int read_exoII_file(int Proc,
int Num_Proc,
PROB_INFO_PTR prob,
PARIO_INFO_PTR pio_info,
MESH_INFO_PTR mesh)
{
#ifndef ZOLTAN_NEMESIS
Gen_Error(0, "Fatal: Nemesis requested but not linked with driver.");
return 0;
#else /* ZOLTAN_NEMESIS */
/* Local declarations. */
char *yo = "read_exoII_mesh";
char par_nem_fname[FILENAME_MAX+1], title[MAX_LINE_LENGTH+1];
char cmesg[256];
float ver;
int i, pexoid, cpu_ws = 0, io_ws = 0;
int *nnodes = NULL, *etypes = NULL;
#ifdef DEBUG_EXO
int j, k, elem;
#endif
FILE *fdtmp;
/***************************** BEGIN EXECUTION ******************************/
DEBUG_TRACE_START(Proc, yo);
/* since this is a test driver, set error reporting in exodus */
ex_opts(EX_VERBOSE | EX_DEBUG);
/* generate the parallel filename for this processor */
gen_par_filename(pio_info->pexo_fname, par_nem_fname, pio_info, Proc,
Num_Proc);
/*
* check whether parallel file exists. do the check with fopen
* as ex_open coredumps on the paragon when files do not exist.
*/
if ((fdtmp = fopen(par_nem_fname, "r")) == NULL) {
sprintf(cmesg,"fatal: parallel Exodus II file %s does not exist",
par_nem_fname);
Gen_Error(0, cmesg);
return 0;
}
else
fclose(fdtmp);
/*
* now open the existing parallel file using Exodus calls.
*/
if ((pexoid = ex_open(par_nem_fname, EX_READ, &cpu_ws, &io_ws,
&ver)) < 0) {
sprintf(cmesg,"fatal: could not open parallel Exodus II file %s",
par_nem_fname);
Gen_Error(0, cmesg);
return 0;
}
/* and get initial information */
if (ex_get_init(pexoid, title, &(mesh->num_dims),
&(mesh->num_nodes), &(mesh->num_elems),
&(mesh->num_el_blks), &(mesh->num_node_sets),
&(mesh->num_side_sets)) < 0) {
Gen_Error(0, "fatal: Error returned from ex_get_init");
return 0;
}
/* alocate some memory for the element blocks */
mesh->data_type = MESH;
mesh->vwgt_dim = 1; /* One weight for now. */
mesh->ewgt_dim = 1; /* One weight for now. */
mesh->eb_etypes = (int *) malloc (5 * mesh->num_el_blks * sizeof(int));
if (!mesh->eb_etypes) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
mesh->eb_ids = mesh->eb_etypes + mesh->num_el_blks;
mesh->eb_cnts = mesh->eb_ids + mesh->num_el_blks;
mesh->eb_nnodes = mesh->eb_cnts + mesh->num_el_blks;
mesh->eb_nattrs = mesh->eb_nnodes + mesh->num_el_blks;
mesh->eb_names = (char **) malloc (mesh->num_el_blks * sizeof(char *));
if (!mesh->eb_names) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
mesh->hindex = (int *) malloc(sizeof(int));
mesh->hindex[0] = 0;
if (ex_get_elem_blk_ids(pexoid, mesh->eb_ids) < 0) {
Gen_Error(0, "fatal: Error returned from ex_get_elem_blk_ids");
return 0;
}
/* allocate temporary storage for items needing global reduction. */
/* nemesis does not store most element block info about blocks for */
/* which the processor owns no elements. */
/* we, however, use this information in migration, so we need to */
/* accumulate it for all element blocks. kdd 2/2001 */
if (mesh->num_el_blks > 0) {
nnodes = (int *) malloc(2 * mesh->num_el_blks * sizeof(int));
if (!nnodes) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
etypes = nnodes + mesh->num_el_blks;
}
/* get the element block information */
for (i = 0; i < mesh->num_el_blks; i++) {
/* allocate space for name */
mesh->eb_names[i] = (char *) malloc((MAX_STR_LENGTH+1) * sizeof(char));
if (!mesh->eb_names[i]) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
if (ex_get_elem_block(pexoid, mesh->eb_ids[i], mesh->eb_names[i],
&(mesh->eb_cnts[i]), &(nnodes[i]),
&(mesh->eb_nattrs[i])) < 0) {
Gen_Error(0, "fatal: Error returned from ex_get_elem_block");
return 0;
}
if (mesh->eb_cnts[i] > 0) {
if ((etypes[i] = (int) get_elem_type(mesh->eb_names[i],
nnodes[i],
mesh->num_dims)) == E_TYPE_ERROR) {
Gen_Error(0, "fatal: could not get element type");
return 0;
}
}
else etypes[i] = (int) NULL_EL;
}
/* Perform reduction on necessary fields of element blocks. kdd 2/2001 */
MPI_Allreduce(nnodes, mesh->eb_nnodes, mesh->num_el_blks, MPI_INT, MPI_MAX,
MPI_COMM_WORLD);
MPI_Allreduce(etypes, mesh->eb_etypes, mesh->num_el_blks, MPI_INT, MPI_MIN,
MPI_COMM_WORLD);
for (i = 0; i < mesh->num_el_blks; i++) {
strcpy(mesh->eb_names[i], get_elem_name(mesh->eb_etypes[i]));
}
free(nnodes);
/*
* allocate memory for the elements
* allocate a little extra for element migration latter
*/
mesh->elem_array_len = mesh->num_elems + 5;
mesh->elements = (ELEM_INFO_PTR) malloc (mesh->elem_array_len
* sizeof(ELEM_INFO));
if (!(mesh->elements)) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
/*
* intialize all of the element structs as unused by
* setting the globalID to -1
*/
for (i = 0; i < mesh->elem_array_len; i++)
initialize_element(&(mesh->elements[i]));
/* read the information for the individual elements */
if (!read_elem_info(pexoid, Proc, prob, mesh)) {
Gen_Error(0, "fatal: Error returned from read_elem_info");
return 0;
}
/* read the communication information */
if (!read_comm_map_info(pexoid, Proc, prob, mesh)) {
Gen_Error(0, "fatal: Error returned from read_comm_map_info");
return 0;
}
/* Close the parallel file */
if(ex_close (pexoid) < 0) {
Gen_Error(0, "fatal: Error returned from ex_close");
return 0;
}
/* print out the distributed mesh */
if (Debug_Driver > 3)
print_distributed_mesh(Proc, Num_Proc, mesh);
DEBUG_TRACE_END(Proc, yo);
return 1;
#endif /* ZOLTAN_NEMESIS */
}
void exodus_file_write_mesh(exodus_file_t* file,
fe_mesh_t* mesh)
{
ASSERT(file->writing);
// See whether we have polyhedral blocks, and whether the non-polyhedral
// blocks have supported element types.
int num_blocks = fe_mesh_num_blocks(mesh);
bool is_polyhedral = false;
int pos = 0;
char* block_name;
fe_block_t* block;
while (fe_mesh_next_block(mesh, &pos, &block_name, &block))
{
fe_mesh_element_t elem_type = fe_block_element_type(block);
if (elem_type == FE_POLYHEDRON)
{
is_polyhedral = true;
break;
}
else if (elem_type != FE_INVALID)
{
// Check the number of nodes for the element.
if (!element_is_supported(elem_type, fe_block_num_element_nodes(block, 0)))
polymec_error("exodus_file_write_mesh: Element type in block %s has invalid number of nodes.", block_name);
}
else
polymec_error("exodus_file_write_mesh: Invalid element type for block %s.", block_name);
}
// Write out information about elements, faces, edges, nodes.
file->num_nodes = fe_mesh_num_nodes(mesh);
ex_init_params params;
strcpy(params.title, file->title);
params.num_dim = 3;
params.num_nodes = file->num_nodes;
int num_edges = fe_mesh_num_edges(mesh);
params.num_edge = num_edges;
params.num_edge_blk = 0;
int num_faces = fe_mesh_num_faces(mesh);
params.num_face = num_faces;
params.num_face_blk = (is_polyhedral) ? 1 : 0;
int num_elem = fe_mesh_num_elements(mesh);
params.num_elem = num_elem;
params.num_elem_blk = num_blocks;
params.num_elem_sets = file->num_elem_sets = fe_mesh_num_element_sets(mesh);
params.num_face_sets = file->num_face_sets = fe_mesh_num_face_sets(mesh);
params.num_edge_sets = file->num_edge_sets = fe_mesh_num_edge_sets(mesh);
params.num_node_sets = file->num_node_sets = fe_mesh_num_node_sets(mesh);
params.num_side_sets = file->num_side_sets = fe_mesh_num_side_sets(mesh);
params.num_elem_maps = 0;
params.num_face_maps = 0;
params.num_edge_maps = 0;
params.num_node_maps = 0;
ex_put_init_ext(file->ex_id, ¶ms);
// If we have any polyhedral element blocks, we write out a single face
// block that incorporates all of the polyhedral elements.
if (is_polyhedral)
{
// Generate face->node connectivity information.
int num_pfaces = fe_mesh_num_faces(mesh);
int face_node_size = 0;
int num_face_nodes[num_pfaces];
for (int f = 0; f < num_pfaces; ++f)
{
int num_nodes = fe_mesh_num_face_nodes(mesh, f);
num_face_nodes[f] = num_nodes;
face_node_size += num_nodes;
}
int* face_nodes = polymec_malloc(sizeof(int) * face_node_size);
int offset = 0;
for (int f = 0; f < num_pfaces; ++f)
{
fe_mesh_get_face_nodes(mesh, f, &face_nodes[offset]);
offset += num_face_nodes[f];
}
for (int i = 0; i < face_node_size; ++i)
face_nodes[i] += 1;
// Write an "nsided" face block.
ex_put_block(file->ex_id, EX_FACE_BLOCK, 1, "nsided",
num_pfaces, face_node_size, 0, 0, 0);
ex_put_name(file->ex_id, EX_FACE_BLOCK, 1, "face_block");
ex_put_conn(file->ex_id, EX_FACE_BLOCK, 1, face_nodes, NULL, NULL);
// Clean up.
polymec_free(face_nodes);
// Number of nodes per face.
ex_put_entity_count_per_polyhedra(file->ex_id, EX_FACE_BLOCK,
1, num_face_nodes);
}
// Go over the element blocks and write out the data.
pos = 0;
while (fe_mesh_next_block(mesh, &pos, &block_name, &block))
{
int elem_block = pos;
int num_e = fe_block_num_elements(block);
fe_mesh_element_t elem_type = fe_block_element_type(block);
if (elem_type == FE_POLYHEDRON)
{
// Count up the faces in the block and write the block information.
int tot_num_elem_faces = 0;
int faces_per_elem[num_e];
for (int i = 0; i < num_e; ++i)
{
faces_per_elem[i] = fe_block_num_element_faces(block, i);
tot_num_elem_faces += faces_per_elem[i];
}
ex_put_block(file->ex_id, EX_ELEM_BLOCK, elem_block, "nfaced",
num_e, 0, 0, tot_num_elem_faces, 0);
// Write elem->face connectivity information.
int elem_faces[tot_num_elem_faces], offset = 0;
for (int i = 0; i < num_e; ++i)
{
fe_block_get_element_faces(block, i, &elem_faces[offset]);
offset += faces_per_elem[i];
}
for (int i = 0; i < tot_num_elem_faces; ++i)
elem_faces[i] += 1;
ex_put_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, NULL, NULL, elem_faces);
ex_put_entity_count_per_polyhedra(file->ex_id, EX_ELEM_BLOCK, elem_block, faces_per_elem);
}
else if (elem_type != FE_INVALID)
{
// Get element information.
char elem_type_name[MAX_NAME_LENGTH+1];
get_elem_name(elem_type, elem_type_name);
int num_nodes_per_elem = fe_block_num_element_nodes(block, 0);
// Write the block.
ex_put_block(file->ex_id, EX_ELEM_BLOCK, elem_block, elem_type_name,
num_e, num_nodes_per_elem, 0, 0, 0);
// Write the elem->node connectivity.
int elem_nodes[num_e* num_nodes_per_elem], offset = 0;
for (int i = 0; i < num_e; ++i)
{
fe_block_get_element_nodes(block, i, &elem_nodes[offset]);
offset += num_nodes_per_elem;
}
for (int i = 0; i < num_e* num_nodes_per_elem; ++i)
elem_nodes[i] += 1;
ex_put_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, elem_nodes, NULL, NULL);
}
// Set the element block name.
ex_put_name(file->ex_id, EX_ELEM_BLOCK, elem_block, block_name);
}
// Set node positions.
real_t x[file->num_nodes], y[file->num_nodes], z[file->num_nodes];
point_t* X = fe_mesh_node_positions(mesh);
for (int n = 0; n < file->num_nodes; ++n)
{
x[n] = X[n].x;
y[n] = X[n].y;
z[n] = X[n].z;
}
ex_put_coord(file->ex_id, x, y, z);
char* coord_names[3] = {"x", "y", "z"};
ex_put_coord_names(file->ex_id, coord_names);
// Write sets of entities.
int *set, set_id = 0;
size_t set_size;
char* set_name;
pos = set_id = 0;
while (fe_mesh_next_element_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_ELEM_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_face_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_FACE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_edge_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_EDGE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_node_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_NODE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_side_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_SIDE_SET, ++set_id, set_name, set, set_size);
}
