Fortran API fixed

.gitattributes

@@ -520,6 +520,7 @@ test/H5Fed/tetmesh_write.c -text
 test/H5Fed/tetmesh_write1.c -text
 test/H5Fed/tetmesh_write2.c -text
 test/H5Fed/tetmesh_write_tags.c -text
+test/H5Fed/trimesh_2gnuplot.c -text
 test/H5Fed/trimesh_adjacencies.c -text
 test/H5Fed/trimesh_read.c -text
 test/H5Fed/trimesh_write.c -text

.gitignore

@@ -77,4 +77,6 @@ test/h5u_test
 tools/.deps
 tools/Makefile
 tools/Makefile.in
+tools/h5PartDcToVtk
+tools/h5PartSurfaceToVtk
 tools/h5hutcc

src/Fortran/H5Block_F.c

@@ -116,7 +116,9 @@ h5bl_3d_getview (
 		      k_start, k_end);
 	H5_API_RETURN (h5b_3d_get_view (
 			       fh,
-			       i_start, i_end, j_start, j_end, k_start, k_end ));
+			       (h5_size_t*)i_start, (h5_size_t*)i_end,
+			       (h5_size_t*)j_start, (h5_size_t*)j_end,
+			       (h5_size_t*)k_start, (h5_size_t*)k_end ));
 }
 
 h5_err_t
@@ -142,7 +144,9 @@ h5bl_3d_getreducedview (
 		      k_start, k_end);
 	H5_API_RETURN(h5b_3d_get_reduced_view (
 		fh,
-		i_start, i_end, j_start, j_end, k_start, k_end ));
+		(h5_size_t*)i_start, (h5_size_t*)i_end,
+		(h5_size_t*)j_start, (h5_size_t*)j_end,
+		(h5_size_t*)k_start, (h5_size_t*)k_end ));
 }
 
 h5_int64_t

src/Fortran/H5Part_F.c

@@ -155,14 +155,14 @@ h5pt_setview (
 h5_err_t
 h5pt_setview_indices (
 	const h5_int64_t *f,
-	const h5_int64_t *indices,
+	const h5_int64_t * const indices,
 	const h5_int64_t *nelem
 	) {
 
 	h5_file_t *fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_err_t, "f=%p, indices=%p, nelem=%lld",
 				fh, indices, (long long)*nelem);
-	H5_API_RETURN(h5u_set_view_indices ( fh, indices, *nelem ));
+	H5_API_RETURN(h5u_set_view_indices ( fh, (const h5_size_t*const)indices, *nelem ));
 }
 
 h5_err_t

src/Fortran/H5_F.c

@@ -51,25 +51,6 @@
 
 #endif
 
-static h5_int32_t
-_flagsfor2c (
-	char * flags
-	) {
-
-	h5_int32_t fbits = 0x00;
-
-	flags = strtok ( flags, "," );
-	while ( flags != NULL ) {
-		if ( strcmp ( flags, "vfd_mpiposix" ) == 0 )
-				fbits |= H5_VFD_MPIPOSIX;
-		else if ( strcmp ( flags, "vfd_independent" ) == 0 )
-				fbits |= H5_VFD_INDEPENDENT;
-		flags = strtok ( NULL, "," );
-	}
-
-	return fbits;
-}
-
 /* open/close interface */
 h5_err_t
 h5_openr (
@@ -79,7 +60,7 @@ h5_openr (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_RDONLY, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_RDONLY, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }
@@ -92,7 +73,7 @@ h5_openw (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_WRONLY, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_WRONLY, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }
@@ -105,7 +86,7 @@ h5pt_opena (
 
 	H5_API_ENTER (h5_err_t, "name='%s', l_name=%d", name, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_file_t* f = h5_open_file ( name2, H5_O_APPEND, 0 );
+	h5_file_t* f = h5_open_file ( name2, H5_O_APPEND, 0, 0 );
 	free ( name2 );
 	H5_API_RETURN((h5_int64_t)(size_t)f);
 }

src/h5core/h5_attach.c

@@ -274,7 +274,7 @@ h5_get_attachment (
 	// write file
 	if (f->myproc == 0) {
 		int fd;
-		if ((fd = open (fname, O_WRONLY|O_CREAT|O_TRUNC)) < 0) {
+		if ((fd = open (fname, O_WRONLY|O_CREAT|O_TRUNC, 0600)) < 0) {
 			H5_CORE_API_LEAVE (
 				h5_error (
 					H5_ERR_H5,

src/h5core/h5t_retrieve.c

@@ -310,3 +310,22 @@ h5t_get_vertex_coords_by_id (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
+h5_err_t
+h5t_get_neighbor_indices (
+	h5t_mesh_t* const m,
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* neighbor_indices
+	) {
+	H5_CORE_API_ENTER (h5_err_t,
+			   "m=%p, entity_id=%llu, neighbor_indices=%p",
+			   m,
+			   (long long unsigned)entity_id,
+			   neighbor_indices);
+	h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (entity_id);
+	h5_loc_idx_t* indices = h5tpriv_get_loc_elem_neighbor_indices (m, elem_idx);
+	int num_facets = h5tpriv_ref_elem_get_num_facets (m);
+	for (int i = 0; i < num_facets; i++) {
+		neighbor_indices[i] = indices[i];
+	}
+	H5_CORE_API_RETURN (H5_SUCCESS);
+}

src/include/H5Fed_retrieve.h

@@ -173,6 +173,19 @@ H5FedGetVertexIndicesOfEntity (
 	H5_API_RETURN (h5t_get_vertex_indices_of_entity (m, entity_id, vertex_indices));
 }
 
+static inline h5_err_t
+H5FedGetNeighborIndicesOfElement (
+	h5t_mesh_t* const m,
+	h5_loc_id_t entity_id,
+	h5_loc_idx_t* neighbor_indices
+	) {
+	H5_API_ENTER (h5_err_t,
+		      "m=%p, entity_id=%lld, neighbor_indices=%p",
+		      m, (long long)entity_id, neighbor_indices);
+	H5_API_RETURN (h5t_get_neighbor_indices (m, entity_id, neighbor_indices));
+}
+
+
 #ifdef __cplusplus
 }
 #endif

src/include/h5core/h5t_retrieve.h

@@ -78,6 +78,8 @@ h5t_get_vertex_coords_by_index (h5t_mesh_t* const, h5_loc_idx_t, h5_float64_t[3]
 h5_err_t
 h5t_get_vertex_coords_by_id (h5t_mesh_t* const, h5_loc_id_t, h5_float64_t[3]);
 
+h5_err_t
+h5t_get_neighbor_indices (h5t_mesh_t* const, h5_loc_id_t, h5_loc_idx_t*);
 #ifdef __cplusplus
 }
 #endif

test/H5Fed/Makefile.am

@@ -16,6 +16,7 @@ noinst_PROGRAMS =				\
 		tetmesh_read_tags		\
 		trimesh_read			\
 		trimesh_write			\
+		trimesh_2gnuplot		\
 		trimesh_adjacencies		\
 		trimesh_write_dunetest
 
@@ -28,12 +29,13 @@ EXTRA_DIST =					\
 		tetmesh_read.c			\
 		tetmesh_read_tags.c		\
 		tetmesh_write.c			\
-		tetmesh_write1.c			\
+		tetmesh_write1.c		\
 		tetmesh_write2.c		\
 		tetmesh_write_tags.c		\
 		trimesh_adjacencies.c		\
 		trimesh_read.c			\
 		trimesh_write.c			\
+		trimesh_2gnuplot.c		\
 		trimesh_write_dunetest.c
 
 #		map_tet2globalid.c \

test/H5Fed/trimesh_2gnuplot.c

@@ -0,0 +1,101 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "H5hut.h"
+#if defined (PARALLEL_IO)
+#include <mpi.h>
+#endif
+
+#define H5FedGetNumLeafElementsTotal H5FedGetNumElementsTotal
+/*
+  Traverse elements and output coordinates
+ */
+static h5_err_t
+traverse_elems (
+	h5t_mesh_t* const m
+	) {
+	/* get number of elements we have to expect */
+	h5_size_t num_elems_expect = H5FedGetNumLeafElementsTotal (m);
+
+	/* get iterator for co-dim 0 */
+	h5t_iterator_t* iter = H5FedBeginTraverseEntities (m, 0);
+
+	/* iterate over all co-dim 0 entities, i.e. elements */
+	h5_loc_id_t local_id;
+	h5_size_t num_elems = 0;
+	while ((local_id = H5FedTraverseEntities (iter)) >= 0) {
+		h5_loc_id_t local_vids[4];
+		H5FedGetVertexIndicesOfEntity (m, local_id, local_vids);
+
+		printf ("# cell %llx\n", (long long unsigned)local_id );
+		h5_float64_t P[3];
+		for (int i = 0; i < 3; i++) {
+			H5FedGetVertexCoordsByIndex (m, local_vids[i], P);
+			printf (" %8.6f %8.6f\n", P[0], P[1]);
+		}
+		H5FedGetVertexCoordsByIndex (m, local_vids[0], P);
+		printf (" %8.6f %8.6f\n", P[0], P[1]);
+		printf ("\n");
+		num_elems++;
+	}
+
+	/* done */
+	H5FedEndTraverseEntities (iter);
+
+	/* report error if we got a different number then expected */
+	if (num_elems != num_elems_expect) {
+		fprintf (stderr, "!!! Got %lld elements, but expected %lld.\n",
+			 (long long)num_elems, (long long)num_elems_expect);
+		exit(1);
+	}
+	return H5_SUCCESS;
+}
+
+int
+main (
+	int argc,
+	char* argv[]
+	) {
+
+#if defined (PARALLEL_IO)
+	MPI_Comm comm = MPI_COMM_WORLD;
+	MPI_Init (&argc, &argv);
+#else
+	MPI_Comm comm = 0;
+#endif
+	if (argc < 2 || argc > 3) {
+		fprintf (stderr, "Usage: %s FILE [LEVEL]\n", argv[0]);
+		exit (42);
+	}
+
+	/* abort program on error, so we don't have to handle them */
+	H5SetErrorHandler (H5AbortErrorhandler);
+	H5SetVerbosityLevel (0);
+
+	/* open file and get number of meshes */
+	h5_file_t* f = H5OpenFile (argv[1], H5_O_RDONLY, comm);
+	h5t_mesh_t*  m;
+	H5FedOpenTriangleMeshByIndex (f, 0, &m);
+	int num_levels = H5FedGetNumLevels (m);
+	int level = num_levels-1;
+	if (argc >= 3) {
+		level = atoi (argv[2]);
+	}
+	if (level >= num_levels || level < 0) {
+		fprintf (stderr, "level %d out of range\n", level);
+		goto done;
+	}
+	H5FedSetLevel (m, level);
+	traverse_elems (m);
+
+
+done:
+	H5FedCloseMesh (m);
+	H5CloseFile (f);
+
+#if defined (PARALLEL_IO)
+	MPI_Finalize ();
+#endif
+
+	return 0;
+}

tools/h5PartDcToVtk.cc

@@ -312,7 +312,7 @@ int main(int argc, const char *argv[])
    
   string ifn = string(input_name) + string(".h5");
 
-  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, 0);
    
   if( h5file == NULL ) {
     fprintf(stdout, "unable to open file %s\n", input_name);

tools/h5PartSurfaceToVtk.cc

@@ -336,7 +336,7 @@ int main(int argc, const char *argv[])
    
   string ifn = string(input_name) + string(".h5");
    
-  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, 0);
      
   if( h5file == NULL ) {
     fprintf(stdout, "unable to open file %s\n", input_name);