refactoring

.gitattributes

@@ -353,7 +353,10 @@ src/H5Fed.c -text
 src/H5Fed.h -text
 src/H5Fed_adjacency.c -text
 src/H5Fed_dof.c -text
+src/H5Fed_inquiry.c -text
+src/H5Fed_retrieve.c -text
 src/H5Fed_statistics.c -text
+src/H5Fed_store.c -text
 src/H5Fed_storeretrieve.c -text
 src/H5Part.c -text
 src/H5Part.h -text

src/H5Fed_inquiry.c

@@ -0,0 +1,292 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+/*!
+  \ingroup h5fed_c_api
+  \defgroup h5fed_mesh_inquiry
+*/
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5/h5.h"
+#include "h5/h5_private.h"
+#include "H5Fed.h"
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Check whether a tetrahedral mesh hierarchy exists on level \c level
+
+  \return  \c 1		tetrahedral mesh hierarchy exists on given level. 
+  \return  \c 0		tetrahedral mesh exists, but not on given level.
+  \return  \c -1	tetrahedral mesh doesn't exist
+ */
+h5_int_t H5FedHasTetrahedralMesh (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to check	*/
+	) {
+	SET_FNAME ( __func__ );
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Check whether a triangle mesh hierarchy exists on level \c level
+
+  \return \c 1		boundary mesh hierarchy exists on given level.
+  \return \c 0		boundary mesh hierarchy exists, but not on given level.
+  \return \c -1		boundary mesh doesn't exist.
+*/
+h5_int_t H5FedHasTriangleMesh(
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to check	*/
+	) {
+	SET_FNAME ( __func__ );
+	return -1;
+}
+
+h5_size_t
+H5FedGetNumMeshes (
+	h5_file * f			/*!< file handle		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_num_meshes ( f );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the number of hierarchical mesh levels available in current step.
+
+  \return Number of hierarchical mesh levels
+  \return \c -1 on error
+ */
+h5_size_t
+H5FedGetNumRefinementLevels (
+	h5_file * f			/*!< file handle		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_num_levels ( f );
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Get the total number of vertices used for defining a submesh
+  at level \c level in current step, summed up over all compute nodes.
+
+  \return number of vertices
+  \return \c -1	on error.
+*/
+h5_size_t H5FedGetNumVerticesTotal(
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to query	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Returns the number of vertices used for defining a submesh
+  at level \c level for compute node \c cnode.
+
+  \return number of vertices
+q  \return \c -1	on error.
+*/
+h5_size_t H5FedGetNumVerticesCnode (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level,		/*!< mesh level to query	*/
+	const h5_id_t cnode		/*!< compute node		*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the number of vertices used for defining a submesh
+  at level \c level for this compute node in current step.
+
+  \return number of vertices
+  \return \c -1	on error.
+*/
+h5_size_t
+H5FedGetNumVertices (
+	h5_file * f			/*!< file handle		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_num_vertices ( f );
+}
+
+/******	EDGE statistics routines ********************************************/
+
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Returns the number of edges present in the mesh at level \c level,
+  in current step, summed up over all compute nodes
+
+  \return number of edges
+  \return \c -1	on error.
+*/
+h5_size_t H5FedGetNumEdgesTotal (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to query	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Returns the number of edges present in the mesh at level \c level
+  on compute node \c cnode
+
+  \return number of edges
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumEdgesCnode (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level,		/*!< mesh level to query	*/
+	const h5_id_t cnode		/*!< compute node		*/
+	) {
+	return -1;
+}
+
+/******	TRIANGLE statistics routines *****************************************/
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Get the number of triangles present in the mesh at level \c level in 
+  current time step summed up over all compute notes.
+
+  \return Number of triangles
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumTrianglesTotal (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to query	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Get the number of triangles present in the mesh at level \c level in 
+  current time step on compute node \c cnode.
+
+  \return Number of triangles
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumTrianglesCnode (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level,		/*!< mesh level to query	*/
+	const h5_id_t cnode		/*!< compute node		*/
+	) {
+	return -1;
+}
+
+/******	TETRAHEDRON statistics routines **************************************/
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Returns the number of tetrahedral elements present in the mesh at 
+  level \c level in current step summed up over all compute nodes.
+
+  \return number of tetrahedra
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumTetrahedraTotal(
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to query	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Returns the number of tetrahedral elements present in the mesh at 
+  level \c level in current step on compute nodes \c computenode.
+
+  \return number of tetrahedra
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumTetrahedraCnode (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level,		/*!< mesh level to query	*/
+	const h5_id_t cnode		/*!< compute node		*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Returns the number of tetrahedral elements present in the mesh at 
+  level \c level in current step on this compute node.
+
+  \return number of tetrahedra
+  \return \c -1 on error.
+*/
+h5_size_t
+H5FedGetNumTetrahedra (
+	h5_file * f			/*!< file handle		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_num_tets ( f );
+}
+
+
+/******	BOUNDARY statistics routines ****************************************/
+
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Get the number of boundary triangles present in the mesh at
+  level \c level in current step summed up over all compute nodes.
+
+  \return number of tetrahedras
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumBoundaryTrianglesTotal (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level		/*!< mesh level to query	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_mesh_inquiry
+
+  Get the number of boundary triangles present in the mesh at
+  level \c level in current step on compute node \c cnode.
+
+  \return number of tetrahedras
+  \return \c -1 on error.
+*/
+h5_size_t H5FedGetNumBoundaryTrianglesCnode (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t level,		/*!< mesh level to query	*/
+	const h5_id_t cnode		/*!< compute node		*/
+	) {
+	return -1;
+}

src/H5Fed_retrieve.c

@@ -0,0 +1,63 @@
+/******	RETRIEVAL routines **************************************************/
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5/h5.h"
+#include "h5/h5_private.h"
+#include "H5Fed.h"
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get coordinates of next vertex.
+
+  \return local id
+  \return error code (H5_ERR_NOENT means no more vertices on this level)
+ 
+ */
+h5_id_t
+H5FedGetVertex (
+	h5_file * f,			/*!< file handle		*/
+	h5_id_t	* const id,		/*!< OUT: global id		*/
+	h5_float64_t P[3]		/*!< OUT: coordinates		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_vertex ( f, id, P );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the definition of a specific tetrahedron \c tetra_id, i.e. 
+  a 4-tuple containing the specific indices of the 3-dimensional vertex
+  coordinates.
+
+  \return pointer to 4-tuple of vertex id's defining the tetrahedron.
+  \return NULL-pointer on error.
+*/
+h5_id_t
+H5FedGetTetrahedron (
+	h5_file * f,			/*!< file handle		*/
+	h5_id_t * const id,		/*!< OUT: global tetrahedron id	*/
+	h5_id_t * parent_id,		/*!< OUT: parent id if level
+					     \c >0 else \c -1		*/
+	h5_id_t vertex_ids[4]		/*!< OUT: vertex id's		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_get_tet ( f, id, parent_id, vertex_ids );
+}
+

src/H5Fed_store.c

@@ -0,0 +1,130 @@
+/*
+  Copyright 2007-2008
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <stdarg.h>
+#include <hdf5.h>
+#include "h5/h5.h"
+#include "h5/h5_private.h"
+#include "H5Fed.h"
+
+/*!
+  Add a new level.
+
+  \note
+  values for f->t.num_levels:
+  \c -1		unknown: after opening the file. This is equivalent to
+		"topological data has not been initialized".
+  \c 0		no levels: HDF5 group for meshes may already exist but must not!
+  \c > 0	number of mesh levels
+ 
+  \note
+  write new level:
+	H5FedAddLevel( f );
+	H5FedSetNumVertices( f, nv );
+	H5FedSetNumTetrahedra( f, nt );
+*/
+  
+h5_id_t
+H5FedAddRefinementLevel (
+	h5_file * f			/*!< file handle		*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_add_level ( f );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Set number of additional vertices in current step and level
+
+  ERRORS:
+
+  H5_ERR_INVAL:	It is not possible to add vertices to an existing mesh due
+  to limitation of the library
+
+  H5_ERR_NOMEM: Couldn't allocate enough memory.
+
+  \return number of vertices
+  \return errno	on error
+*/
+
+h5_size_t
+H5FedSetAdditionalNumVerticesToStore (
+	h5_file * f,			/*!< file handle		*/
+	const h5_size_t num		/*!< number of additional vertices */
+	) {
+
+	SET_FNAME ( __func__ );
+	return H5t_add_num_vertices ( f, num );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the the coordinates of a specific vertex at level \c level
+  with id \c vertex_id of the tetrahedral mesh.
+
+  \return local vertex id on success
+  \return errno on error
+*/
+h5_id_t
+H5FedStoreVertex (
+	h5_file * f,			/*!< file handle		*/
+	const h5_id_t id,		/*!< global vertex id or -1	*/
+	const h5_float64_t P[3]		/*!< coordinates		*/
+	) {
+
+	SET_FNAME ( __func__ );
+	return H5t_store_vertex ( f, id, P );
+}
+
+/*** T E T R A H E D R A ****************************************************/
+
+h5_size_t
+H5FedSetAdditionalNumTetrahedraToStore (
+	h5_file * f,			/*!< file handle		*/
+	const h5_size_t num		/*!< number of additional
+					  tetrahedra at level \c level	*/
+	) {
+	SET_FNAME ( __func__ );
+
+	return H5t_add_num_tets ( f, num );
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the 4-tuple, that contains the specific indices describing
+  a tetrahedron with id \c tet_id at level \c level of the tetrahedral
+  mesh.
+
+  Errors:
+  * current level not yet defined
+  * to many tets stored on level
+
+  \return local tetrahedron id
+  \return \c errno on error
+*/
+h5_id_t
+H5FedStoreTetrahedron (
+	h5_file * f,			/*!< file handle		*/
+	const h5_id_t id,		/*!< global tetrahedron id	*/
+	const h5_id_t parent_id,	/*!< global parent id
+					     if level \c >0 else \c -1	*/
+	const h5_id_t vertex_ids[4]	/*!< tuple with vertex id's	*/
+	) {
+	SET_FNAME ( __func__ );
+	return H5t_store_tet ( f, id, parent_id, vertex_ids );
+}