added

.gitattributes

@@ -32,6 +32,7 @@ src/H5Fed_adjacency.c -text
 src/H5Fed_dof.c -text
 src/H5Fed_retrieve.c -text
 src/H5Fed_statistics.c -text
+src/H5Fed_storeretrieve.c -text
 src/H5Part.c -text
 src/H5Part.h -text
 src/H5PartErrors.h -text

src/H5Fed_storeretrieve.c

@@ -0,0 +1,540 @@
+/******	RETRIEVAL routines **************************************************/
+/*
+  Copyright 2006-2007
+ 	Paul Scherrer Institut, Villigen, Switzerland;
+ 	Benedikt Oswald;
+ 	Achim Gsell
+ 	All rights reserved.
+ 
+  Authors
+ 	Achim Gsell
+  
+  Warning
+	This code is under development.
+ 
+ */
+
+#include <hdf5.h>
+#include "h5/h5_types.h"
+#include "h5/h5.h"
+#include "H5Fed.h"
+
+
+/*
+  Retrieval for all objects:
+
+  SetLevel()
+  while ( getObj() >=0 ) {
+	...
+  }
+
+  For the implementation of "getObj()" we need the information whether an
+  object has been refined or not. If we are on level n and an object has been
+  refined on level i<n, we have to skip this object. Since we have a consecutive
+  enumberation of objects, we have a simple mapping from the parent id of the 
+  object to 
+  
+*/
+
+/*** V E R T I C E S *********************************************************/
+
+/*!
+  \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 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 */
+	) {
+
+	struct h5t_fdata *t = &f->t;
+
+	ssize_t num_elems = (t->cur_level > 0 ? t->num_vertices[t->cur_level-1] : 0)
+		+ num;
+
+	t->num_vertices[t->cur_level] = num_elems;
+	t->vertices = realloc ( t->vertices, num_elems*sizeof ( t->vertices[0] ) );
+
+	if ( t->vertices == NULL ) {
+		return H5_ERR_NOMEM;
+	}
+
+	return num;
+}
+
+/*!
+  \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		*/
+	) {
+	return -1;
+}
+
+/*!
+  \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		*/
+	) {
+
+	struct h5t_fdata *t = &f->t;
+
+	if ( t->cur_level < 0 )
+		return H5_ERR_INVAL;
+
+	if ( t->last_stored_vertex_id+1 >= t->num_vertices[t->cur_level] )
+		return H5_ERR_INVAL;
+
+	h5_vertex *vertex = &t->vertices[++t->last_stored_vertex_id];
+	vertex->id = id;
+	memcpy ( &vertex->P, P, sizeof ( vertex->P ) );
+	
+	return t->last_stored_vertex_id;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get coordinates of the vertex \c vertex_id.
+
+  \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 * const P[3]	/*!< OUT: coordinates		*/
+	) {
+	return -1;
+}
+
+/*** E D G E S ***************************************************************/
+
+h5_size_t
+H5FedSetNumEdges (
+	h5_file * f,
+	const h5_size_t num
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Returns the number of edges present in the mesh at level \c level in 
+  current time step on this compute node.
+
+  \return number of edges
+  \return \c -1	on error.
+*/
+h5_size_t
+H5FedGetNumEdges (
+	h5_file * f			/*!< file handle		*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the 2-tuple, that contains the specific indices describing
+  an edge with id \c edge_id at level \c level of the tetrahedral mesh.
+
+  \return local edge id
+  \return \c -1 on error
+*/
+h5_id_t
+H5FedStoreEdge (
+	h5_file * f,			/*!< file handle		*/
+	const h5_id_t id,		/*!< global edge id or -1	*/
+	const h5_id_t parent_id,	/*!< local parent id
+					     if level \c >0 else \x -1	*/
+	const h5_id_t vertex_ids[2]	/*!< tuple with vertex id's	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the definition of a specific edge \edge_id, i.e. a 2-tuple
+  containing the specific indices of the 3-dimensional vertex
+  coordinates.
+
+  \return local id
+  \return error code (H5_ERR_NOENT means no more vertices on this level)
+*/
+h5_id_t
+H5FedGetEdge (
+	h5_file * f,			/*!< file handle		*/
+	h5_id_t * const id,		/*!< OUT: global edge id	*/
+	h5_id_t * const parent_id,	/*!< OUT: global parent id
+					     if level \c >0 else \c -1	*/
+	h5_id_t * const vertex_ids[2]	/*!< OUT: vertex id's		*/
+	) {
+	return -1;
+}
+
+/*** T R I A N G L E S *******************************************************/
+
+h5_size_t
+H5FedSetNumTriangles (
+	h5_file * f,
+	const h5_size_t num
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the number of triangles present in the mesh at level \c level in 
+  current time step on this compute note.
+
+  \return Number of triangles
+  \return \c -1 on error.
+
+*/
+h5_size_t
+H5FedGetNumTriangles (
+	h5_file * f			/*!< file handle		*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the 3-tuple, that contains the specific indices describing a
+  triangle with id \c triangle_id at level \c level of the tetrahedral mesh.
+
+  \return local triangle id
+  \return \c -1 on error
+*/
+h5_int_t
+H5FedStoreTriangle (
+	h5_file * f,			/*!< file handle		*/
+	const h5_id_t id,		/*!< global triangle id	or -1	*/
+	const h5_id_t parent_id,	/*!< local parent id
+					     if level \c >0 else \x -1	*/
+	const h5_id_t vertex_ids[3]	/*!< tuple with vertex id's	*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the definition of a specific triangle \triangle_id, i.e. 
+  a 3-tuple containing the specific indices of the 3-dimensional vertex
+  coordinates.
+
+  \return local id
+  \return error code (H5_ERR_NOENT means no more vertices on this level)
+*/
+h5_id_t
+H5FedGetTriangle (
+	h5_file * f,			/*!< file handle		*/
+	h5_id_t * const id,		/*!< OUT: global triangle id	*/
+	h5_id_t * const parent_id,	/*!< OUT: parent id if level
+					     \c >0 else \c -1		*/
+	h5_id_t * const vertex_ids[3]	/*!< OUT: vertex id's		*/
+	) {
+	return -1;
+}
+
+/*** B O U N D A R Y   T R I A N G L E S *************************************/
+ 
+/*!
+  \ingroup h5fed_c_api
+
+  Get the number of boundary triangles present in the mesh at
+  level \c level in current step on this compute node.
+
+  \return number of tetrahedras
+  \return \c -1 on error.
+*/
+h5_size_t
+H5FedGetNumBoundaryTriangles (
+	h5_file * f			/*!< file handle		*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Writes the vector, that contains the specific indices that describe
+  a boundary triangle \c btriangle with id \c btriangle_id at level
+  \c level of the tetrahedral mesh.
+
+  \return local boundary triangle id
+  \return \c -1 on error
+*/
+h5_id_t H5FedStoreBoundaryTriangle (
+	h5_file * fh,			/*!< file handle		*/
+	const h5_id_t btriangle_id,	/*!< global boundary triangle id*/
+	const h5_id_t parent_id,	/*!< parent id if level \c >0
+					     else \c -1			*/
+	const h5_id_t btriangle[3]	/*!< tuple with vertex id's*/
+	) {
+	return -1;
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Get the definition of the boundary triangle \c triangle_id at level
+  \c level, i.e. the indices of the 3-dimensional vertex coordinates.
+
+  \return pointer to 3-tuple of vertex id's defining the boundary triangle.
+  \return NULL-pointer on error.
+*/
+h5_id_t H5FedGetBoundaryTriangle (
+	h5_file * f,			/*!< file handle		*/
+	h5_id_t * const id,		/*!< global btriangle_id	*/
+	h5_id_t * const parent_id,	/*!< OUT: parent id if level
+					     \c >0 else \c -1		*/
+	h5_id_t * const vertex_ids[3]	/*!< OUT: vertex id's		*/
+	) {
+	return -1;
+}
+
+/*** 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	*/
+	) {
+
+	struct h5t_fdata *t = &f->t;
+
+	ssize_t num_elems = (t->cur_level > 0 ? t->num_tets[t->cur_level-1] : 0)
+		+ num;
+
+	t->num_tets[t->cur_level] = num_elems;
+	t->tets = realloc ( t->tets, num_elems*sizeof ( t->tets[0] ) );
+	if ( t->tets == NULL ) {
+		return H5_ERR_NOMEM;
+	}
+	t->map_tets_g2l = realloc (
+		t->map_tets_g2l,
+		num_elems*sizeof ( t->map_tets_g2l[0] ) );
+
+	return num;
+}
+
+/*!
+  \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		*/
+	) {
+	return -1;
+}
+
+/*!
+  \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 tet_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	*/
+	) {
+
+	struct h5t_fdata *t = &f->t;
+
+	/*
+	  more than allocated
+	*/
+	if ( t->last_stored_tet_id+1 >= t->num_tets[t->cur_level] ) 
+		return H5_ERR_INVAL;
+
+	/*
+	  missing call to add the first level
+	 */
+	if ( t->cur_level < 0 )
+		return H5_ERR_INVAL;
+
+	/*
+	  check parent id
+	*/
+	if ( (t->cur_level == 0) && (parent_id != -1) ) {
+		return H5_ERR_INVAL;
+	} 
+	if ( (t->cur_level >  0) && (parent_id < 0) ) {
+		return H5_ERR_INVAL;
+	}
+	if ( (t->cur_level >  0) && (parent_id >= t->num_tets[t->cur_level-1]) ) {
+		return H5_ERR_INVAL;
+	}
+	/*
+	  check tet_id
+	*/
+	if ( (t->cur_level == 0) && (
+		     (tet_id < 0) || (tet_id >= t->num_tets[0]) ) ) {
+		return H5_ERR_INVAL;
+	}
+	if ( (t->cur_level > 0) && (
+		     (tet_id <  t->num_tets[t->cur_level-1]) ||
+		     (tet_id >= t->num_tets[t->cur_level]) ) ) {
+		return H5_ERR_INVAL;
+	}
+	
+
+	h5_tetrahedron *tet = &t->tets[++t->last_stored_tet_id];
+	tet->id = tet_id;
+	tet->parent_id = parent_id;
+	tet->refined_on_level = -1;
+	tet->unused = 0;
+	memcpy ( &tet->vertex_ids, vertex_ids, sizeof ( tet->vertex_ids ) );
+
+	t->map_tets_g2l[tet_id] = t->last_stored_tet_id;
+	if ( parent_id >= 0 ) {
+		h5_id_t local_parent_id = t->map_tets_g2l[parent_id];
+		t->tets[local_parent_id].refined_on_level = t->cur_level;
+	}
+	return t->last_stored_vertex_id;
+}
+
+/*!
+  \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 * const vertex_ids[4]	/*!< OUT: vertex id's		*/
+	) {
+	return -1;
+}
+
+h5_err_t
+H5FedSetStep (
+	h5_file *f,			/*!< Handle to open file */
+	const h5_id_t step		/*!< Time-step to set. */
+	) {
+
+	return (h5_err_t) H5_set_step ( f, step );
+}
+
+
+h5_id_t
+H5FedAddMesh (
+	h5_file * f
+	) {
+	return H5t_add_mesh ( f );
+}
+
+/*****************************************************************************/
+/*!
+  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
+H5FedAddLevel (
+	h5_file * f			/*!< file handle		*/
+	) {
+	struct h5t_fdata *t = &f->t;
+
+	if ( f->mode == H5_O_RDONLY ) {
+		return H5_ERR_INVAL;
+	}
+
+	/* t->num_levels will be set to zero on file creation(!) */
+	if ( t->num_levels == -1 ) {	/* unknown number of levels	*/
+		/* determine number of levels */
+		return -1;		/* not implemented		*/
+	}
+	t->cur_level = t->num_levels++;
+
+	ssize_t num_bytes = t->num_levels*sizeof ( h5_size_t );
+	t->num_vertices = realloc ( t->num_vertices, num_bytes );
+	t->num_vertices[t->cur_level] = -1;
+
+	t->num_tets = realloc ( t->num_tets, num_bytes );
+	t->num_tets[t->cur_level] = -1;
+
+	t->new_level = t->cur_level;
+	if ( t->cur_level == 0 ) {
+		/* nothing stored yet */
+		t->last_stored_vertex_id = -1;
+		t->last_stored_tet_id = -1;
+	}
+	return t->cur_level;
+}