bugfixes, implementation of adjacency functions

src/H5.h

@@ -31,7 +31,7 @@ H5CloseFile (
 	);
 
 h5_err_t
-H5DefineStepNameFormat (
+H5SetStepNameFormat (
 	h5_file_t *f,
 	const char *name,
 	const h5_int64_t width
@@ -61,11 +61,16 @@ H5StartTraverseSteps (
 	h5_file_t *f
 	);
 
-h5_err_t
+h5_id_t
 H5TraverseSteps (
 	h5_file_t *f
 	);
 
+h5_err_t
+H5EndTraverseSteps (
+	h5_file_t *f
+	);
+
 h5_err_t
 H5SetVerbosityLevel (
 	const h5_id_t level

src/H5Fed.c

@@ -29,6 +29,13 @@ H5FedOpenMesh (
 	return h5t_open_mesh ( f, mesh_id, mesh_type_id );
 }
 
+h5_err_t
+H5FedCloseMesh (
+	h5_file_t * const f
+	) {
+	return -1;
+}
+
 h5_err_t
 H5FedSetLevel (
 	h5_file_t * const f,
@@ -37,3 +44,11 @@ H5FedSetLevel (
 	SET_FNAME ( f, __func__ );
 	return h5t_open_level ( f, level_id );
 }
+
+h5_err_t
+H5FedLinkMeshToStep (
+	h5_file_t * f,
+	const h5_id_t mesh_id
+	) {
+	return -1;
+}

src/H5Fed.h

@@ -20,18 +20,15 @@
 #define __H5FED_H
 
 #include "H5.h"
+#include "H5Fed_adjacency.h"
 #include "H5Fed_boundaries.h"
+#include "H5Fed_inquiry.h"
 #include "H5Fed_map.h"
+#include "H5Fed_retrieve.h"
 #include "H5Fed_store.h"
 
 /******	General routines *****************************************************/
 
-h5_size_t
-H5FedGetNumMeshes (
-	h5_file_t * const f,
-	const h5_oid_t mesh_type_id
-	);
-
 h5_err_t
 H5FedOpenMesh (
 	h5_file_t * const f,
@@ -39,90 +36,24 @@ H5FedOpenMesh (
 	const h5_oid_t mesh_type_id
 	);
 
-h5_size_t
-H5FedGetNumLevels (
-	h5_file_t * f
+h5_err_t
+H5FedCloseMesh (
+	h5_file_t * const f
 	);
 
 h5_err_t
 H5FedSetLevel (
 	h5_file_t * f,
-	const h5_id_t id
-	);
-
-h5_id_t
-H5FedGetLevel (
-	h5_file_t * f
-	);
-
-h5_size_t
-H5FedGetNumVertices (
-	h5_file_t * f
-	);
-
-h5_size_t
-H5FedGetNumVerticesTotal(
-	h5_file_t * f
-	);
-
-h5_size_t
-H5FedGetNumVerticesCnode (
-	h5_file_t * f,
-	const h5_id_t cnode
-	);
-
-h5_size_t
-H5FedGetNumElements (
-	h5_file_t * f
-	);
-
-h5_size_t
-H5FedGetNumElementsTotal (
-	h5_file_t * f
-	);
-
-h5_size_t
-H5FedGetNumElementsCnode (
-	h5_file_t * f,
-	const h5_id_t cnode
-	);
-
-/******	STORE / RETRIEVAL routines ********************************************/
-
-h5_err_t
-H5FedStartTraverseVertices (
-	h5_file_t * f
-	);
-
-h5_id_t
-H5FedTraverseVertices (
-	h5_file_t * f,
-	h5_id_t	* const	id,
-	h5_float64_t P[3]
+	const h5_id_t level_id
 	);
 
 h5_err_t
-H5FedEndTraverseVertices (
-	h5_file_t * f
-	);
-
-h5_err_t
-H5FedStartTraverseElements (
-	h5_file_t * f
-	);
-
-h5_id_t
-H5FedTraverseElements (
+H5FedLinkMeshToStep (
 	h5_file_t * f,
-	h5_id_t * const id,
-	h5_id_t * const parent_id,
-	h5_id_t * const vertex_ids
+	const h5_id_t mesh_id
 	);
 
-h5_err_t
-H5FedEndTraverseElements (
-	h5_file_t * f
-	);
+
 
 #endif
 

src/H5Fed_adjacency.c

@@ -15,250 +15,45 @@
 
 #include <hdf5.h>
 #include "h5_core/h5_types.h"
+#include "h5_core/h5_core.h"
 #include "H5Fed.h"
 
 /******	UPWARD ADJACENCY routines *********************************************/
 
 /*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the edges that are
-  adjacent to the vertex with id \c vertex_id and in \c num_adj_edges
-  the number of edges to which this vertex is adjacent, i.e. the size 
-  of the returned vector.
-
-  \return n-tuple of upward adjacent edges
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetEdgesUAdjacentToVertex (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t vertex_id,	/*!< global vertex id		*/
-	h5_size_t * const num_adj_edges	/*!< OUT: size of returned vector */
+  \return	number of upward adjacent edges 
+ */
+h5_err_t
+H5FedGetEdgesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
 	) {
-	return NULL;
+	return h5t_get_edges_upadjacent_to_vertex ( f, local_vid, list );
 }
 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the triangles that are
-  adjacent to the vertex with id \c vertexid and  \c num_adj_triangles
-  the number of triangle to which this vertex is adjacent, i.e. the size 
-  of the returned vector.
-
-  \return n-tuple of upward adjacent triangles.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTrianglesUAdjacentToVertex (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t vertex_id,	/*!< global vertex id		*/
-	h5_size_t * const num_adj_triangles
-					/*!< OUT: size of returned vector */
+h5_err_t
+H5FedGetTrianglesUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
 	) {
-	return NULL;
+	return h5t_get_triangles_upadjacent_to_vertex ( f, local_vid, list );
 }
 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the tetrahedra that are
-  adjacent to the vertex with id \c vertex_id and in
-  \c num_adj_tetrahedra the number of tetrahera to which this vertex is
-  adjacent, i.e. the size of the returned vector.
-
-  \return n-tuple of upward adjacent tetrahedra.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTetrahedrasUAdjacentToVertex (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t vertex_id,	/*!< global vertex id		*/
-	h5_size_t * const num_adj_tetrahedra
-					/*!< OUT: size of returned vector */
+h5_err_t
+H5FedGetTetsUpAdjacentToVertex (
+	h5_file_t * const f,
+	const h5_id_t local_vid,
+	h5_idlist_t **list
 	) {
-	return NULL;
+	return h5t_get_tets_upadjacent_to_vertex ( f, local_vid, list );
 }
 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the triangles that are
-  adjacent to the edge with id \c vertex_id and in
-  \c num_adj_triangles the number of triangles adjacent to the edge, i.e.
-  the size of the return vector.
-
-  \return n-tuple of upward adjacent triangles.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTrianglesUAdjacentToEdge (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t edge_id,		/*!< global edge id		*/
-	h5_size_t * const num_adj_triangles
-					/*!< OUT: size of returned vector */
+h5_err_t
+H5FedReleaseListOfAdjacencies (
+	h5_file_t * const f,
+	h5_idlist_t **list
 	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the tetrahedra that
-  are adjacent to the edge with id \c edge_id and in
-  \c num_adj_tetrahedra the number of tetrahedra that are adjacent to
-  the edge, i.e. the size of the returned vector.
-
-  \return n-tuple of upward adjacent tetrahedra.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTetrahedraUAdjacentToEdge (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t edge_id,		/*!< global edge id		*/
-	h5_size_t * const num_adj_tets	/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the tetrahedra that
-  are adjacent to the triangle with id \c triangle_id and in
-  \c num_adj_tetrahedra the number of tetrahedra that are adjacent to
-  this triangle.
-
-  There are only  two different cases: either the triangle is an internal,
-  including interprocessor boundaries, triangle or an external triangle,
-  i.e. a part of the mesh boundary; in the first case, there are \c 2
-  adjacent tetrahedra, in the second case the triangle has exactly one
-  sinle adjacent tetrahedron.
-
-  \return n-tuple of upward adjacent tetrahedra.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTetrahedraUAdjacentToTriangle (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t triangle_id,	/*!< global triangle id		*/
-	h5_size_t * const num_adj_tets	/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/******	DOWNWARD ADJACENCY routines *********************************************/
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the vertices that are
-  adjacent to the edge with id \c vertex_id.
-
-  \return n-tuple of downward adjacent vertices.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetVerticesDAdjacentToEdge (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query 	*/
-	const h5_id_t edge_id,		/*!< global edge id		*/
-	h5_size_t * const num_adj_vertices
-					/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the edges that are
-  adjacent to the triangle with id \c triangle_id.
-
-  \return n-tuple of downward adjacent edges.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetEdjesDAdjacentToTriangle (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query 	*/
-	const h5_id_t triangle_id,	/*!< global triangle id		*/
-	h5_size_t * const num_adj_triangles
-					/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the vertices that are
-  adjacent to the triangle with id \c triangle_id.
-
-  \return n-tuple of downward adjacent vertices.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetVerticesDAdjacentToTriangle (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t triangle_id,	/*!< global triangle id		*/
-	h5_size_t * const num_adj_vertices
-					/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
- 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the triangles that are
-  adjacent to the tetrahedron with id \c tet_id
-
-  \return n-tuple of downward adjacent triangles.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetTrianglesDAdjacentToTetrahedron (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t tet_id,		/*!< global tetrahedron id	*/
-	h5_size_t * const num_adj_triangles
-					/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the edges that are
-  adjacent to the tetrahedron with id \c tet_id.
-
-  \return n-tuple of downward adjacent edges.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetEdjesDAdjacentToTetrahedron (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t tet_id,		/*!< global tetrahedron id	*/
-	h5_size_t * const num_adj_edges	/*!< OUT: size of returned vector */
-	) {
-	return NULL;
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Returns a vector, that contains the id's of all the vertices that are
-  adjacent to the tetrahedron with id \c tet_id.
-
-  \return n-tuple of downward adjacent vertices.
-  \return NULL-pointer on error.
-*/
-h5_id_t * H5FedGetVerticesDAdjacentToTetrahedron (
-	h5_file_t * fh,			/*!< file handle		*/
-	const h5_id_t level,		/*!< mesh level to query	*/
-	const h5_id_t tet_id,		/*!< global tetrahedron id	*/
-	h5_size_t * const num_adj_vertices
-					/*!< OUT: size of returned vector */
-	) {
-	return NULL;
+	return _h5_free_idlist ( f, list );
 }

src/H5Fed_map.c

@@ -1,5 +1,5 @@
 /*
-  Copyright 2007-2008
+  Copyright 2007-2009
  	Paul Scherrer Institut, Villigen, Switzerland;
  	Benedikt Oswald;
  	Achim Gsell
@@ -40,3 +40,13 @@ H5FedMapTriangle2GlobalID (
 	SET_FNAME ( f, __func__ );
 	return h5t_get_global_triangle_id ( f, global_vids );
 }
+
+h5_err_t
+H5FedMapEntityID2LocalVids (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *local_vids
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_get_local_vids_of_entity ( f, local_id, local_vids );
+}

src/H5Fed_map.h

@@ -31,5 +31,11 @@ H5FedMapTriangle2GlobalID (
 	h5_id_t * const global_vids
 	);
 
+h5_err_t
+H5FedMapEntityID2LocalVids (
+	h5_file_t * const f,
+	h5_id_t local_id,
+	h5_id_t *localvids
+	);
 #endif
 

src/H5Fed_retrieve.c

@@ -20,7 +20,7 @@
 #include "H5Fed.h"
 
 h5_err_t
-H5FedStartTraverseVertices (
+H5FedBeginTraverseVertices (
 	h5_file_t * const f		/*!< file handle		*/
 	) {
 	SET_FNAME ( f, __func__ );
@@ -56,7 +56,7 @@ H5FedEndTraverseVertices (
 
 
 h5_err_t
-H5FedStartTraverseElements (
+H5FedBeginTraverseElements (
 	h5_file_t * const f  		/*!< file handle		*/
 	) {
 	SET_FNAME ( f, __func__ );

src/Makefile.am

@@ -62,7 +62,6 @@ libH5_a_SOURCES = \
 	H5Fed.c \
 	H5Fed_adjacency.c \
 	H5Fed_boundaries.c \
-	H5Fed_dof.c \
 	H5Fed_inquiry.c \
 	H5Fed_map.c \
 	H5Fed_retrieve.c \