bug fixes, some private functions renamed, formating changes

src/C/Makefile.am

@@ -1,5 +1,5 @@
-# src/C level Makefile.am
 
+if ENABLE_C
 # Header files that I wish to install in $(prefix)/include
 include_HEADERS =				\
 	../include/H5.h				\
@@ -22,6 +22,7 @@ include_HEADERS =				\
 
 # Listing of all possible headers that I may include
 EXTRA_HEADERS =
+endif
 
 clean-local:
 	$(RM) *~

src/Fortran/Makefile.am

@@ -1,33 +1,28 @@
-# src/Fortran level Makefile.am
 
-OBJEXT=o
+if ENABLE_FORTRAN
+AM_CPPFLAGS += -I$(top_srcdir)/src/include
 
-AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
-
-F90_FILES =     	H5F.f90			\
-			H5_constF.f90		\
-			H5_attribsF.f90		\
-			H5PartF.f90		\
-			H5Part_ioF.f90		\
-			H5BlockF.f90		\
-			H5Block_attribsF.f90	\
-			H5Block_ioF.f90
+F90_FILES =			\
+	H5F.f90			\
+	H5_constF.f90		\
+	H5_attribsF.f90		\
+	H5PartF.f90		\
+	H5Part_ioF.f90		\
+	H5BlockF.f90		\
+	H5Block_attribsF.f90	\
+	H5Block_ioF.f90
 
 EXTRA_HEADERS =
 
-# Extra files that I wish to include in the dist tar ball.
-EXTRA_DIST =		TestUnderscoreC.c \
-			TestUnderscore.f \
-			$(F90_FILES)
+EXTRA_DIST =			\
+	TestUnderscoreC.c	\
+	TestUnderscore.f	\
+	$(F90_FILES)
 
-# Files that I don't want to include in the dist tar ball
-nodist_include_HEADERS = ../include/H5hutF.h
+nodist_include_HEADERS = 	\
+	$(top_srcdir)/src/include/H5hutF.h
 
-# What to build... Will be determined by configure script.
-lib_LTLIBRARIES = @LIB_FORTRAN@
-
-# Listing of all possible targets that I may build.
-EXTRA_LTLIBRARIES = libH5hutF.la
+lib_LTLIBRARIES = libH5hutF.la
 
 include_HEADERS =		\
 	../include/H5hutF.h
@@ -41,17 +36,19 @@ libH5hutF_la_SOURCES =		\
 	H5Block_attribs.c	\
 	H5Block_io.c
 
-libH5hutF_la_DEPENDENCIES =
+libH5hutF_la_DEPENDENCIES =	\
+	$(top_srcdir)/src/include/H5hutF.h
 
 libH5hutF_la_LDFLAGS = -version-info 2:0:0 -rpath '$(libdir)'
 
-../include/H5hutF.h: $(F90_FILES)
+$(top_srcdir)/src/include/H5hutF.h: $(F90_FILES)
 	awk '/INTEGER\*8 :: /{print "\t" $$0}' $^ >$@
 	awk '/PARAMETER /{print "\t" $$0}' $^ >> $@
 	awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >>$@
 
 all-local: ../include/H5hutF.h
 	$(INSTALL) -m644 .libs/libH5hutF.a ../lib
+endif
 
 clean: clean-am
 

src/Makefile.am

@@ -1,4 +1,2 @@
-# test level Makefile.am
-
-SUBDIRS = h5core @BINDINGS@
 
+SUBDIRS = h5core C Fortran include

src/h5core/Makefile.am

@@ -1,6 +1,3 @@
-# src level Makefile.am
-
-OBJEXT=o
 
 AM_CPPFLAGS = -I$(top_srcdir)/src/include @AM_CPPFLAGS@
 
@@ -103,13 +100,13 @@ libH5hut_la_DEPENDENCIES = $(EXTRA_HEADERS)
 libH5hut_la_LDFLAGS = -version-info 2:0:0
 
 all-local:
-	$(INSTALL) -m755 -d ../lib
-	$(INSTALL) -m644 .libs/libH5hut.a ../lib
+	$(INSTALL) -m0755 -d $(top_builddir)/src/lib
+	$(INSTALL) -m644 .libs/libH5hut.a $(top_builddir)/src/lib
 
 install-exec-local:
 	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core
-	@$(INSTALL) -m644 ../include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
+	@$(INSTALL) -m644 $(top_srcdir)/src/include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
 
 clean-local:
-	$(RM) -f ../lib/libH5hut.*
+	$(RM) -f $(top_srcdir)/src/lib/libH5hut.*
 	$(RM) -f *~

src/h5core/h5t_access_tetm.c

@@ -205,7 +205,8 @@ copy_glb_elems (
 	return (h5_glb_elem_t*)dst;
 }
 
-int compare_glb_elems(const void *p_a, const void *p_b) {
+static int
+compare_glb_elems(const void *p_a, const void *p_b) {
 	return ((h5_glb_tet_t*) p_a)->idx - ((h5_glb_tet_t*) p_b)->idx;
 }
 

src/h5core/h5t_access_trim.c

@@ -203,7 +203,8 @@ copy_glb_elems (
 	return (h5_glb_elem_t*)dst;
 }
 
-int compare_glb_elems(const void *p_a, const void *p_b) {
+static int
+compare_glb_elems(const void *p_a, const void *p_b) {
 	return ((h5_glb_tri_t*) p_a)->idx - ((h5_glb_tri_t*) p_b)->idx;
 }
 

src/h5core/h5t_adjacencies_tetm.c

@@ -292,7 +292,7 @@ get_edges_uadj_to_vertex (
 	                    "m=%p, entity_id=%llu, list=%p",
 	                    m, (long long unsigned)entity_id, list);
 	h5_loc_idx_t vertex_idx;
-	TRY( h5tpriv_get_vertex_index_of_vertex (m, entity_id, &vertex_idx) );
+	TRY( h5tpriv_get_loc_vtx_idx_of_vtx (m, entity_id, &vertex_idx) );
 	h5_loc_idlist_t* tv = m->adjacencies.tv.v[vertex_idx];
 
 	TRY( h5priv_alloc_loc_idlist (list, 8) );
@@ -335,7 +335,7 @@ get_triangles_uadj_to_vertex (
 	   Note: this list may include tetrahedra which are not in
 	   the (current) leaf grid */
 	h5_loc_idx_t vertex_idx;
-	TRY( h5tpriv_get_vertex_index_of_vertex (m, entity_id, &vertex_idx) );
+	TRY( h5tpriv_get_loc_vtx_idx_of_vtx (m, entity_id, &vertex_idx) );
 	h5_loc_idlist_t* tv = m->adjacencies.tv.v[vertex_idx];
 
 	// build list of upward adjacent triangles
@@ -375,7 +375,7 @@ get_tets_uadj_to_vertex (
 	                    "m=%p, entity_id=%llu, list=%p",
 	                    m, (long long unsigned)entity_id, list);
 	h5_loc_idx_t vertex_idx;
-	TRY( h5tpriv_get_vertex_index_of_vertex (m, entity_id, &vertex_idx) );
+	TRY( h5tpriv_get_loc_vtx_idx_of_vtx (m, entity_id, &vertex_idx) );
 	h5_loc_idlist_t* tv = m->adjacencies.tv.v[vertex_idx];
 
 	TRY( h5priv_alloc_loc_idlist (list, 8) );

src/h5core/h5t_adjacencies_trim.c

@@ -168,7 +168,7 @@ get_edges_uadj_to_vertex (
 	                    "m=%p, entity_id=%llu, list=%p",
 	                    m, (long long unsigned)entity_id, list);
 	h5_loc_idx_t vertex_idx;
-	TRY( h5tpriv_get_vertex_index_of_vertex (m, entity_id, &vertex_idx) );
+	TRY( h5tpriv_get_loc_vtx_idx_of_vtx (m, entity_id, &vertex_idx) );
 	h5_loc_idlist_t* tv = m->adjacencies.tv.v[vertex_idx];
 
 	TRY( h5priv_alloc_loc_idlist (list, 8) );
@@ -204,7 +204,7 @@ get_triangles_uadj_to_vertex (
 	                    "m=%p, entity_id=%llu, list=%p",
 	                    m, (long long unsigned)entity_id, list);
 	h5_loc_idx_t vertex_idx;
-	TRY( h5tpriv_get_vertex_index_of_vertex (m, entity_id, &vertex_idx) );
+	TRY( h5tpriv_get_loc_vtx_idx_of_vtx (m, entity_id, &vertex_idx) );
 	h5_loc_idlist_t* tv = m->adjacencies.tv.v[vertex_idx];
 
 	TRY ( h5priv_alloc_loc_idlist (list, 8) );

src/h5core/h5t_core.c

@@ -32,7 +32,7 @@ h5tpriv_enter_tv2 (
 	                   m, (long long)face_idx, (long long)elem_idx, idlist);
 
 	h5_loc_idx_t vertex_idx;
-	TRY (h5t_get_loc_vertex_index_of_vertex2 (
+	TRY (h5tpriv_get_loc_vtx_idx_of_vtx2 (
 	             m,
 	             face_idx, elem_idx,
 	             &vertex_idx));

src/h5core/h5t_map.c

@@ -303,7 +303,7 @@ h5t_get_glb_vertex_indices_of_entity (
 }
 
 h5_err_t
-h5tpriv_get_vertex_index_of_vertex (
+h5tpriv_get_loc_vtx_idx_of_vtx (
 	h5t_mesh_t* const m,
 	const h5_loc_id_t entity_id,
 	h5_loc_idx_t* vertex_index
@@ -315,12 +315,12 @@ h5tpriv_get_vertex_index_of_vertex (
 	                   (long long unsigned)*vertex_index);
 	h5_loc_idx_t face_idx = h5tpriv_get_face_idx (entity_id);
 	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
-	H5_CORE_API_RETURN (h5tpriv_get_vertex_index_of_vertex2 (
+	H5_CORE_API_RETURN (h5tpriv_get_loc_vtx_idx_of_vtx2 (
 				    m, face_idx, elem_idx, vertex_index));
 }
 
 h5_err_t
-h5tpriv_get_vertex_index_of_vertex2 (
+h5tpriv_get_loc_vtx_idx_of_vtx2 (
 	h5t_mesh_t* const m,
 	const h5_loc_idx_t face_idx,	// vertex index according ref. element
 	const h5_loc_idx_t elem_idx,	// local element index

src/h5core/h5t_map_private.h

@@ -69,14 +69,14 @@ h5priv_find_in_idlist (glb_id)
 h5priv_search_in_xlist (glb_id)
 
 h5_err_t
-h5tpriv_get_vertex_index_of_vertex (
+h5tpriv_get_loc_vtx_idx_of_vtx (
 	h5t_mesh_t* const m,
 	const h5_loc_id_t entity_id,
 	h5_loc_idx_t* vertex_index
 	);
 
 h5_err_t
-h5tpriv_get_vertex_index_of_vertex2 (
+h5tpriv_get_loc_vtx_idx_of_vtx2 (
 	h5t_mesh_t* const m,
 	const h5_loc_idx_t face_idx,
 	const h5_loc_idx_t elem_idx,

src/h5core/h5t_model.c

@@ -191,7 +191,8 @@ h5tpriv_init_mesh (
 		             "__num_leaf_levels__",
 		             H5T_NATIVE_INT16,
 		             &m->num_leaf_levels));
-		m->leaf_level = m->num_leaf_levels-1; //seems not to be set otherwise but for reading vtx it should be...
+                //seems not to be set otherwise but for reading vtx it should be...
+		m->leaf_level = m->num_leaf_levels-1;
 		TRY (m->num_glb_elems = h5_calloc (m->num_leaf_levels, sizeof(*m->num_glb_elems)));
 		TRY (m->num_glb_leaf_elems = h5_calloc (m->num_leaf_levels, sizeof(*m->num_glb_leaf_elems)));
 		TRY (m->num_glb_vertices = h5_calloc (m->num_leaf_levels, sizeof (*m->num_glb_vertices)));

src/h5core/h5t_model_tetm.c

@@ -137,6 +137,7 @@ h5_err_t
 h5t_add_tetrahedral_mesh (
 	const h5_file_t fh,
 	const char* name,
+        const h5_weight_t num_weights,
 	h5t_mesh_t** mesh
 	) {
         h5_file_p f = (h5_file_p)fh;
@@ -177,11 +178,13 @@ h5t_add_tetrahedral_mesh (
 
 	m->leaf_level = 0;
 	m->num_leaf_levels = 0;
+        m->num_weights = num_weights;
 	TRY (h5tpriv_add_level (m));
 	m->mesh_changed = 1;
 
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
+
 /*!
    Add new mesh
 
@@ -191,6 +194,7 @@ h5_err_t
 h5t_add_chunked_tetrahedral_mesh (
 	const h5_file_t fh,
         const char* name,
+        const h5_weight_t num_weights,
         h5t_mesh_t** mesh
         ) {
         h5_file_p f = (h5_file_p)fh;

src/h5core/h5t_model_trim.c

@@ -153,6 +153,7 @@ h5_err_t
 h5t_add_triangle_mesh (
 	const h5_file_t fh,
 	const char* name,
+        const h5_weight_t num_weights,
 	h5t_mesh_t** mesh
 	) {
         h5_file_p f = (h5_file_p)fh;
@@ -207,6 +208,7 @@ h5_err_t
 h5t_add_chunked_triangle_mesh(
         const h5_file_t fh,
         const char* name,
+        const h5_weight_t num_weights,
         h5t_mesh_t** mesh
         ) {
         h5_file_p f = (h5_file_p)fh;

src/h5core/h5t_retrieve.c

@@ -319,7 +319,7 @@ h5t_get_vertex_coords_by_id (
 	                   (long long unsigned)vertex_id,
 	                   P);
 	h5_loc_idx_t vertex_index;
-	TRY (h5tpriv_get_vertex_index_of_vertex (m, vertex_id, &vertex_index));
+	TRY (h5tpriv_get_loc_vtx_idx_of_vtx (m, vertex_id, &vertex_index));
 	TRY (h5t_get_vertex_coords_by_index (m, vertex_index, P));
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
@@ -336,7 +336,7 @@ h5t_get_vertex_by_id (
 	                   m, (long long)vertex_id, glb_idx, P);
 	// get loc index of vertex
 	h5_loc_idx_t idx;
-	TRY (h5t_get_loc_vertex_index_of_vertex (m, vertex_id, &idx));
+	TRY (h5tpriv_get_loc_vtx_idx_of_vtx (m, vertex_id, &idx));
 	*glb_idx = m->vertices[idx].idx;
 	*P = m->vertices[idx].P;
 	H5_CORE_API_RETURN (H5_SUCCESS);

src/h5core/h5t_store.c

@@ -497,12 +497,11 @@ h5t_end_store_vertices (
 h5_err_t
 h5t_begin_store_elems (
         h5t_mesh_t* const m,
-        const h5_size_t num,
-        const h5_weight_t num_weights
+        const h5_size_t num
         ) {
 	H5_CORE_API_ENTER (h5_err_t,
-	                   "m=%p, num=%llu, num_weights=%d",
-	                   m, (long long unsigned)num, num_weights);
+	                   "m=%p, num=%llu",
+	                   m, (long long unsigned)num);
 
 	h5_debug ("begin storing %llu elements", (long long)num);
 	size_t cur = m->leaf_level > 0 ? m->num_interior_elems[m->leaf_level-1] : 0;
@@ -515,9 +514,8 @@ h5t_begin_store_elems (
 	m->num_interior_leaf_elems[m->leaf_level] = m->leaf_level > 0 ?
 	                                            num + m->num_interior_leaf_elems[m->leaf_level-1] : num;
 
-	m->num_weights = num_weights;
 	if (m->leaf_level == 0) {
-		TRY (m->weights = h5_calloc(num_weights * num, sizeof (* m->weights) ));
+		TRY (m->weights = h5_calloc(m->num_weights * num, sizeof (* m->weights) ));
 		if (m->num_weights < 1) {
 			m->weights = NULL;
 		}
@@ -541,13 +539,13 @@ h5t_begin_store_elems (
                                         tetrahedron.
  */
 h5_loc_idx_t
-h5t_store_elem (
+h5tpriv_add_cell (
         h5t_mesh_t* const m,
         const h5_loc_idx_t parent_idx,
         const h5_loc_idx_t* vertex_indices,
         const h5_weight_t* weights
         ) {
-	H5_CORE_API_ENTER (h5_loc_idx_t,
+	H5_PRIV_FUNC_ENTER (h5_loc_idx_t,
 	                   "m=%p, parent_idx=%lld, vertex_indices=%p, weights=%p",
 	                   m,
 	                   (long long)parent_idx,
@@ -602,20 +600,19 @@ h5t_store_elem (
 	}
 	H5_CORE_API_RETURN (elem_idx);
 }
+
 h5_loc_idx_t
-h5t_store_elem2 (
+h5t_add_lvl0_cell (
         h5t_mesh_t* const m,
-        const h5_loc_idx_t parent_idx,
         const h5_loc_idx_t* vertex_indices,
         const h5_weight_t* weights
         ) {
 	H5_CORE_API_ENTER (h5_loc_idx_t,
-		                   "m=%p, parent_idx=%lld, vertex_indices=%p, weights=%p",
+		                   "m=%p, vertex_indices=%p, weights=%p",
 		                   m,
-		                   (long long)parent_idx,
 		                   vertex_indices,
 		                   weights);
-	h5t_store_elem (m, parent_idx, vertex_indices, weights);
+	h5tpriv_add_cell (m, -1, vertex_indices, weights);
 	h5_loc_idx_t* loc_vertex_indices = h5tpriv_get_loc_elem_vertex_indices (
 	        m, m->last_stored_eid);
 	int num_vertices = h5tpriv_ref_elem_get_num_vertices (m);
@@ -682,7 +679,11 @@ h5t_end_store_elems (
         h5t_mesh_t* const m
         ) {
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
-	h5_debug ("end storing elements");
+
+        if (m->leaf_level == 0) {
+                m->num_glb_leaf_elems[0] = m->num_glb_elems[0];
+        }
+
 	m->num_interior_elems[m->leaf_level] = m->last_stored_eid+1;
 	m->num_glb_elems[m->leaf_level] = m->last_stored_eid+1;
 	m->num_glb_leaf_elems[m->leaf_level] = m->num_interior_leaf_elems[m->leaf_level];
@@ -1787,7 +1788,8 @@ h5t_refine_marked_elems_chk (
 
 	// refine elements
 	for (int i = 0; i < num_midpoints; i++) {
-		TRY (h5tpriv_refine_elem (m, h5t_map_glb_elem_idx2loc(m,midpoints[i].elem))); // needs to be ordered acc to octants
+                // needs to be ordered acc to octants
+		TRY (h5tpriv_refine_elem (m, h5t_map_glb_elem_idx2loc(m,midpoints[i].elem)));
 	}
 	TRY (h5_free (oct_c_list.items));
 	TRY (h5_free (elem_range));
@@ -2147,7 +2149,9 @@ store_exchanged_elems (
 
 
 	// create list of new glb_vtx
-	h5_glb_vertex_t* new_vtx = h5_calloc(new_elems_c * 4, sizeof (*new_vtx));// TODO should be by far enough -> could be optimzed
+
+        // TODO should be by far enough -> could be optimzed
+	h5_glb_vertex_t* new_vtx = h5_calloc(new_elems_c * 4, sizeof (*new_vtx));
 	int new_vtx_c = 0;
 
 

src/h5core/h5t_store_private.h

@@ -37,6 +37,11 @@ h5tpriv_alloc_loc_elems (
 	return m->methods->store->alloc_loc_elems (m, cur, new);
 }
 
+h5_loc_idx_t
+h5tpriv_add_cell (
+        h5t_mesh_t* const, const h5_loc_idx_t, const h5_loc_idx_t*, const h5_weight_t*);
+
+
 static inline h5_loc_idx_t
 h5tpriv_refine_elem (
         h5t_mesh_t * const m,

src/h5core/h5t_store_tetm.c

@@ -126,7 +126,7 @@ pre_refine_tet (
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p", m);
 	unsigned int num_interior_elems_to_refine = m->marked_entities->num_items;
 	TRY (h5t_begin_store_vertices (m, num_interior_elems_to_refine*3 + 192));
-	TRY (h5t_begin_store_elems (m, num_interior_elems_to_refine*8, m->num_weights));
+	TRY (h5t_begin_store_elems (m, num_interior_elems_to_refine*8));
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
@@ -170,61 +170,87 @@ refine_tet (
 	// add new tets
 	h5_loc_idx_t new_elem[4];
 
+        /*
+          Add refined cells with pre-sorted vertices!
+          This is actually importend: sorting refined cells may produce wrong
+          orientated cells. This can easily be shown with triangle:
+
+         0
+          * 
+               
+                     *4
+          2*                 
+                               *2
+                     *
+            *        5
+            1
+
+          The parent triangle is (0,1,2) with a counter-clockwise orientation.
+          Since we must use an epsilon comparision, we run into a problem, if
+          the comparision returns X(0) < X(1), but X(0) == X(2). This happens,
+          if
+             X(0) - X(1) < 2*epsilon
+          The refined triangle (0,2,4) would be stored as (2,0,4), if we try 
+          to sort the vertices. The orientation of (2,0,4) is clockwise! But
+          we assume that (0,2,4), (2,1,5) and (4,5,2) have the same orientation
+          as the parent and (2,4,5) the opposite orientation.
+        */
+
 	// child 0
 	new_elem[0] = vertices[0];      // vertex 0
 	new_elem[1] = vertices[4];      // split point (0,1)
 	new_elem[2] = vertices[5];      // split point (0,2)
 	new_elem[3] = vertices[7];      // split point (0,3)
-	TRY( elem_idx_of_first_child = h5t_store_elem (m, elem_idx, new_elem, NULL) ); //TODO check use of h5t_store_elem2
+	TRY (elem_idx_of_first_child = h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 1
 	new_elem[0] = vertices[4];      // split point (0,1)
 	new_elem[1] = vertices[1];      // vertex 1
 	new_elem[2] = vertices[6];      // split point (1,2)
 	new_elem[3] = vertices[8];      // split point (1,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) ); //TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 2
 	new_elem[0] = vertices[5];      // split point (0,2)
 	new_elem[1] = vertices[6];      // split point (1,2)
 	new_elem[2] = vertices[2];      // vertex 2
 	new_elem[3] = vertices[9];      // split point (2,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) ); //TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 3
 	new_elem[0] = vertices[7];      // split point (0,3)
 	new_elem[1] = vertices[8];      // split point (1,3)
 	new_elem[2] = vertices[9];      // split point (2,3)
 	new_elem[3] = vertices[3];      // vertex 3
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );//TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 4
 	new_elem[0] = vertices[4];      // split point (0,1)
 	new_elem[1] = vertices[5];      // split point (0,2)
 	new_elem[2] = vertices[6];      // split point (1,2)
 	new_elem[3] = vertices[8];      // split point (1,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );//TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 5
 	new_elem[0] = vertices[4];      // split point (0,1)
 	new_elem[1] = vertices[5];      // split point (0,2)
 	new_elem[2] = vertices[7];      // split point (0,3)
 	new_elem[3] = vertices[8];      // split point (1,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );//TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 6
 	new_elem[0] = vertices[5];      // split point (0,2)
 	new_elem[1] = vertices[6];      // split point (1,2)
 	new_elem[2] = vertices[8];      // split point (1,3)
 	new_elem[3] = vertices[9];      // split point (2,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );//TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	// child 7
 	new_elem[0] = vertices[5];      // split point (0,2)
 	new_elem[1] = vertices[7];      // split point (0,3)
 	new_elem[2] = vertices[8];      // split point (1,3)
 	new_elem[3] = vertices[9];      // split point (2,3)
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );//TODO check use of h5t_store_elem2
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	((h5_loc_tet_t*)m->loc_elems)[elem_idx].child_idx = elem_idx_of_first_child;
 	m->num_interior_leaf_elems[m->leaf_level]--;

src/h5core/h5t_store_trim.c

@@ -108,7 +108,7 @@ pre_refine_triangle (
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p", m);
 	unsigned int num_interior_elems_to_refine = m->marked_entities->num_items;
 	TRY (h5t_begin_store_vertices (m, num_interior_elems_to_refine*3 + 64));
-	TRY (h5t_begin_store_elems (m, num_interior_elems_to_refine*4, m->num_weights));
+	TRY (h5t_begin_store_elems (m, num_interior_elems_to_refine*4));
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
@@ -149,22 +149,22 @@ refine_triangle (
 	new_elem[0] = vertices[0]; // V[0] < V[3] , V[4]
 	new_elem[1] = vertices[3];
 	new_elem[2] = vertices[4];
-	TRY( elem_idx_of_first_child = h5t_store_elem (m, elem_idx, new_elem, NULL) );
+	TRY (elem_idx_of_first_child = h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	new_elem[0] = vertices[3];  // V[3] < V[1] , V[5]
 	new_elem[1] = vertices[1];
 	new_elem[2] = vertices[5];
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	new_elem[0] = vertices[4];  // V[4] < V[5] , V[2]
 	new_elem[1] = vertices[5];
 	new_elem[2] = vertices[2];
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	new_elem[0] = vertices[3];  // V[3] < V[4] , V[5]
 	new_elem[1] = vertices[5];
 	new_elem[2] = vertices[4]; // TODO check if that ordering is correct!
-	TRY( h5t_store_elem (m, elem_idx, new_elem, NULL) );
+	TRY (h5tpriv_add_cell (m, elem_idx, new_elem, NULL));
 
 	((h5_loc_tri_t*)m->loc_elems)[elem_idx].child_idx = elem_idx_of_first_child;
 	m->num_interior_leaf_elems[m->leaf_level]--;

src/h5core/h5t_tags.c

@@ -29,7 +29,7 @@
 
 static h5_err_t
 read_dataset (
-		h5t_mesh_t* const m,
+        h5t_mesh_t* const m,
         const h5_file_p f,
         hid_t dset_id,
         h5_dsinfo_t* dsinfo,
@@ -421,11 +421,13 @@ read_tagset (
 	TRY (dset_id = hdf5_open_dataset (loc_id, "elems"));
 	TRY (num_interior_elems = hdf5_get_npoints_of_dataset (dset_id));
 	TRY (elems = h5_calloc (num_interior_elems, sizeof(*elems)));
+
 	h5_dsinfo_t dsinfo;
 	memset (&dsinfo, 0, sizeof (dsinfo));
 	dsinfo.type_id = h5_dta_types.h5t_glb_tag_idx_t;
-	TRY (h5priv_read_dataset (
-		     tagset->m->f,
+	TRY (read_dataset (
+                     tagset->m,
+                     tagset->m->f,
 		     dset_id,
 		     &dsinfo,
 		     open_space_all,
@@ -442,7 +444,7 @@ read_tagset (
 	TRY (num_entities = hdf5_get_npoints_of_dataset (dset_id));
 	TRY (entities = h5_calloc (num_entities, sizeof(*entities)));
 	TRY (read_dataset (
-				 tagset->m,
+                     tagset->m,
 	             tagset->m->f,
 	             dset_id,
 	             &dsinfo,

src/include/H5.h

@@ -215,10 +215,6 @@ static inline H5SetThrottle (
 	H5_API_RETURN (h5_set_throttle(f, factor));
 }
 #endif // PARALLEL_IO
-#ifdef __cplusplus
-}
-#endif
-
 
 /*!
   \ingroup h5hut_file

src/include/H5Fed.h

@@ -109,15 +109,6 @@ H5FedSetMeshChanged (
 	H5_API_RETURN (h5t_set_mesh_changed (m));
 }
 
-static inline h5_err_t
-H5FedLinkMeshToStep (
-        h5_file_t* const m,
-        const h5_id_t mesh_id
-        ) {
-	H5_API_ENTER (h5_err_t, "m=%p, mesh_id=%lld", m, (long long)mesh_id);
-	H5_API_RETURN (h5_error_not_implemented ());
-}
-
 #ifdef __cplusplus
 }
 #endif

src/include/H5Fed_store.h

@@ -28,7 +28,7 @@ H5FedAddTetrahedralMesh (
 	H5_API_ENTER (h5_err_t,
                       "f=%p, name=%s, mesh=%p",
                       (h5_file_p)f, name, mesh);
-	H5_API_RETURN (h5t_add_tetrahedral_mesh (f, name, mesh));
+	H5_API_RETURN (h5t_add_tetrahedral_mesh (f, name, 0, mesh));
 }
 
 static inline h5_err_t
@@ -40,7 +40,7 @@ H5FedAddChunkedTetrahedralMesh (
 	H5_API_ENTER (h5_err_t,
                       "f=%p, name=%s, mesh=%p",
                       (h5_file_p)f, name, mesh);
-	H5_API_RETURN (h5t_add_chunked_tetrahedral_mesh (f, name, mesh));
+	H5_API_RETURN (h5t_add_chunked_tetrahedral_mesh (f, name, 0, mesh));
 }
 
 
@@ -53,7 +53,7 @@ H5FedAddTriangleMesh (
 	H5_API_ENTER (h5_err_t,
                       "f=%p, name=%s, mesh=%p",
                       (h5_file_p)f, name, mesh);
-	H5_API_RETURN (h5t_add_triangle_mesh (f, name, mesh));
+	H5_API_RETURN (h5t_add_triangle_mesh (f, name, 0, mesh));
 }
 
 static inline h5_err_t
@@ -65,8 +65,9 @@ H5FedAddChunkedTriangleMesh (
 	H5_API_ENTER(h5_err_t,
                      "f=%p, name=%s, mesh=%p",
                      (h5_file_p)f, name, mesh);
-	H5_API_RETURN (h5t_add_chunked_triangle_mesh (f, name, mesh));
+	H5_API_RETURN (h5t_add_chunked_triangle_mesh (f, name, 0, mesh));
 }
+
 /*!
    \ingroup h5fed_c_api
 
@@ -136,13 +137,12 @@ H5FedEndStoreVertices (
 static inline h5_err_t
 H5FedBeginStoreElements (
         h5t_mesh_t* const m,
-        const h5_size_t num,
-        const h5_weight_t num_weights
+        const h5_size_t num
         ) {
 	H5_API_ENTER (h5_err_t,
-	              "m=%p, num=%llu, num_weights=%d",
-	              m, (long long unsigned)num, num_weights);
-	H5_API_RETURN (h5t_begin_store_elems (m, num, num_weights));
+	              "m=%p, num=%llu",
+	              m, (long long unsigned)num);
+	H5_API_RETURN (h5t_begin_store_elems (m, num));
 }
 
 /*!
@@ -161,6 +161,21 @@ H5FedBeginStoreElements (
  */
 static inline h5_loc_idx_t
 H5FedStoreElement (
+        h5t_mesh_t* const m,            /*!< file handle		*/
+        const h5_loc_idx_t local_vids[] /*!< tuple with vertex id's	*/
+        ) {
+	H5_API_ENTER (h5_loc_idx_t, "m=%p, local_vids=%p", m, local_vids);
+	if (h5t_get_level (m) != 0) {
+		H5_API_LEAVE (
+		        h5_error (
+		                H5_ERR_INVAL,
+		                "Elements can be added to level 0 only!"));
+	}
+	H5_API_RETURN (h5t_add_lvl0_cell (m, local_vids, NULL));
+}
+
+static inline h5_loc_idx_t
+H5FedStoreWeightedElement (
         h5t_mesh_t* const m,            /*!< file handle		*/
         const h5_loc_idx_t local_vids[], /*!< tuple with vertex id's	*/
         const h5_weight_t weights[]    // tuple with weights
@@ -172,7 +187,7 @@ H5FedStoreElement (
 		                H5_ERR_INVAL,
 		                "Elements can be added to level 0 only!"));
 	}
-	H5_API_RETURN (h5t_store_elem2 (m, -1, local_vids, weights));
+	H5_API_RETURN (h5t_add_lvl0_cell (m, local_vids, weights));
 }
 
 static inline h5_err_t

src/include/Makefile.am

@@ -1,29 +1,5 @@
-# src/C level Makefile.am
 
-# Header files that I wish to install in $(prefix)/include
-include_HEADERS =				\
-	../include/h5core/h5.h			\
-	../include/h5core/h5_attribs.h		\
-	../include/h5core/h5_debug.h		\
-	../include/h5core/h5_errorhandling.h	\
-	../include/h5core/h5_model.h		\
-	../include/h5core/h5_syscall.h		\
-	../include/h5core/h5_types.h		\
-	../include/h5core/h5b_attribs.h		\
-	../include/h5core/h5b_model.h		\
-	../include/h5core/h5b_io.h	\
-	../include/h5core/h5t_adjacencies.h	\
-	../include/h5core/h5t_map.h		\
-	../include/h5core/h5t_model.h		\
-	../include/h5core/h5t_retrieve.h	\
-	../include/h5core/h5t_store.h		\
-	../include/h5core/h5t_tags.h		\
-	../include/h5core/h5u_model.h		\
-	../include/h5core/h5u_io.h
-
-# Listing of all possible headers that I may include
-EXTRA_HEADERS =
+SUBDIRS = h5core
 
 clean-local:
 	$(RM) *~
-	$(RM) h5core/*~

src/include/h5core/h5.h

@@ -69,7 +69,6 @@ h5_err_t
 h5_close_hdf5 (
 	void);
 
-
 h5_err_t
 h5_flush_step (
 	const h5_file_t);

src/include/h5core/h5_types.h

@@ -25,21 +25,21 @@ extern "C" {
    H5_O_APPEND: allows to append a new datasets to an existing file
    H5_O_RDWR:   dataset may exist
  */
-
-#define H5_O_RDWR               0x001
-#define H5_O_RDONLY             0x002
-#define H5_O_WRONLY             0x004
-#define H5_O_APPEND             0x008
+#define H5_O_RDWR		0x00000001
+#define H5_O_RDONLY		0x00000002
+#define H5_O_WRONLY		0x00000004
+#define H5_O_APPEND		0x00000008
 
 #define H5_VFD_MPIPOSIX         0x00000010
 #define H5_VFD_MPIIO_IND        0x00000020
+#define H5_VFD_INDEPENDENT      H5_VFD_MPIIO_IND // obsolete(?)
 #define H5_VFD_CORE		0x00000040
 
-#define H5_FLUSH_FILE           0x040
-#define H5_FLUSH_STEP           0x080
-#define H5_FLUSH_DATASET        0x100
+#define H5_FLUSH_FILE		0x00001000
+#define H5_FLUSH_STEP		0x00002000
+#define H5_FLUSH_DATASET	0x00004000
 
-#define H5_FS_LUSTRE            0x200
+#define H5_FS_LUSTRE		0x00010000
 
 #define H5_ID_T                 H5T_NATIVE_INT64
 #define H5_FLOAT64_T            H5T_NATIVE_DOUBLE

src/include/h5core/h5t_map.h

@@ -44,21 +44,6 @@ h5t_map_glb_elem_indices2loc (
         h5_loc_idx_t* loc_indices
         );
 
-h5_err_t
-h5t_get_loc_vertex_index_of_vertex (
-        h5t_mesh_t* const m,
-        const h5_loc_id_t entity_id,
-        h5_loc_idx_t* vertex_index
-        );
-
-h5_err_t
-h5t_get_loc_vertex_index_of_vertex2 (
-        h5t_mesh_t* const m,
-        const h5_loc_idx_t face_idx,
-        const h5_loc_idx_t elem_idx,
-        h5_loc_idx_t* vertex_indices
-        );
-
 h5_err_t
 h5t_get_loc_vertex_indices_of_edge (
         h5t_mesh_t* const m,

src/include/h5core/h5t_model.h

@@ -42,48 +42,76 @@ h5t_open_triangle_mesh_by_idx (
 
 h5_err_t
 h5t_open_triangle_mesh_part (
-        const h5_file_t, const char*, h5t_mesh_t** mesh,
+        const h5_file_t, const char*, h5t_mesh_t**,
         h5_glb_idx_t*, h5_glb_idx_t);
 
-h5_lvl_idx_t h5t_is_chunked (h5t_mesh_t* const);
+h5_lvl_idx_t
+h5t_is_chunked (
+        h5t_mesh_t* const);
 
-h5_ssize_t h5t_get_num_trimeshes (const h5_file_t f);
+h5_ssize_t
+h5t_get_num_trimeshes (
+        const h5_file_t f);
 
-h5_ssize_t h5t_get_num_leaf_levels (h5t_mesh_t* const);
+h5_ssize_t
+h5t_get_num_leaf_levels (
+        h5t_mesh_t* const);
 
-h5_ssize_t h5t_get_num_vertices (h5t_mesh_t* const, const h5_id_t);
+h5_ssize_t
+h5t_get_num_vertices (
+        h5t_mesh_t* const, const h5_id_t);
 
-h5_ssize_t h5t_get_num_leaf_elems (h5t_mesh_t* const, const h5_id_t);
+h5_ssize_t
+h5t_get_num_leaf_elems (
+        h5t_mesh_t* const, const h5_id_t);
 
-h5_id_t h5t_add_chunked_tetrahedral_mesh (const h5_file_t, const char* name, h5t_mesh_t**);
+h5_id_t
+h5t_add_chunked_tetrahedral_mesh (
+        const h5_file_t, const char*, const h5_weight_t, h5t_mesh_t**);
 
-h5_id_t h5t_add_triangle_mesh (const h5_file_t, const char*, h5t_mesh_t**);
+h5_id_t
+h5t_add_chunked_triangle_mesh (
+        const h5_file_t, const char*, const h5_weight_t, h5t_mesh_t**);
 
-h5_id_t h5t_add_chunked_triangle_mesh (const h5_file_t, const char*, h5t_mesh_t**);
+h5_lvl_idx_t
+h5t_get_level (
+        h5t_mesh_t* const);
 
-h5_lvl_idx_t h5t_get_level (h5t_mesh_t* const);
+h5_err_t
+h5t_open_tetrahedral_mesh (
+        const h5_file_t, const char*, h5t_mesh_t**);
 
-h5_err_t h5t_open_tetrahedral_mesh (const h5_file_t ,
-                                    const char*, h5t_mesh_t**);
-h5_err_t h5t_open_tetrahedral_mesh_by_idx (const h5_file_t ,
-                                           const h5_id_t, h5t_mesh_t**);
+h5_err_t
+h5t_open_tetrahedral_mesh_by_idx (
+        const h5_file_t, const h5_id_t, h5t_mesh_t**);
 
-h5_err_t h5t_open_triangle_mesh (const h5_file_t,
-                                 const char*,	h5t_mesh_t**);
-h5_err_t h5t_open_triangle_mesh_by_idx (const h5_file_t,
-                                        const h5_id_t, h5t_mesh_t**);
-h5_id_t h5t_add_tetrahedral_mesh (const h5_file_t,
-                                  const char* name, h5t_mesh_t**);
-h5_id_t h5t_add_triangle_mesh (const h5_file_t,
-                               const char*, h5t_mesh_t**);
+h5_err_t
+h5t_open_triangle_mesh (
+        const h5_file_t, const char*, h5t_mesh_t**);
 
-h5_err_t h5t_set_level (h5t_mesh_t* const, const h5_lvl_idx_t);
+h5_err_t
+h5t_open_triangle_mesh_by_idx (
+        const h5_file_t, const h5_id_t, h5t_mesh_t**);
 
-h5_err_t h5t_set_mesh_changed (h5t_mesh_t* const m);
+h5_id_t
+h5t_add_tetrahedral_mesh (
+        const h5_file_t, const char*, const h5_weight_t, h5t_mesh_t**);
 
-h5_err_t h5t_close_mesh (h5t_mesh_t* const);
+h5_id_t
+h5t_add_triangle_mesh (
+        const h5_file_t, const char*, const h5_weight_t, h5t_mesh_t**);
 
+h5_err_t
+h5t_set_level (
+        h5t_mesh_t* const, const h5_lvl_idx_t);
 
+h5_err_t
+h5t_set_mesh_changed (
+        h5t_mesh_t* const m);
+
+h5_err_t
+h5t_close_mesh (
+        h5t_mesh_t* const);
 
 #ifdef __cplusplus
 }

src/include/h5core/h5t_store.h

@@ -30,15 +30,11 @@ h5t_end_store_vertices (
 
 h5_err_t
 h5t_begin_store_elems (
-        h5t_mesh_t* const, const h5_size_t, const h5_weight_t);
+        h5t_mesh_t* const, const h5_size_t);
 
 h5_loc_idx_t
-h5t_store_elem (
-        h5t_mesh_t* const, const h5_loc_idx_t, const h5_loc_idx_t*, const h5_weight_t*);
-
-h5_loc_idx_t
-h5t_store_elem2 (
-        h5t_mesh_t* const, const h5_loc_idx_t, const h5_loc_idx_t*, const h5_weight_t*);
+h5t_add_lvl0_cell (
+        h5t_mesh_t* const, const h5_loc_idx_t*, const h5_weight_t*);
 
 h5_err_t
 h5t_end_store_elems (

src/include/h5core/h5u_model.h

@@ -41,7 +41,7 @@ h5u_set_num_particles (
 
 h5_err_t
 h5u_has_view (
-	const const h5_file_t);
+	const h5_file_t);
 
 h5_err_t
 h5u_reset_view (