void use_case_5_generate_mesh(
const std::string& mesh_options ,
stk::mesh::BulkData & mesh ,
const VectorFieldType & node_coord ,
stk::mesh::Part & hex_block ,
stk::mesh::Part & quad_shell_block )
{
mesh.modification_begin();
const unsigned parallel_size = mesh.parallel_size();
const unsigned parallel_rank = mesh.parallel_rank();
double t = 0 ;
size_t num_hex = 0 ;
size_t num_shell = 0 ;
size_t num_nodes = 0 ;
size_t num_block = 0 ;
int error_flag = 0 ;
try {
Iogn::GeneratedMesh gmesh( mesh_options, parallel_size, parallel_rank );
num_nodes = gmesh.node_count_proc();
num_block = gmesh.block_count();
t = stk::wall_time();
std::vector<int> node_map( num_nodes , 0 );
gmesh.node_map( node_map );
{
for ( size_t i = 1 ; i <= num_block ; ++i ) {
const size_t num_elem = gmesh.element_count_proc(i);
const std::pair<std::string,int> top_info = gmesh.topology_type(i);
std::vector<int> elem_map( num_elem , 0 );
std::vector<int> elem_conn( num_elem * top_info.second );
gmesh.element_map( i, elem_map );
gmesh.connectivity( i , elem_conn );
if ( top_info.second == 8 ) {
for ( size_t j = 0 ; j < num_elem ; ++j ) {
const int * const local_node_id = & elem_conn[ j * 8 ] ;
const stk::mesh::EntityId node_id[8] = {
local_node_id[0] ,
local_node_id[1] ,
local_node_id[2] ,
local_node_id[3] ,
local_node_id[4] ,
local_node_id[5] ,
local_node_id[6] ,
local_node_id[7]
};
const stk::mesh::EntityId elem_id = elem_map[ j ];
stk::mesh::fem::declare_element( mesh , hex_block , elem_id , node_id );
++num_hex ;
}
}
else if ( top_info.second == 4 ) {
for ( size_t j = 0 ; j < num_elem ; ++j ) {
const int * const local_node_id = & elem_conn[ j * 4 ] ;
const stk::mesh::EntityId node_id[4] = {
local_node_id[0] ,
local_node_id[1] ,
local_node_id[2] ,
local_node_id[3]
};
const stk::mesh::EntityId elem_id = elem_map[ j ];
stk::mesh::fem::declare_element( mesh , quad_shell_block , elem_id , node_id );
++num_shell ;
}
}
}
}
std::vector<double> node_coordinates( 3 * node_map.size() );
gmesh.coordinates( node_coordinates );
if ( 3 * node_map.size() != node_coordinates.size() ) {
std::ostringstream msg ;
msg << " P" << mesh.parallel_rank()
<< ": ERROR, node_map.size() = "
<< node_map.size()
<< " , node_coordinates.size() / 3 = "
<< ( node_coordinates.size() / 3 );
throw std::runtime_error( msg.str() );
}
for ( unsigned i = 0 ; i < node_map.size() ; ++i ) {
const unsigned i3 = i * 3 ;
stk::mesh::Entity * const node = mesh.get_entity( stk::mesh::fem::FEMMetaData::NODE_RANK , node_map[i] );
if ( NULL == node ) {
std::ostringstream msg ;
msg << " P:" << mesh.parallel_rank()
<< " ERROR, Node not found: "
<< node_map[i] << " = node_map[" << i << "]" ;
throw std::runtime_error( msg.str() );
}
double * const data = field_data( node_coord , *node );
data[0] = node_coordinates[ i3 + 0 ];
data[1] = node_coordinates[ i3 + 1 ];
data[2] = node_coordinates[ i3 + 2 ];
}
}
catch ( const std::exception & X ) {
std::cout << " P:" << mesh.parallel_rank() << ": " << X.what()
<< std::endl ;
std::cout.flush();
error_flag = 1 ;
}
catch( ... ) {
std::cout << " P:" << mesh.parallel_rank()
<< " Caught unknown exception"
<< std::endl ;
std::cout.flush();
error_flag = 1 ;
}
stk::all_reduce( mesh.parallel() , stk::ReduceMax<1>( & error_flag ) );
if ( error_flag ) {
std::string msg( "Failed mesh generation" );
throw std::runtime_error( msg );
}
mesh.modification_end();
double dt = stk::wall_dtime( t );
stk::all_reduce( mesh.parallel() , stk::ReduceMax<1>( & dt ) );
std::cout << " P" << mesh.parallel_rank()
<< ": Meshed Hex = " << num_hex
<< " , Shell = " << num_shell
<< " , Node = " << num_nodes
<< " in " << dt << " sec"
<< std::endl ;
std::cout.flush();
}
int write_vis(std::string &nemI_out_file,
std::string &exoII_inp_file,
Machine_Description* machine,
Problem_Description* prob,
Mesh_Description<INT>* mesh,
LB_Description<INT>* lb)
{
int exid_vis, exid_inp;
char title[MAX_LINE_LENGTH+1];
const char *coord_names[] = {"X", "Y", "Z"};
/*-----------------------------Execution Begins------------------------------*/
/* Generate the file name for the visualization file */
std::string vis_file_name = remove_extension(nemI_out_file);
vis_file_name += "-vis.exoII";
/* Generate the title for the file */
strcpy(title, UTIL_NAME);
strcat(title, " ");
strcat(title, ELB_VERSION);
strcat(title, " load balance visualization file");
/*
* If the vis technique is to be by element block then calculate the
* number of element blocks.
*/
int vis_nelem_blks;
if(prob->type == ELEMENTAL)
vis_nelem_blks = machine->num_procs;
else
vis_nelem_blks = machine->num_procs + 1;
/* Create the ExodusII file */
std::cout << "Outputting load balance visualization file " << vis_file_name.c_str() << "\n";
int cpu_ws = 0;
int io_ws = 0;
int mode = EX_CLOBBER;
if (prob->int64db|prob->int64api) {
mode |= EX_NETCDF4|EX_NOCLASSIC|prob->int64db|prob->int64api;
}
if((exid_vis=ex_create(vis_file_name.c_str(), mode, &cpu_ws, &io_ws)) < 0) {
Gen_Error(0, "fatal: unable to create visualization output file");
return 0;
}
ON_BLOCK_EXIT(ex_close, exid_vis);
/*
* Open the original input ExodusII file, read the values for the
* element blocks and output them to the visualization file.
*/
int icpu_ws=0;
int iio_ws=0;
float vers=0.0;
mode = EX_READ | prob->int64api;
if((exid_inp=ex_open(exoII_inp_file.c_str(), mode, &icpu_ws, &iio_ws, &vers)) < 0) {
Gen_Error(0, "fatal: unable to open input ExodusII file");
return 0;
}
ON_BLOCK_EXIT(ex_close, exid_inp);
char **elem_type = (char**)array_alloc(2, mesh->num_el_blks, MAX_STR_LENGTH+1,
sizeof(char));
if(!elem_type) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
ON_BLOCK_EXIT(free, elem_type);
std::vector<INT> el_blk_ids(mesh->num_el_blks);
std::vector<INT> el_cnt_blk(mesh->num_el_blks);
std::vector<INT> node_pel_blk(mesh->num_el_blks);
std::vector<INT> nattr_el_blk(mesh->num_el_blks);
if(ex_get_elem_blk_ids(exid_inp, TOPTR(el_blk_ids)) < 0) {
Gen_Error(0, "fatal: unable to get element block IDs");
return 0;
}
int acc_vis = ELB_TRUE; // Output a different element block per processor
if (prob->vis_out == 2)
acc_vis = ELB_FALSE; // Output a nodal/element variable showing processor
size_t nsize = 0;
/*
* Find out if the mesh consists of mixed elements. If not then
* element blocks will be used to visualize the partitioning. Otherwise
* nodal/element results will be used.
*/
for(size_t ecnt=0; ecnt < mesh->num_el_blks; ecnt++) {
if(ex_get_elem_block(exid_inp, el_blk_ids[ecnt], elem_type[ecnt],
&el_cnt_blk[ecnt], &node_pel_blk[ecnt],
&nattr_el_blk[ecnt]) < 0) {
Gen_Error(0, "fatal: unable to get element block parameters");
return 0;
}
nsize += el_cnt_blk[ecnt]*node_pel_blk[ecnt];
if(strcmp(elem_type[0], elem_type[ecnt]) == 0) {
if(node_pel_blk[0] != node_pel_blk[ecnt])
acc_vis = ELB_FALSE;
}
else
acc_vis = ELB_FALSE;
}
if(acc_vis == ELB_TRUE) {
/* Output the initial information */
if(ex_put_init(exid_vis, title, mesh->num_dims, mesh->num_nodes,
mesh->num_elems, vis_nelem_blks, 0, 0) < 0) {
Gen_Error(0, "fatal: unable to output initial params to vis file");
return 0;
}
/* Output the nodal coordinates */
float *xptr = nullptr;
float *yptr = nullptr;
float *zptr = nullptr;
switch(mesh->num_dims) {
case 3:
zptr = (mesh->coords) + 2*mesh->num_nodes;
/* FALLTHRU */
case 2:
yptr = (mesh->coords) + mesh->num_nodes;
/* FALLTHRU */
case 1:
xptr = mesh->coords;
}
if(ex_put_coord(exid_vis, xptr, yptr, zptr) < 0) {
Gen_Error(0, "fatal: unable to output coords to vis file");
return 0;
}
if(ex_put_coord_names(exid_vis, (char**)coord_names) < 0) {
Gen_Error(0, "fatal: unable to output coordinate names");
return 0;
}
std::vector<INT> elem_block(mesh->num_elems);
std::vector<INT> elem_map(mesh->num_elems);
std::vector<INT> tmp_connect(nsize);
for(size_t ecnt=0; ecnt < mesh->num_elems; ecnt++) {
elem_map[ecnt] = ecnt+1;
if(prob->type == ELEMENTAL)
elem_block[ecnt] = lb->vertex2proc[ecnt];
else {
int proc = lb->vertex2proc[mesh->connect[ecnt][0]];
int nnodes = get_elem_info(NNODES, mesh->elem_type[ecnt]);
elem_block[ecnt] = proc;
for(int ncnt=1; ncnt < nnodes; ncnt++) {
if(lb->vertex2proc[mesh->connect[ecnt][ncnt]] != proc) {
elem_block[ecnt] = machine->num_procs;
break;
}
}
}
}
int ccnt = 0;
std::vector<INT> vis_el_blk_ptr(vis_nelem_blks+1);
for(INT bcnt=0; bcnt < vis_nelem_blks; bcnt++) {
vis_el_blk_ptr[bcnt] = ccnt;
int pos = 0;
int old_pos = 0;
INT* el_ptr = TOPTR(elem_block);
size_t ecnt = mesh->num_elems;
while(pos != -1) {
pos = in_list(bcnt, ecnt, el_ptr);
if(pos != -1) {
old_pos += pos + 1;
ecnt = mesh->num_elems - old_pos;
el_ptr = TOPTR(elem_block) + old_pos;
int nnodes = get_elem_info(NNODES, mesh->elem_type[old_pos-1]);
for(int ncnt=0; ncnt < nnodes; ncnt++)
tmp_connect[ccnt++] = mesh->connect[old_pos-1][ncnt] + 1;
}
}
}
vis_el_blk_ptr[vis_nelem_blks] = ccnt;
/* Output the element map */
if(ex_put_map(exid_vis, TOPTR(elem_map)) < 0) {
Gen_Error(0, "fatal: unable to output element number map");
return 0;
}
/* Output the visualization element blocks */
for(int bcnt=0; bcnt < vis_nelem_blks; bcnt++) {
/*
* Note this assumes all the blocks contain the same type
* element.
*/
int ecnt = (vis_el_blk_ptr[bcnt+1]-vis_el_blk_ptr[bcnt])/node_pel_blk[0];
if(ex_put_elem_block(exid_vis, bcnt+1, elem_type[0],
ecnt, node_pel_blk[0], 0) < 0) {
Gen_Error(0, "fatal: unable to output element block params");
return 0;
}
/* Output the connectivity */
if(ex_put_elem_conn(exid_vis, bcnt+1,
&tmp_connect[vis_el_blk_ptr[bcnt]]) < 0) {
Gen_Error(0, "fatal: unable to output element connectivity");
return 0;
}
}
}
else { /* For nodal/element results visualization of the partioning. */
// Copy the mesh portion to the vis file.
ex_copy(exid_inp, exid_vis);
/* Set up the file for nodal/element results */
float time_val = 0.0;
if(ex_put_time(exid_vis, 1, &time_val) < 0) {
Gen_Error(0, "fatal: unable to output time to vis file");
return 0;
}
const char *var_names[] = {"proc"};
if(prob->type == NODAL) {
/* Allocate memory for the nodal values */
std::vector<float> proc_vals(mesh->num_nodes);
if(ex_put_variable_param(exid_vis, EX_NODAL, 1) < 0) {
Gen_Error(0, "fatal: unable to output var params to vis file");
return 0;
}
if(ex_put_variable_names(exid_vis, EX_NODAL, 1, (char**)var_names) < 0) {
Gen_Error(0, "fatal: unable to output variable name");
return 0;
}
/* Do some problem specific assignment */
for(size_t ncnt=0; ncnt < mesh->num_nodes; ncnt++)
proc_vals[ncnt] = lb->vertex2proc[ncnt];
for(int pcnt=0; pcnt < machine->num_procs; pcnt++) {
for(auto & elem : lb->bor_nodes[pcnt])
proc_vals[elem] = machine->num_procs + 1;
}
/* Output the nodal variables */
if(ex_put_nodal_var(exid_vis, 1, 1, mesh->num_nodes, TOPTR(proc_vals)) < 0) {
Gen_Error(0, "fatal: unable to output nodal variables");
return 0;
}
}
else if(prob->type == ELEMENTAL) {
/* Allocate memory for the element values */
std::vector<float> proc_vals(mesh->num_elems);
if(ex_put_variable_param(exid_vis, EX_ELEM_BLOCK, 1) < 0) {
Gen_Error(0, "fatal: unable to output var params to vis file");
return 0;
}
if(ex_put_variable_names(exid_vis, EX_ELEM_BLOCK, 1, (char**)var_names) < 0) {
Gen_Error(0, "fatal: unable to output variable name");
return 0;
}
/* Do some problem specific assignment */
for(int proc=0; proc < machine->num_procs; proc++) {
for (size_t e = 0; e < lb->int_elems[proc].size(); e++) {
size_t ecnt = lb->int_elems[proc][e];
proc_vals[ecnt] = proc;
}
for (size_t e = 0; e < lb->bor_elems[proc].size(); e++) {
size_t ecnt = lb->bor_elems[proc][e];
proc_vals[ecnt] = proc;
}
}
/* Output the element variables */
size_t offset = 0;
for (size_t i=0; i < mesh->num_el_blks; i++) {
if(ex_put_var(exid_vis, 1, EX_ELEM_BLOCK, 1, el_blk_ids[i],
el_cnt_blk[i], &proc_vals[offset]) < 0) {
Gen_Error(0, "fatal: unable to output nodal variables");
return 0;
}
offset += el_cnt_blk[i];
}
}
}
return 1;
} /*---------------------------End write_vis()-------------------------------*/
