hid_t
mhdf_createAdjacency( mhdf_FileHandle file,
const char* elem_handle,
long adj_list_size,
mhdf_Status* status )
{
FileHandle* file_ptr;
hid_t elem_id, table_id;
hsize_t dim = (hsize_t)adj_list_size;
API_BEGIN;
file_ptr = (FileHandle*)(file);
if (!mhdf_check_valid_file( file_ptr, status ))
return -1;
if (adj_list_size < 1)
{
mhdf_setFail( status, "Invalid argument.\n" );
return -1;
}
if (elem_handle == mhdf_node_type_handle())
{
table_id = mhdf_create_table( file_ptr->hdf_handle,
NODE_ADJCY_PATH,
file_ptr->id_type,
1, &dim,
status );
}
else
{
elem_id = mhdf_elem_group_from_handle( file_ptr, elem_handle, status );
if (elem_id < 0) return -1;
table_id = mhdf_create_table( elem_id,
ADJACENCY_NAME,
file_ptr->id_type,
1, &dim,
status );
H5Gclose( elem_id );
}
API_END_H(1);
return table_id;
}
int
mhdf_haveAdjacency( mhdf_FileHandle file,
const char* elem_group,
mhdf_Status* status )
{
FileHandle* file_ptr;
hid_t elem_id;
int result;
API_BEGIN;
file_ptr = (FileHandle*)(file);
if (!mhdf_check_valid_file( file_ptr, status ))
return -1;
if (elem_group == mhdf_node_type_handle())
{
#if defined(H5Gopen_vers) && H5Gopen_vers > 1
elem_id = H5Gopen( file_ptr->hdf_handle, NODE_GROUP, H5P_DEFAULT );
#else
elem_id = H5Gopen( file_ptr->hdf_handle, NODE_GROUP );
#endif
if (elem_id < 0)
{
mhdf_setFail( status, "H5Gopen( \"%s\" ) failed.\n", NODE_GROUP );
return -1;
}
}
else
{
elem_id = mhdf_elem_group_from_handle( file_ptr, elem_group, status );
if (elem_id < 0)
return -1;
}
result = mhdf_is_in_group( elem_id, ADJACENCY_NAME, status );
H5Gclose( elem_id );
mhdf_setOkay( status );
API_END;
return result;
}
static int check_valid_tag( int tag_idx, mhdf_FileHandle file, struct mhdf_FileDesc* desc )
{
long *ids = 0, count, junk;
long *ranges;
int nranges;
hid_t handles[3];
mhdf_Status status;
const struct mhdf_TagDesc* tag = &(desc->tags[tag_idx]);
int i, result = 0;
long srange[2];
const char* name;
struct mhdf_EntDesc* group;
hid_t h5type;
hsize_t size;
if (tag->have_sparse) {
mhdf_openSparseTagData( file, tag->name, &count, &junk, handles, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error opening sparse data for tag \"%s\": %s\n", tag->name, mhdf_message(&status));
return 1;
}
ids = malloc( sizeof(long) * count );
mhdf_readSparseTagEntities( handles[0], 0, count, H5T_NATIVE_LONG, ids, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error reading sparse entities for tag \"%s\": %s\n", tag->name, mhdf_message(&status));
mhdf_closeData( file, handles[0], &status );
mhdf_closeData( file, handles[1], &status );
free(ids);
return 1;
}
mhdf_closeData( file, handles[0], &status );
ranges = all_id_ranges( desc, 0, &nranges );
if (!ids_contained( ids, count, ranges, nranges )) {
++result;
printf("Sparse data for tag \"%s\" has values for invalid IDs\n", tag->name );
}
else if (contains_duplicates( ids, count )) {
++result;
printf("Sparse data for tag \"%s\" has duplicate values for one or more entities\n", tag->name );
}
free(ranges);
for (i = 0; i < tag->num_dense_indices; ++i) {
if (tag->dense_elem_indices[i] == -2) {
name = mhdf_set_type_handle();
group = &desc->sets;
}
else if (tag->dense_elem_indices[i] == -1) {
name = mhdf_node_type_handle();
group = &desc->nodes;
}
else {
name = desc->elems[ tag->dense_elem_indices[i] ].handle;
group = &desc->elems[ tag->dense_elem_indices[i] ].desc;
}
srange[0] = group->start_id;
srange[1] = group->count;
if (ids_contained( ids, count, srange, 2 )) {
++result;
printf("Tag \"%s\" has both sparse values and dense values for one or more entities in \"%s\"\n", tag->name, name );
}
}
free(ids);
}
if (tag->type != mhdf_ENTITY_ID) {
if (tag->have_sparse)
mhdf_closeData( file, handles[1], &status );
return result;
}
ranges = all_id_ranges( desc, 1, &nranges );
if (tag->default_value && !ids_contained( tag->default_value, tag->size, ranges, nranges )) {
++result;
printf("Handle tag \"%s\" has invalid ID(s) in its default value.\n", tag->name );
}
if (tag->global_value && !ids_contained( tag->global_value, tag->size, ranges, nranges )) {
++result;
printf("Handle tag \"%s\" has invalid ID(s) in its global/mesh value.\n", tag->name );
}
h5type = H5T_NATIVE_LONG;
if (tag->size > 1) {
size = tag->size;
#if defined(H5Tarray_create_vers) && H5Tarray_create_vers > 1
h5type = H5Tarray_create( H5T_NATIVE_LONG, 1, &size );
#else
h5type = H5Tarray_create( H5T_NATIVE_LONG, 1, &size, NULL );
#endif
}
if (tag->have_sparse) {
ids = malloc( tag->size * count * sizeof(long) );
mhdf_readTagValues( handles[1], 0, count, h5type, ids, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error reading sparse values for handle tag \"%s\": %s\n", tag->name, mhdf_message(&status));
mhdf_closeData( file, handles[1], &status );
free(ids);
free(ranges);
if (tag->size > 1)
H5Tclose( h5type );
return 1;
}
mhdf_closeData( file, handles[1], &status );
if (!ids_contained( ids, tag->size * count, ranges, nranges )) {
++result;
printf("Sparse data for one or more entities with handle tag \"%s\" has invalid ID(s).\n", tag->name );
}
free(ids);
}
for (i = 0; i < tag->num_dense_indices; ++i) {
if (tag->dense_elem_indices[i] == -2) {
name = mhdf_set_type_handle();
/*group = &desc->sets;*/
}
else if (tag->dense_elem_indices[i] == -1) {
name = mhdf_node_type_handle();
/*group = &desc->nodes;*/
}
else {
name = desc->elems[ tag->dense_elem_indices[i] ].handle;
/*group = &desc->elems[ tag->dense_elem_indices[i] ].desc;*/
}
handles[0] = mhdf_openDenseTagData( file, tag->name, name, &count, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal dense values for handle tag \"%s\" on \"%s\": %s\n", tag->name, name, mhdf_message(&status));
++result;
continue;
}
ids = malloc( tag->size * count * sizeof(long) );
mhdf_readTagValues( handles[0], 0, count, h5type, ids, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error reading dense values for handle tag \"%s\" on \"%s\": %s\n", tag->name, name, mhdf_message(&status));
mhdf_closeData( file, handles[0], &status );
free(ids);
++result;
continue;
}
mhdf_closeData( file, handles[1], &status );
if (!ids_contained( ids, count, ranges, nranges )) {
++result;
printf("Dense data on \"%s\" for handle tag \"%s\" has invalid ID(s) for one or more entities.\n", name, tag->name );
}
free(ids);
}
if (tag->size > 1)
H5Tclose( h5type );
return result;
}
int main( int argc, char* argv[] )
{
/* input file */
const char* filename;
mhdf_FileHandle file;
mhdf_Status status;
mhdf_Status *const sptr = &status;
hid_t handle; /* generic handle used to refer to any data block in file */
/* output file */
const char* gmsh_filename;
FILE* gmsh;
unsigned gmsh_type; /* hexahedral element type number */
double x, y, z; /* temp storage of node coordinates */
unsigned node_offset, node_id; /* temporary values */
unsigned* connectivity; /* temporary value */
/* node data */
long numnode; /* total number of nodes */
long nodestart; /* file id of first node in list */
int dimension; /* coordinate values per node */
double* nodecoords; /* interleaved node coordinates */
unsigned* nodeids; /* GLOBAL_ID value for nodes */
int have_nodeids = 0;
/* hex data */
char* hexgroup = NULL; /* name of element group containing hexes */
long numhex; /* total number of hexahedral elements */
long hexstart; /* file id of first hex in group */
int nodes_per_hex; /* length of connectivity list for a hex */
unsigned* hexconnectivity; /* hex connectivity data */
unsigned* hexids; /* GLOBAL_ID value for hexes */
int have_hexids = 0;
/* list of element groups in file */
char** elem_groups;
unsigned num_elem_groups;
char namebuffer[64];
/* tag data for accessing GLOBAL_ID */
int tagsize; /* number of values for each entity */
int ts, td, tg; /* unused tag properties */
int havesparse, havedense; /* Boolean values */
enum mhdf_TagDataType tagtype; /* base data type of tag */
hid_t sparse_handle[2]; /* handle pair for sparse tag data */
unsigned* sparse_entities; /* temp storage of sparse tag file ids */
unsigned* sparse_ids; /* temp storage of GLOBAL_ID values in spasre tag */
long junk, numtag; /* number of entities for which tag data is available */
long fileid, globalid; /* temporary values */
long ncount = 0, hcount = 0; /* temporary count of number of tag values */
/* iteration */
long i;
int j;
unsigned k;
/* process CL args (expect input .h5m file and output .gmsh file name) */
if (argc != 3)
{
fprintf(stderr, "Usage: %s <input_file> <output_file>\n", argv[0] );
return 1;
}
filename = argv[1];
gmsh_filename = argv[2];
/* Open the file */
file = mhdf_openFile( filename, 0, 0, sptr ); CHK_ERR(sptr);
/* Read node coordinates. */
handle = mhdf_openNodeCoords( file, &numnode, &dimension, &nodestart, sptr ); CHK_ERR(sptr);
nodecoords = (double*)malloc( dimension * numnode * sizeof(double) );
mhdf_readNodeCoords( handle, 0, numnode, nodecoords, sptr ); CHK_ERR(sptr);
mhdf_closeData( file, handle, sptr ); CHK_ERR(sptr);
/* Find first element group containing hexahedra */
elem_groups = mhdf_getElemHandles( file, &num_elem_groups, sptr ); CHK_ERR(sptr);
for (k = 0; k < num_elem_groups; ++k)
{
mhdf_getElemTypeName( file, elem_groups[k], namebuffer, sizeof(namebuffer), sptr ); CHK_ERR(sptr);
if (!hexgroup && !strcmp(mdhf_HEX_TYPE_NAME, namebuffer))
hexgroup = strdup(elem_groups[k]);
else
printf( "Skipping element group '%s' containing element of type '%s'\n", elem_groups[k], namebuffer );
}
free( elem_groups );
if (!hexgroup) {
fprintf( stderr, "No Hexahedra defined in file\n" );
return 4;
}
/* Read Hexahedron connectivity */
handle = mhdf_openConnectivity( file, hexgroup, &nodes_per_hex,
&numhex, &hexstart, sptr ); CHK_ERR(sptr);
hexconnectivity = (unsigned*)malloc(numhex * nodes_per_hex * sizeof(unsigned));
mhdf_readConnectivity( handle, 0, numhex, H5T_NATIVE_UINT, hexconnectivity, sptr ); CHK_ERR(sptr);
mhdf_closeData( file, handle, sptr ); CHK_ERR(sptr);
/* Note: hex connectivity list contains file-space node IDs, which are
the nodes in the sequence they are read from the file, with
the first node having an ID of 'nodestart' */
/* Check for "GLOBAL_ID" tag */
nodeids = (unsigned*)malloc( numnode * sizeof(unsigned) );
hexids = (unsigned*)malloc( numhex * sizeof(unsigned) );
mhdf_getTagInfo( file, "GLOBAL_ID", &tagtype, &tagsize, &ts, &td, &tg, &havesparse, sptr );
/* If have GLOBAL_ID tag, try to read values for nodes and hexes */
if (!mhdf_isError(sptr))
{
/* Check that the tag contains what we expect */
if (tagtype != mhdf_INTEGER || tagsize != 1)
{
fprintf(stderr, "ERROR: Invalid data type for 'GLOBAL_ID' tag.\n");
exit(3);
}
/* Check for and read dense-format tag data for nodes */
havedense = mhdf_haveDenseTag( file, "GLOBAL_ID", mhdf_node_type_handle(), sptr ); CHK_ERR(sptr);
if (havedense)
{
handle = mhdf_openDenseTagData( file, "GLOBAL_ID", mhdf_node_type_handle(), &numtag, sptr ); CHK_ERR(sptr);
assert( numtag == numnode );
mhdf_readDenseTag( handle, 0, numtag, H5T_NATIVE_UINT, nodeids, sptr ); CHK_ERR(sptr);
mhdf_closeData( file, handle, sptr ); CHK_ERR(sptr);
have_nodeids = 1;
}
/* Check for and read dense-format tag data for hexes */
havedense = mhdf_haveDenseTag( file, "GLOBAL_ID", hexgroup, sptr ); CHK_ERR(sptr);
if (havedense)
{
handle = mhdf_openDenseTagData( file, "GLOBAL_ID", hexgroup, &numtag, sptr ); CHK_ERR(sptr);
assert( numtag == numhex );
mhdf_readDenseTag( handle, 0, numtag, H5T_NATIVE_UINT, hexids, sptr ); CHK_ERR(sptr);
mhdf_closeData( file, handle, sptr ); CHK_ERR(sptr);
have_hexids = 1;
}
/* Check for and read sparse-format tag data */
if (havesparse)
{
mhdf_openSparseTagData( file, "GLOBAL_ID", &numtag, &junk, sparse_handle, sptr ); CHK_ERR(sptr);
sparse_entities = (unsigned*)malloc(numtag * sizeof(unsigned));
mhdf_readSparseTagEntities( sparse_handle[0], 0, numtag, H5T_NATIVE_UINT,
sparse_entities, sptr ); CHK_ERR(sptr);
sparse_ids = (unsigned*)malloc(numtag * sizeof(unsigned));
mhdf_readSparseTagValues( sparse_handle[1], 0, numtag, H5T_NATIVE_UINT,
sparse_ids, sptr ); CHK_ERR(sptr);
mhdf_closeData( file, sparse_handle[0], sptr ); CHK_ERR(sptr);
mhdf_closeData( file, sparse_handle[1], sptr ); CHK_ERR(sptr);
/* Set hex and node ids from sparse tag data */
for (i = 0; i < numtag; ++i)
{
fileid = sparse_entities[i];
globalid = sparse_ids[i];
if (fileid >= nodestart && fileid - nodestart < numnode)
{
nodeids[fileid - nodestart] = globalid;
++ncount;
}
else if (fileid >= hexstart && fileid - hexstart < numhex)
{
hexids[fileid - hexstart] = globalid;
++hcount;
}
}
free( sparse_ids );
free( sparse_entities );
/* make sure there was an ID for each node and each hex */
if (ncount == numnode)
have_nodeids = 1;
if (hcount == numhex)
have_hexids = 1;
} /* end have sparse tag for GLOBAL_ID */
} /* end have GLOBAL_ID tag */
/* done with input file */
free( hexgroup );
mhdf_closeFile( file, sptr ); CHK_ERR(sptr);
/* if no GLOBAL_ID, just use incrementing values */
if (!have_nodeids)
for (i = 0; i < numnode; ++i)
nodeids[i] = i+1;
if (!have_hexids)
for (i = 0; i < numhex; ++i)
hexids[i] = i+1;
/* write out as gmesh file version 1.0 */
/* get gmsh type for hexahedrons */
if (nodes_per_hex == 8)
gmsh_type = 5;
else if (nodes_per_hex == 27)
gmsh_type = 12;
else {
fprintf(stderr, "Cannot store %d node hex in gmsh file.\n", nodes_per_hex);
exit(4);
}
/* open file */
gmsh = fopen( gmsh_filename, "w" );
/* Write node data. If dimension is less than 3,
write zero for other coordinate values. In the
(highly unlikely) case that dimension is greater
than three, disregard higher-dimension coordinate
values. */
fprintf(gmsh, "$NOD\n" );
fprintf(gmsh, "%lu\n", numnode );
for (i = 0; i < numnode; ++i)
{
x = nodecoords[dimension*i];
y = z = 0.0;
if (dimension > 1) {
y = nodecoords[dimension*i+1];
if (dimension > 2) {
z = nodecoords[dimension*i+2];
}
}
fprintf(gmsh, "%u %f %f %f\n", nodeids[i], x, y, z );
}
/* Write element connectivity data */
fprintf(gmsh, "$ENDNOD\n$ELM\n" );
fprintf(gmsh, "%lu\n", numhex );
for (i = 0; i < numhex; ++i)
{
fprintf( gmsh, "%u %u 1 1 %d", hexids[i], gmsh_type, nodes_per_hex );
/* connectivity list for this hex */
connectivity = hexconnectivity + i*nodes_per_hex;
for (j = 0; j < nodes_per_hex; ++j)
{
/* get offset in node list from file id */
node_offset = connectivity[j] - nodestart;
/* get node id from ID list */
node_id = nodeids[node_offset];
fprintf( gmsh, " %u", node_id );
}
fprintf( gmsh, "\n" );
}
fprintf( gmsh, "$ENDELM\n" );
fclose( gmsh );
return 0;
}
