- refactored 'num_elems_on_level' to 'num_elems_on_leaf_level'

- introduced new refinement level

src/h5core/h5t_inquiry.c

@@ -94,7 +94,7 @@ h5t_get_num_elems (
 	if (t->cur_level < 0) {
 		return h5tpriv_error_undef_level (f);
 	}
-	return t->num_elems_on_level[t->cur_level];
+	return t->num_elems_on_leaf_level[t->cur_level];
 }
 
 /*!

src/h5core/h5t_openclose.c

@@ -235,7 +235,7 @@ init_fdata (
 	t->glb_elems.data =		NULL;
 	t->loc_elems.data =		NULL;
 	t->num_elems =			NULL;
-	t->num_elems_on_level =		NULL;
+	t->num_elems_on_leaf_level =	NULL;
 	t->map_elem_g2l.items =		NULL;
 	t->vertices =			NULL; 
 	t->num_vertices =		NULL;
@@ -310,21 +310,21 @@ init_fdata (
 	t->dsinfo_num_elems.access_prop = H5P_DEFAULT;
 
 	/* NumElemsOnLevel */
-	strcpy (t->dsinfo_num_elems_on_level.name, "NumElemsOnLevel");
-	t->dsinfo_num_elems_on_level.rank = 1;
-	t->dsinfo_num_elems_on_level.dims[0] = 0;
-	t->dsinfo_num_elems_on_level.max_dims[0] = H5S_UNLIMITED;
-	t->dsinfo_num_elems_on_level.chunk_dims[0] = 4096;
-	t->dsinfo_num_elems_on_level.type_id = t->dtypes.h5_glb_idx_t;
-	TRY( t->dsinfo_num_elems_on_level.create_prop = h5priv_create_hdf5_property (
+	strcpy (t->dsinfo_num_elems_on_leaf_level.name, "NumElemsOnLeafLevel");
+	t->dsinfo_num_elems_on_leaf_level.rank = 1;
+	t->dsinfo_num_elems_on_leaf_level.dims[0] = 0;
+	t->dsinfo_num_elems_on_leaf_level.max_dims[0] = H5S_UNLIMITED;
+	t->dsinfo_num_elems_on_leaf_level.chunk_dims[0] = 4096;
+	t->dsinfo_num_elems_on_leaf_level.type_id = t->dtypes.h5_glb_idx_t;
+	TRY( t->dsinfo_num_elems_on_leaf_level.create_prop = h5priv_create_hdf5_property (
 		     f,
 		     H5P_DATASET_CREATE) );
 	TRY( h5priv_set_hdf5_chunk_property (
 		     f,
-		     t->dsinfo_num_elems_on_level.create_prop,
-		     t->dsinfo_num_elems_on_level.rank,
-		     t->dsinfo_num_elems_on_level.chunk_dims) );
-	t->dsinfo_num_elems_on_level.access_prop = H5P_DEFAULT;
+		     t->dsinfo_num_elems_on_leaf_level.create_prop,
+		     t->dsinfo_num_elems_on_leaf_level.rank,
+		     t->dsinfo_num_elems_on_leaf_level.chunk_dims) );
+	t->dsinfo_num_elems_on_leaf_level.access_prop = H5P_DEFAULT;
 
 	return H5_SUCCESS;
 }
@@ -499,7 +499,7 @@ release_elems (
 	TRY( h5_free (f, t->glb_elems.data) );
 	TRY( h5_free (f, t->loc_elems.data) );
 	TRY( h5_free (f, t->num_elems) );
-	TRY( h5_free (f, t->num_elems_on_level) );
+	TRY( h5_free (f, t->num_elems_on_leaf_level) );
 	TRY( h5_free (f, t->map_elem_g2l.items) );
 
 	return H5_SUCCESS;

src/h5core/h5t_readwrite.c

@@ -73,10 +73,10 @@ write_elems (
 	TRY( h5priv_write_dataset_by_name (
 		     f,
 		     t->mesh_gid,
-		     &t->dsinfo_num_elems_on_level,
+		     &t->dsinfo_num_elems_on_leaf_level,
 		     open_space_all,
 		     open_space_all,
-		     t->num_elems_on_level) );
+		     t->num_elems_on_leaf_level) );
 
 	return H5_SUCCESS;
 }
@@ -192,8 +192,8 @@ read_num_elems (
 		return h5_error_internal (f, __FILE__, __func__, __LINE__);
 	}
 	size_t size = t->num_levels * sizeof (t->num_elems[0]);
-	TRY( t->num_elems = h5_alloc (f, NULL, size) );
-	TRY( t->num_elems_on_level = h5_alloc (f, NULL, size) );
+	TRY( t->num_elems = h5_calloc (f, 1, size) );
+	TRY( t->num_elems_on_leaf_level = h5_calloc (f, 1, size) );
 	TRY( h5priv_read_dataset_by_name (
 		     f,
 		     t->mesh_gid,
@@ -205,10 +205,10 @@ read_num_elems (
 	TRY( h5priv_read_dataset_by_name (
 		     f,
 		     t->mesh_gid,
-		     &t->dsinfo_num_elems_on_level,
+		     &t->dsinfo_num_elems_on_leaf_level,
 		     open_space_all,
 		     open_space_all,
-		     t->num_elems_on_level) );
+		     t->num_elems_on_leaf_level) );
 	
 	return H5_SUCCESS;
 }

src/h5core/h5t_readwrite_tetm.c

@@ -36,6 +36,14 @@ init_loc_elems_struct (
 		}
 		loc_elem->level_idx = level_idx;
 
+		// refinement level
+		loc_elem->refinement_level = 0;
+		h5_loc_tet_t* elem = loc_elem;
+		while (elem->parent_idx > 0) {
+			elem = t->loc_elems.tets + elem->parent_idx;
+			loc_elem->refinement_level++;
+		}
+
 		// vertex indices
 		TRY( h5t_map_global_vertex_indices2local (
 			     f,
@@ -49,17 +57,6 @@ init_loc_elems_struct (
 			     glb_elem->neighbor_indices,
 			     num_facets,
 			     loc_elem->neighbor_indices) );
-#if 0
-		// done in function below
-                // on boundary?
-		int i;
-		for (i=0; i < num_facets; i++) {
-			if (loc_elem->neighbor_indices[i] == -1) {
-				loc_elem->flags |= H5T_BOUNDARY_ELEM_FLAG;
-				break;
-			}
-		}
-#endif
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_readwrite_trim.c

@@ -36,6 +36,14 @@ init_loc_elems_struct (
 		}
 		loc_elem->level_idx = level_idx;
 
+		// refinement level
+		loc_elem->refinement_level = 0;
+		h5_loc_triangle_t* elem = loc_elem;
+		while (elem->parent_idx > 0) {
+			elem = t->loc_elems.tris + elem->parent_idx;
+			loc_elem->refinement_level++;
+		}
+
 		// vertex indices
 		TRY( h5t_map_global_vertex_indices2local (
 			     f,
@@ -49,16 +57,7 @@ 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++) {
-			if (loc_elem->neighbor_indices[i] == -1) {
-				loc_elem->flags |= H5T_BOUNDARY_ELEM_FLAG;
-				break;
-			}
-		}
-#endif
+
 	}
 	return H5_SUCCESS;
 }

src/h5core/h5t_retrieve.c

@@ -220,7 +220,7 @@ h5t_init_boundary_face_iterator (
 	H5_CORE_API_ENTER;
 	h5_err_t h5err = H5_SUCCESS;
 	h5t_leaf_iterator_t* it;
-	it->face_idx = 999; // just a high enough number
+	it->face_idx = 999; // something > max number of faces
 	it->elem_idx = -1;
 	it->codim = codim;
 	it->leaf_level = f->t->cur_level;

src/h5core/h5t_store.c

@@ -139,7 +139,7 @@ h5t_add_level (
 	t->num_loaded_levels = t->num_levels;
 	t->dsinfo_num_vertices.dims[0] = t->num_levels;
 	t->dsinfo_num_elems.dims[0] = t->num_levels;
-	t->dsinfo_num_elems_on_level.dims[0] = t->num_levels;
+	t->dsinfo_num_elems_on_leaf_level.dims[0] = t->num_levels;
 
 	ssize_t num_bytes = t->num_levels*sizeof (h5_size_t);
 	TRY( t->num_vertices = h5_alloc (f, t->num_vertices, num_bytes) );
@@ -147,9 +147,9 @@ h5t_add_level (
 
 	TRY( t->num_elems = h5_alloc (f, t->num_elems, num_bytes) );
 	t->num_elems[t->cur_level] = -1;
-	TRY( t->num_elems_on_level = h5_alloc (
-		     f, t->num_elems_on_level, num_bytes) );
-	t->num_elems_on_level[t->cur_level] = -1;
+	TRY( t->num_elems_on_leaf_level = h5_alloc (
+		     f, t->num_elems_on_leaf_level, num_bytes) );
+	t->num_elems_on_leaf_level[t->cur_level] = -1;
 
 	if (t->cur_level == 0) {
 		/* nothing stored yet */
@@ -238,8 +238,8 @@ h5t_begin_store_elems (
 	t->num_elems[t->cur_level] = new;
 	t->dsinfo_elems.dims[0] = new;
 
-	t->num_elems_on_level[t->cur_level] = t->cur_level > 0 ?
-		num + t->num_elems_on_level[t->cur_level-1] : num;
+	t->num_elems_on_leaf_level[t->cur_level] = t->cur_level > 0 ?
+		num + t->num_elems_on_leaf_level[t->cur_level-1] : num;
 	/*
 	  We allocate a hash table for a minimum of 2^21 edges to
 	  avoid resizing.

src/h5core/h5t_store_tetm.c

@@ -217,7 +217,7 @@ refine_tet (
 
 	// 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]--;
+	t->num_elems_on_leaf_level[t->cur_level]--;
 
 	return elem_idx_of_first_child;
 }

src/h5core/h5t_store_trim.c

@@ -181,7 +181,7 @@ refine_triangle (
 
 	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]--;
+	t->num_elems_on_leaf_level[t->cur_level]--;
 
 	return elem_idx_of_first_child;
 }

src/h5core/h5t_types_private.h

@@ -20,11 +20,11 @@ typedef struct h5_glb_triangle {
 } h5_glb_triangle_t;
 
 typedef struct h5_loc_triangle {
-	h5_glb_idx_t	glb_idx;
-	h5_loc_idx_t	parent_idx;
-	h5_loc_idx_t	child_idx;
-	h5t_lvl_idx_t	level_idx;
-	h5t_lvl_idx_t	refinement_level;
+	h5_glb_idx_t	glb_idx;	// global index of element
+	h5_loc_idx_t	parent_idx;	// index of parent element
+	h5_loc_idx_t	child_idx;	// index of (first) children
+	h5t_lvl_idx_t	level_idx;	// leaf level on which this element has been created
+	h5t_lvl_idx_t	refinement_level; // refinements of father in macro-grid
 	h5t_elem_flags_t flags;
 	h5_loc_idx_t	vertex_indices[3];
 	h5_loc_idx_t	neighbor_indices[3];
@@ -158,13 +158,13 @@ typedef struct h5t_fdata {
 	h5_loc_elems_t	loc_elems;
 
 	h5_size_t	*num_elems;
-	h5_size_t	*num_elems_on_level;
+	h5_size_t	*num_elems_on_leaf_level;
 	h5_idxmap_t	map_elem_g2l;	/* map global id to local id */
 
 	h5_loc_idx_t	last_stored_eid;
 	h5_dsinfo_t	dsinfo_elems;
 	h5_dsinfo_t	dsinfo_num_elems;
-	h5_dsinfo_t	dsinfo_num_elems_on_level;
+	h5_dsinfo_t	dsinfo_num_elems_on_leaf_level;
 
 	h5_idlist_t	marked_entities;