added

.gitattributes

@@ -521,6 +521,7 @@ test/H5Fed/tetmesh_read_tags.c -text
 test/H5Fed/tetmesh_write.c -text
 test/H5Fed/tetmesh_write2.c -text
 test/H5Fed/tetmesh_write_tags.c -text
+test/H5Fed/trimesh_adjacencies.c -text
 test/H5Fed/trimesh_read.c -text
 test/H5Fed/trimesh_write.c -text
 test/H5Fed/trimesh_write_dunetest.c -text

test/H5Fed/trimesh_adjacencies.c

@@ -0,0 +1,316 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+
+#include "H5hut.h"
+
+#define PRINT_UPADJACENCIES 1
+#define PRINT_DOWNADJACENCIES 0
+
+const h5_oid_t MESH_TYPE = H5_TRIANGLE_MESH;
+const char* FNAME = "simple_triangle.h5";
+
+static h5_err_t
+print_adjacencies_of_vertex (
+	h5_file_t* const f,
+	h5_id_t local_id,
+	clock_t* time_used
+	) {
+	h5_idlist_t* uadj_edges;
+	h5_idlist_t* uadj_triangles;
+	clock_t time_used_before = clock();
+	H5FedGetAdjacencies (f, local_id, 1, &uadj_edges);
+	H5FedGetAdjacencies (f, local_id, 2, &uadj_triangles);
+	*time_used = clock() - time_used_before;
+	int n = 0;
+	if (uadj_triangles->num_items > n) n = uadj_triangles->num_items;
+	if (uadj_edges->num_items > n) n = uadj_edges->num_items;
+	int i;
+	for (i = 0; i < n; i++) {
+		char v[256];
+		char k[256];
+		char d[256];
+		h5_id_t local_vids[4];
+		if (i == 0) {
+			H5FedGetVertexIndicesOfEntity (
+				f, local_id, local_vids);
+			snprintf (v, sizeof(v), "=[%lld]=", local_vids[0]);
+		} else {
+			*v = '\0';
+		}
+		if (i < uadj_edges->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, uadj_edges->items[i], local_vids);
+			snprintf (k, sizeof(k), "=[%lld,%lld]=",
+				   local_vids[0], local_vids[1]);
+		} else {
+			*k = '\0';
+		}
+		if (i < uadj_triangles->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, uadj_triangles->items[i], local_vids);
+			snprintf (d, sizeof(d), "=[%lld,%lld,%lld]=",
+				   local_vids[0], local_vids[1], local_vids[2]);
+		} else {
+			*d = '\0';
+		}
+		printf ("| %-18s | %-18s | %-18s |\n", v, k, d);
+	}
+	H5FedReleaseListOfAdjacencies (f, &uadj_edges);
+	H5FedReleaseListOfAdjacencies (f, &uadj_triangles);
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+print_adjacencies_of_edge (
+	h5_file_t* const f,
+	h5_id_t local_id,
+	clock_t* time_used
+	) {
+	h5_idlist_t* dadj_vertices;
+	h5_idlist_t* uadj_triangles;
+	clock_t time_used_before = clock();
+	H5FedGetAdjacencies (f, local_id, 0, &dadj_vertices);
+	H5FedGetAdjacencies (f, local_id, 2, &uadj_triangles);
+	*time_used = clock() - time_used_before;
+	int n = dadj_vertices->num_items;
+	if (uadj_triangles->num_items > n) n = uadj_triangles->num_items;
+
+	int i;
+	for (i = 0; i < n; i++) {
+		char v[256];
+		char k[256];
+		char d[256];
+		h5_id_t local_vids[4];
+		if (i < dadj_vertices->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, dadj_vertices->items[i], local_vids);
+			snprintf (v, sizeof(v), "=[%lld]=",
+				   local_vids[0]);
+		} else {
+			*v = '\0';
+		}
+		if (i == 0) {
+			H5FedGetVertexIndicesOfEntity (
+				f, local_id, local_vids);
+			snprintf (k, sizeof(k), "=[%lld,%lld]=",
+				  local_vids[0], local_vids[1]);
+		} else {
+			*k = '\0';
+		}
+		if (i < uadj_triangles->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, uadj_triangles->items[i], local_vids);
+			snprintf (d, sizeof(d), "=[%lld,%lld,%lld]=",
+				  local_vids[0], local_vids[1], local_vids[2]);
+		} else {
+			*d = '\0';
+		}
+		printf ("| %-18s | %-18s | %-18s |\n", v, k, d);
+	}
+	H5FedReleaseListOfAdjacencies (f, &dadj_vertices);
+	H5FedReleaseListOfAdjacencies (f, &uadj_triangles);
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+print_adjacencies_of_elem (
+	h5_file_t* const f,
+	h5_id_t local_id,
+	clock_t* time_used
+	) {
+	h5_idlist_t* dadj_vertices;
+	h5_idlist_t* dadj_edges;
+	clock_t time_used_before = clock();
+	H5FedGetAdjacencies (f, local_id, 0, &dadj_vertices);
+	H5FedGetAdjacencies (f, local_id, 1, &dadj_edges);
+	*time_used = clock() - time_used_before;
+	int n = dadj_vertices->num_items;
+	if (dadj_edges->num_items > n) n = dadj_edges->num_items;
+	int i;
+	for (i = 0; i < n; i++) {
+		char v[256];
+		char k[256];
+		char d[256];
+		h5_id_t local_vids[4];
+		if (i < dadj_vertices->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, dadj_vertices->items[i], local_vids);
+			snprintf (v, sizeof(v), "=[%lld]=",
+				   local_vids[0]);
+		} else {
+			*v = '\0';
+		}
+		if (i < dadj_edges->num_items) {
+			H5FedGetVertexIndicesOfEntity (
+				f, dadj_edges->items[i], local_vids);
+			snprintf (k, sizeof(k), "=[%lld,%lld]=",
+				   local_vids[0], local_vids[1]);
+		} else {
+			*k = '\0';
+		}
+		if (i == 0) {
+			H5FedGetVertexIndicesOfEntity (
+				f, local_id, local_vids);
+			snprintf (d, sizeof(k), "=[%lld,%lld,%lld]=",
+				  local_vids[0], local_vids[1], local_vids[2]);
+		} else {
+			*d = '\0';
+		}
+		printf ( "| %-18s | %-18s | %-18s |\n", v, k, d );
+	}
+	H5FedReleaseListOfAdjacencies (f, &dadj_vertices);
+	H5FedReleaseListOfAdjacencies (f, &dadj_edges);
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+traverse_vertices (
+	h5_file_t* const f
+	) {
+	h5_id_t local_id;
+	h5_id_t num = 0;
+	clock_t t_total = 0;
+	clock_t t_min = CLOCKS_PER_SEC;
+	clock_t t_max = 0;
+	clock_t t = 0;
+	printf ("\nAdjacencies to vertices\n");
+	h5t_iterator_t* iter = H5FedBeginTraverseEntities (f, 2);
+	while ((local_id = H5FedTraverseEntities (f, iter)) >= 0) {
+		print_adjacencies_of_vertex (f, local_id, &t);
+		num++;
+		t_total += t;
+		if (t < t_min) t_min = t;
+		if (t > t_max) t_max = t;
+	}
+	fprintf (
+		stderr,
+		"%lld\ttotal: %f\tmin: %f\tavg: %f\tmax: %f\n",
+		num,
+		(double)t_total / (double)CLOCKS_PER_SEC,
+		(double)t_min / (double)CLOCKS_PER_SEC,
+		(double)t_total / (double)CLOCKS_PER_SEC / (double)num,
+		(double)t_max / (double)CLOCKS_PER_SEC );
+	return H5FedEndTraverseEntities (f, iter);
+}
+
+static h5_err_t
+traverse_edges (
+	h5_file_t* const f
+	) {
+	h5_id_t local_id;
+	h5_id_t num = 0;
+	clock_t t_total = 0;
+	clock_t t_min = CLOCKS_PER_SEC;
+	clock_t t_max = 0;
+	clock_t t = 0;
+	printf ("\nAdjacencies to edges\n");
+	h5t_iterator_t* iter = H5FedBeginTraverseEntities (f, 1);
+	while ((local_id = H5FedTraverseEntities (f, iter)) >= 0) {
+		print_adjacencies_of_edge (f, local_id, &t);
+		num++;
+		t_total += t;
+		if (t < t_min) t_min = t;
+		if (t > t_max) t_max = t;
+	}
+	fprintf (
+		stderr,
+		"%lld\ttotal: %f\tmin: %f\tavg: %f\tmax: %f\n",
+		num,
+		(double)t_total / (double)CLOCKS_PER_SEC,
+		(double)t_min / (double)CLOCKS_PER_SEC,
+		(double)t_total / (double)CLOCKS_PER_SEC / (double)num,
+		(double)t_max / (double)CLOCKS_PER_SEC );
+	return H5FedEndTraverseEntities (f, iter);
+}
+
+static h5_err_t
+traverse_elems (
+	h5_file_t* const f
+	) {
+	h5_id_t local_id;
+	h5_id_t num = 0;
+	clock_t t_total = 0;
+	clock_t t_min = CLOCKS_PER_SEC;
+	clock_t t_max = 0;
+	clock_t t = 0;
+	printf ("\nAdjacencies to tetrahedra\n");
+	h5t_iterator_t* iter = H5FedBeginTraverseEntities (f, 0);
+	while ((local_id = H5FedTraverseEntities (f, iter)) >= 0) {
+		print_adjacencies_of_elem (f, local_id, &t);
+		num++;
+		t_total += t;
+		if (t < t_min) t_min = t;
+		if (t > t_max) t_max = t;
+	}
+	fprintf (
+		stderr,
+		"%lld\ttotal: %f\tmin: %f\tavg: %f\tmax: %f\n",
+		num,
+		(double)t_total / (double)CLOCKS_PER_SEC,
+		(double)t_min / (double)CLOCKS_PER_SEC,
+		(double)t_total / (double)CLOCKS_PER_SEC / (double)num,
+		(double)t_max / (double)CLOCKS_PER_SEC);
+	return H5FedEndTraverseEntities (f, iter);
+}
+
+static h5_err_t
+traverse_level (
+	h5_file_t* const f,
+	const h5_id_t level_id
+	) {
+	printf ("    Setting level to %lld\n", level_id);
+	H5FedSetLevel (f, level_id);
+	traverse_vertices (f);
+	traverse_edges (f);
+	traverse_elems (f);
+	return H5_SUCCESS;
+}
+
+static h5_err_t
+traverse_mesh (
+	h5_file_t* const f,
+	const h5_id_t mesh_id,
+	const h5_oid_t mesh_type
+	) {
+	/* open mesh and get number of levels */
+	printf ("    Opening mesh with id %lld\n", mesh_id);
+	H5FedOpenMesh (f, mesh_id, mesh_type);
+	h5_size_t num_levels = H5FedGetNumLevels (f);
+	printf ("    Number of levels in mesh: %lld\n", (long long)num_levels);
+
+	/* loop over all levels */
+	h5_id_t level_id;
+	for (level_id = 0; level_id < num_levels; level_id++) {
+		traverse_level (f, level_id);
+	}
+	/* done */
+	H5FedCloseMesh (f);
+	return H5_SUCCESS;
+}
+
+int
+main (
+	int argc,
+	char* argv[]
+	) {
+
+	/* abort program on error, so we don't have to handle them */
+	H5SetErrorHandler (H5AbortErrorhandler);
+	H5SetVerbosityLevel (2);
+
+	/* open file and get number of meshes */
+	h5_file_t *f = H5OpenFile (FNAME, H5_O_RDONLY, 0);
+	h5_size_t num_meshes = H5FedGetNumMeshes (f, MESH_TYPE);
+	printf ("    Number of meshes: %lld\n", (long long)num_meshes);
+
+	/* loop over all meshes */
+	h5_id_t mesh_id;
+	for (mesh_id = 0; mesh_id < num_meshes; mesh_id++) {
+		traverse_mesh (f, mesh_id, MESH_TYPE);
+	}
+
+	/* done */
+	H5CloseFile (f);
+	return 0;
+}