	}
+		(new-cur) * sizeof (t->loc_elems.tris[0]) );
 
 	/* alloc mem for global to local ID mapping */
 	TRY ( h5priv_alloc_idmap ( f, &t->map_elem_g2l, new ) );
@@ -62,7 +44,7 @@ get_direct_children_of_edge (
 	const h5_id_t elem_idx, // index of the first child!
 	h5_id_t	children[2]
 	) {
-	int num_faces = f->t->ref_element->num_faces[1];
+	int num_faces = f->t->ref_elem->num_faces[1];
 	/*
 	  Please note: The face index of the children and the father is
 	  always the same. The only think we have to know, is the offset
@@ -89,12 +71,12 @@ get_direct_children_of_edge (
 
 static h5_id_t
 bisect_edge (
-	h5_file_t * const f,
-	h5_id_t face_idx,
-	h5_id_t elem_idx
+	h5_file_t* const f,
+	const h5_id_t face_idx,
+	const h5_id_t elem_idx
 	) {
-	h5t_fdata_t *t = f->t;
-	h5_idlist_t *retval;
+	h5t_fdata_t* t = f->t;
+	h5_idlist_t* retval;
 	/*
 	  get all elements sharing the given edge
 	 */
@@ -104,9 +86,9 @@ bisect_edge (
 	 */
 	size_t i;
 	for ( i = 0; i < retval->num_items; i++ ) {
-		h5_id_t local_id = h5tpriv_get_elem_idx ( retval->items[i] );
-		h5_elem_ldta_t *tet = &t->elems_ldta[local_id];
-		if ( tet->local_child_idx >= 0 ) {
+		h5_id_t idx = h5tpriv_get_elem_idx ( retval->items[i] );
+		h5_id_t child_idx = h5tpriv_get_loc_elem_child_idx (f, idx);
+		if ( child_idx >= 0 ) {
 			/*
 			  this element has been refined!
 			  return bisecting point
@@ -117,7 +99,7 @@ bisect_edge (
 			TRY ( get_direct_children_of_edge (
 				      f,
 				      face_id,
-				      tet->local_child_idx,
+				      child_idx,
 				      kids ) );
 			TRY ( h5t_get_vertex_indices_of_edge ( f, kids[0], edge0 ) );
 			TRY ( h5t_get_vertex_indices_of_edge ( f, kids[1], edge1 ) );
@@ -130,10 +112,10 @@ bisect_edge (
 	/*
 	  None of the elements has been refined -> add new vertex.
 	 */
-	h5_id_t vindices[2];
-	TRY( h5t_get_vertex_indices_of_edge2 (f, face_idx, elem_idx, vindices) );
-	h5_float64_t *P0 = t->vertices[vindices[0]].P;
-	h5_float64_t *P1 = t->vertices[vindices[1]].P;
+	h5_id_t indices[2];
+	TRY( h5t_get_vertex_indices_of_edge2 (f, face_idx, elem_idx, indices) );
+	h5_float64_t *P0 = t->vertices[indices[0]].P;
+	h5_float64_t *P1 = t->vertices[indices[1]].P;
 	h5_float64_t P[3];
 
 	P[0] = ( P0[0] + P1[0] ) / 2.0;
@@ -156,18 +138,18 @@ refine_triangle (
 	h5t_fdata_t *t = f->t;
 	h5_id_t vertices[6];	// local vertex indices
 	h5_id_t elem_idx_of_first_child;
-	h5_elem_ldta_t *el = &t->elems_ldta[elem_idx];
+	h5_triangle_t *el = &t->loc_elems.tris[elem_idx];
 
-	if ( el->local_child_idx >= 0 )
+	if ( el->child_idx >= 0 )
 		return h5_error (
 			f,
 			H5_ERR_INVAL,
 			"Element %lld already refined.",
 			(long long)elem_idx );
 
-	vertices[0] = el->local_vertex_indices[0];
-	vertices[1] = el->local_vertex_indices[1];
-	vertices[2] = el->local_vertex_indices[2];
+	vertices[0] = el->vertex_indices[0];
+	vertices[1] = el->vertex_indices[1];
+	vertices[2] = el->vertex_indices[2];
 
 	vertices[3] = bisect_edge( f, 0, elem_idx );
 	vertices[4] = bisect_edge( f, 1, elem_idx );
@@ -195,15 +177,78 @@ refine_triangle (
 	new_elem[2] = vertices[5];
 	TRY( h5t_store_elem (f, elem_idx, new_elem) );
 
-	t->elems.tris[elem_idx].global_child_idx = elem_idx_of_first_child;
-	t->elems_ldta[elem_idx].local_child_idx = elem_idx_of_first_child;
+	t->glb_elems.tris[elem_idx].child_idx = elem_idx_of_first_child;
+	t->loc_elems.tris[elem_idx].child_idx = elem_idx_of_first_child;
 	t->num_elems_on_level[t->cur_level]--;
 
 	return elem_idx_of_first_child;
 }
 
+/*
+  Compute the neighbors in the macro-grid. 
+ */
+static h5_err_t
+compute_neighbors_in_macrogrid (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t *t = f->t;
+	h5_id_t elem_idx = 0;
+	h5_triangle_t *el = &t->loc_elems.tris[0];
+	h5_id_t num_elems = t->num_elems[0];
+	for (;elem_idx < num_elems; elem_idx++, el++) {
+		int face_idx = 0;
+		for (; face_idx < 3; face_idx++) {
+			h5_idlist_t* te;
+
+			TRY( h5tpriv_find_te2 (
+				     f,
+				     face_idx,
+				     elem_idx,
+				     &te) );
+			if (te == NULL) {
+			} else {
+			}
+		}
+	}
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+compute_neighbors_for_refined_elems (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t *t = f->t;
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+compute_neighbors (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t *t = f->t;
+
+	if (t->cur_level == 0) {
+		TRY( compute_neighbors_in_macrogrid (f) );
+	} else {
+		TRY( compute_neighbors_for_refined_elems (f) );
+	}
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+end_store_elems (
+	h5_file_t* const f
+	) {
+	h5t_fdata_t *t = f->t;
+
+	TRY( (t->methods.adjacency->update_internal_structs)(f, t->cur_level) );
+	TRY( compute_neighbors (f) );
+	return H5_SUCCESS;
+}
+
 struct h5t_store_methods h5tpriv_trim_store_methods = {
 	alloc_triangles,
 	refine_triangle,
+	end_store_elems,
 	get_direct_children_of_edge
 };

src/h5core/h5t_store_trim_private.h

@@ -1,5 +1,4 @@
 #ifndef __H5T_TRIM_STORE_PRIVATE_H
 #define __H5T_TRIM_STORE_PRIVATE_H
 
-extern struct h5t_store_methods h5tpriv_trim_store_methods;
 #endif

src/h5core/h5t_types_private.h

@@ -1,9 +1,72 @@
 #ifndef __H5T_TYPES_PRIVATE_H
 #define __H5T_TYPES_PRIVATE_H
 
+typedef struct h5_vertex {
+	h5_id_t		global_idx;
+	h5_coord3d_t	P;
+} h5_vertex_t;
+
+typedef struct h5_vertex_data {
+	h5_idlist_t	tv;
+} h5_vertex_data_t;
+
+typedef struct h5_triangle {
+	h5_id_t		idx;
+	h5_id_t		parent_idx;
+	h5_id_t		child_idx;
+	h5_id_t		level_idx;
+	h5_3id_t	vertex_indices;
+	h5_3id_t	neighbor_indices;
+} h5_triangle_t;
+
+typedef struct h5_tetrahedron {
+	h5_id_t		idx;
+	h5_id_t		parent_idx;
+	h5_id_t		child_idx;
+	h5_id_t		level_idx;
+	h5_4id_t	vertex_indices;
+	h5_4id_t	neighbor_indices;
+} h5_tetrahedron_t;
+typedef h5_tetrahedron_t	h5_tet_t;
+
+typedef struct h5_generic_elem {
+	h5_id_t		idx;
+	h5_id_t		parent_idx;
+	h5_id_t		child_idx;
+	h5_id_t		level_idx;
+	h5_id_t		indices[1];
+} h5_generic_elem_t;
+
+
+typedef union h5_elems {
+	h5_tet_t	*tets;
+	h5_triangle_t	*tris;
+	void		*data;
+} h5_elems_t;
+
+/*** type ids' for compound types ***/
+typedef struct h5_dtypes {
+	hid_t		h5_id_t;		/* ID's */
+	hid_t		h5_int64_t;		/* 64 bit signed integer */
+	hid_t		h5_float64_t;		/* 64 bit floating point */
+	hid_t		h5_coord3d_t;		/* 3-tuple of 64-bit float */
+	hid_t		h5_3id_t;		/* 3-tuple of ID's */
+	hid_t		h5_4id_t;		/* 4-tuple of ID's */
+	hid_t		h5_vertex_t;		/* vertex structure */
+	hid_t		h5_triangle_t;		/* triangle structure */
+	hid_t		h5_tet_t;		/* tetrahedron structure */
+	hid_t		h5t_tag_idx_t;
+} h5_dtypes_t;
+
+typedef struct h5t_adjacencies {
+	h5_hashtable_t te_hash;
+	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_id_t (*refine_elem)(h5_file_t* const, const h5_id_t);
+	h5_err_t (*end_store_elems)(h5_file_t* const);
 	h5_id_t (*get_direct_children_of_edge)(h5_file_t* const, const h5_id_t, const h5_id_t, h5_id_t*);
 };
 
@@ -11,6 +74,76 @@ struct h5t_retrieve_methods {
 	h5_err_t (*init_iterator)(h5_file_t* const, h5t_entity_iterator_t*, const int);
 };
 
+
+struct h5t_access_methods {
+	h5_generic_elem_t* (*get_loc_elem)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_loc_elem_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_loc_elem_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_loc_elem_parent_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_loc_elem_parent_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_loc_elem_child_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_loc_elem_child_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_loc_elem_level_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_loc_elem_level_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t* (*get_loc_elem_vertex_indices)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_loc_elem_vertex_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*set_loc_elem_vertex_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
+	h5_id_t* (*get_loc_elem_neighbor_indices)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_loc_elem_neighbor_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*set_loc_elem_neighbor_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
+
+	h5_generic_elem_t* (*get_glb_elem)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_glb_elem_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_glb_elem_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_glb_elem_parent_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_glb_elem_parent_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_glb_elem_child_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_glb_elem_child_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*get_glb_elem_level_idx)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*set_glb_elem_level_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t* (*get_glb_elem_vertex_indices)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_glb_elem_vertex_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*set_glb_elem_vertex_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
+	h5_id_t* (*get_glb_elem_neighbor_indices)(
+		h5_file_t* const, const h5_id_t);
+	h5_id_t (*get_glb_elem_neighbor_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t);
+	h5_id_t (*set_glb_elem_neighbor_idx)(
+		h5_file_t* const, const h5_id_t, const h5_id_t, const h5_id_t);
+
+};
+
+struct h5t_read_methods {
+	h5_err_t (*init_loc_elems_struct)(h5_file_t* const);
+};
+
 struct h5t_adjacency_methods {
 	h5_err_t (*update_internal_structs)(h5_file_t* const, h5_id_t);
 	h5_err_t (*release_internal_structs)(h5_file_t* const);
@@ -40,101 +173,21 @@ struct h5t_adjacency_methods {
 		h5_file_t * const, const h5_id_t, h5_idlist_t**);
 };
 
-struct h5t_methods {
+typedef struct h5t_methods {
+	struct h5t_read_methods *read;
 	struct h5t_store_methods *store;
 	struct h5t_retrieve_methods *retrieve;
+	struct h5t_access_methods *access;
 	struct h5t_adjacency_methods *adjacency;
-};
+} h5t_methods_t;
 
-typedef struct h5_vertex {
-	h5_id_t		global_idx;
-	h5_coord3d_t	P;
-} h5_vertex_t;
-
-typedef struct h5_vertex_data {
-	h5_idlist_t	tv;
-} h5_vertex_data_t;
-
-typedef struct h5_triangle {
-	h5_id_t		global_idx;
-	h5_id_t		global_parent_idx;
-	h5_id_t		global_child_idx;
-	h5_3id_t	global_vertex_indices;
-} h5_triangle_t;
-
-typedef struct h5_tetrahedron {
-	h5_id_t		global_idx;
-	h5_id_t		global_parent_idx;
-	h5_id_t		global_child_idx;
-	h5_4id_t	global_vertex_indices;
-} h5_tetrahedron_t;
-typedef h5_tetrahedron_t	h5_tet_t;
-
-typedef struct h5_elem {
-	h5_id_t		global_idx;
-	h5_id_t		global_parent_idx;
-	h5_id_t		global_child_idx;
-	h5_id_t		global_vertex_indices[1];
-} h5_elem_t;
-
-typedef struct h5_elem_ldta {
-	h5_id_t		local_parent_idx;
-	h5_id_t		local_child_idx;
-	h5_id_t		level_id;
-	h5_id_t		*local_vertex_indices;
-} h5_elem_ldta_t;
-
-
-typedef union h5_elems {
-	h5_tet_t	*tets;
-	h5_triangle_t	*tris;
-	void		*data;
-} h5_elems_t;
-
-
-
-
-typedef struct boundary {
-	char		name[16];
-	char		label[256];
-	h5_id_t		id;			/* name of boundary as integer */
-	h5_id_t		changed;		/* true if boundary is new or
-						   has been changed */
-	h5_id_t		gid;			/* hdf5 grp id boundary */
-	h5_id_t		*faces;
-	h5_id_t		*lfaces;
-	h5_size_t	*num_faces;		/* addit. num of faces per level */
-	h5_size_t	*num_faces_on_level;	/* real num of faces per level */
-	
-	h5_id_t		last_accessed_face;
-	h5_dsinfo_t	dsinfo;
-} boundary_t;
-
-/*** type ids' for compound types ***/
-typedef struct h5_dtypes {
-	hid_t		h5_id_t;		/* ID's */
-	hid_t		h5_int64_t;		/* 64 bit signed integer */
-	hid_t		h5_float64_t;		/* 64 bit floating point */
-	hid_t		h5_coord3d_t;		/* 3-tuple of 64-bit float */
-	hid_t		h5_3id_t;		/* 3-tuple of ID's */
-	hid_t		h5_4id_t;		/* 4-tuple of ID's */
-	hid_t		h5_vertex_t;		/* vertex structure */
-	hid_t		h5_triangle_t;		/* triangle structure */
-	hid_t		h5_tet_t;		/* tetrahedron structure */
-	hid_t		h5t_tag_idx_t;
-} h5_dtypes_t;
-
-typedef struct h5t_adjacencies {
-	h5_hashtable_t te_hash;
-	h5_hashtable_t td_hash;
-} h5t_adjacencies_t;
 
 typedef struct h5t_fdata {
 	/*** book-keeping ***/
 	char		mesh_name[16];
 	char		mesh_label[256];
 	h5_oid_t	mesh_type;	/* object id of element type */
-	const h5t_ref_element_t*  ref_element;
+	const h5t_ref_elem_t*  ref_elem;
 	h5_id_t		cur_mesh;	/* id of current mesh */
 	h5_id_t		mesh_changed;	/* true if new or has been changed */
 	h5_id_t		num_meshes;	/* number of meshes */
@@ -166,9 +219,9 @@ typedef struct h5t_fdata {
 	
 
 	/*** Elements ***/
-	h5_elems_t	elems;
-	h5_elem_ldta_t	*elems_ldta;	/* local, per element data */
-	h5_id_t		*elems_lvids;
+	h5_elems_t	glb_elems;
+	h5_elems_t	loc_elems;
+
 	h5_size_t	*num_elems;
 	h5_size_t	*num_elems_on_level;
 	h5_idmap_t	map_elem_g2l;	/* map global id to local id */
@@ -188,13 +241,6 @@ typedef struct h5t_fdata {
 
 	h5_idlist_t	marked_entities;
 
-#if 0
-	/*** Boundary Meshes ***/
-	h5_id_t		num_boundaries;		/* number of boundaries */
-	h5_id_t		boundaries_gid;		/* hdf5 grp id container group */
-
-	boundary_t	boundary;
-#endif
 	/*** Adjacencies ***/
 	h5t_adjacencies_t adjacencies;