int check_valid_elem_conn( int idx, mhdf_FileHandle file, struct mhdf_FileDesc* desc, int conn_dim )
{
long *ranges, *buffer, *iter;
int num_ranges;
long i, invalid = 0;
hid_t handle;
mhdf_Status status;
const long count = desc->elems[idx].desc.count;
const long len = desc->elems[idx].desc.vals_per_ent;
ranges = get_dim_ranges( desc, conn_dim, &num_ranges );
handle = mhdf_openConnectivitySimple( file, desc->elems[idx].handle, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error opening connectivity for %s: %s\n",
desc->elems[idx].handle, mhdf_message(&status));
free(ranges);
return 1;
}
buffer = malloc( sizeof(long) * count * len );
mhdf_readConnectivity( handle, 0, count, H5T_NATIVE_LONG, buffer, &status );
if (mhdf_isError(&status)) {
fprintf(stderr,"Internal error reading connectivity for %s: %s\n",
desc->elems[idx].handle, mhdf_message(&status));
free(ranges);
free(buffer);
mhdf_closeData( file, handle, &status );
return 1;
}
mhdf_closeData( file, handle, &status );
iter = buffer;
for (i = 0; i < count; ++i, iter += len) {
if (!ids_contained( iter, len, ranges, num_ranges)) {
if (VERBOSE)
printf("Invalid connectivity for element %ld (ID %ld) in %s\n",
i, i + desc->elems[idx].desc.start_id, desc->elems[idx].handle );
++invalid;
}
}
free( buffer );
free( ranges );
if (invalid) {
printf("%ld elements with invalid connectivity in %s\n", invalid, desc->elems[idx].handle );
return 1;
}
return 0;
}
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;
}