// element ids / proc_id:
// |-------|-------|-------|
// | | | |
// | 1/0 | 4/2 | 7/2 |
// | | | |
// |-------|-------|-------|
// | | | |
// | 2/0 | 5/1 | 8/2 |
// | | | |
// |-------|-------|-------|
// | | | |
// | 3/0 | 6/2 | 9/2 |
// | | | |
// |-------|-------|-------|
inline
void setupKeyholeMesh3D_case1(stk::mesh::BulkData& bulk)
{
ThrowRequire(bulk.parallel_size() == 3);
stk::io::fill_mesh("generated:3x1x3", bulk);
stk::mesh::EntityProcVec elementProcChanges;
if (bulk.parallel_rank() == 1) {
elementProcChanges.push_back(stk::mesh::EntityProc(bulk.get_entity(stk::topology::ELEM_RANK,4u),2));
elementProcChanges.push_back(stk::mesh::EntityProc(bulk.get_entity(stk::topology::ELEM_RANK,6u),2));
}
bulk.change_entity_owner(elementProcChanges);
}
void unpack_and_update_part_ordinals(stk::CommSparse &comm, const stk::mesh::BulkData& bulkData, const ElemElemGraph& graph, ParallelPartInfo ¶llelPartInfo)
{
for(int i=0;i<bulkData.parallel_size();++i)
{
while(comm.recv_buffer(i).remaining())
{
stk::mesh::GraphEdge edge = unpack_edge(comm, bulkData, graph, i);
size_t num_ordinals = 0;
comm.recv_buffer(i).unpack<size_t>(num_ordinals);
std::vector<stk::mesh::PartOrdinal> partOrdinals(num_ordinals);
for(stk::mesh::PartOrdinal &partOrdinal : partOrdinals)
comm.recv_buffer(i).unpack<stk::mesh::PartOrdinal>(partOrdinal);
parallelPartInfo[edge.elem2()] = partOrdinals;
}
}
}
inline
void setupKeyholeMesh3D_case2(stk::mesh::BulkData& bulk)
{
ThrowRequire(bulk.parallel_size() == 3);
stk::io::fill_mesh("generated:3x1x3", bulk);
stk::mesh::EntityProcVec elementProcChanges;
if (bulk.parallel_rank() == 1) {
elementProcChanges.push_back(stk::mesh::EntityProc(bulk.get_entity(stk::topology::ELEM_RANK,4),2));
elementProcChanges.push_back(stk::mesh::EntityProc(bulk.get_entity(stk::topology::ELEM_RANK,6),2));
}
bulk.change_entity_owner(elementProcChanges);
bulk.modification_begin();
if (bulk.parallel_rank() == 1) {
stk::mesh::Entity local_element5 = bulk.get_entity(stk::topology::ELEM_RANK,5);
const bool delete_success = bulk.destroy_entity(local_element5);
ThrowRequire(delete_success);
}
bulk.modification_end();
}
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();
}
void communicate_field_data( const stk::mesh::BulkData & mesh ,
const std::vector< const stk::mesh::FieldBase * > & fields )
{
if ( fields.empty() ) { return; }
const unsigned parallel_size = mesh.parallel_size();
const unsigned parallel_rank = mesh.parallel_rank();
// Sizing for send and receive
const unsigned zero = 0 ;
std::vector<unsigned> send_size( parallel_size , zero );
std::vector<unsigned> recv_size( parallel_size , zero );
std::vector<unsigned> procs ;
for ( std::vector<stk::mesh::Entity*>::const_iterator
i = mesh.entity_comm().begin() ;
i != mesh.entity_comm().end() ; ++i ) {
stk::mesh::Entity & e = **i ;
unsigned size = 0 ;
for ( std::vector<const stk::mesh::FieldBase *>::const_iterator
fi = fields.begin() ; fi != fields.end() ; ++fi ) {
const stk::mesh::FieldBase & f = **fi ;
size += stk::mesh::field_data_size( f , e );
}
if ( size ) {
if ( e.owner_rank() == parallel_rank ) {
// owner sends
stk::mesh::comm_procs( e , procs );
for ( std::vector<unsigned>::iterator
ip = procs.begin() ; ip != procs.end() ; ++ip ) {
send_size[ *ip ] += size ;
}
}
else {
// non-owner receives
recv_size[ e.owner_rank() ] += size ;
}
}
}
// Allocate send and receive buffers:
stk::CommAll sparse ;
{
const unsigned * const s_size = & send_size[0] ;
const unsigned * const r_size = & recv_size[0] ;
sparse.allocate_buffers( mesh.parallel(), parallel_size / 4 , s_size, r_size);
}
// Send packing:
for ( std::vector<stk::mesh::Entity*>::const_iterator
i = mesh.entity_comm().begin() ;
i != mesh.entity_comm().end() ; ++i ) {
stk::mesh::Entity & e = **i ;
if ( e.owner_rank() == parallel_rank ) {
stk::mesh::comm_procs( e , procs );
for ( std::vector<const stk::mesh::FieldBase *>::const_iterator
fi = fields.begin() ; fi != fields.end() ; ++fi ) {
const stk::mesh::FieldBase & f = **fi ;
const unsigned size = stk::mesh::field_data_size( f , e );
if ( size ) {
unsigned char * ptr =
reinterpret_cast<unsigned char *>(stk::mesh::field_data( f , e ));
for ( std::vector<unsigned>::iterator
ip = procs.begin() ; ip != procs.end() ; ++ip ) {
stk::CommBuffer & b = sparse.send_buffer( *ip );
b.pack<unsigned char>( ptr , size );
}
}
}
}
}
// Communicate:
sparse.communicate();
// Unpack for recv:
for ( std::vector<stk::mesh::Entity*>::const_iterator
i = mesh.entity_comm().begin() ;
i != mesh.entity_comm().end() ; ++i ) {
stk::mesh::Entity & e = **i ;
if ( e.owner_rank() != parallel_rank ) {
for ( std::vector<const stk::mesh::FieldBase *>::const_iterator
fi = fields.begin() ; fi != fields.end() ; ++fi ) {
const stk::mesh::FieldBase & f = **fi ;
const unsigned size = stk::mesh::field_data_size( f , e );
if ( size ) {
unsigned char * ptr =
reinterpret_cast<unsigned char *>(stk::mesh::field_data( f , e ));
stk::CommBuffer & b = sparse.recv_buffer( e.owner_rank() );
b.unpack<unsigned char>( ptr , size );
}
}
}
}
}
void Gear::mesh( stk::mesh::BulkData & M )
{
stk::mesh::EntityRank element_rank = stk::topology::ELEMENT_RANK;
stk::mesh::EntityRank side_rank = m_mesh_meta_data.side_rank();
M.modification_begin();
m_mesh = & M ;
const unsigned p_size = M.parallel_size();
const unsigned p_rank = M.parallel_rank();
std::vector<size_t> counts ;
stk::mesh::comm_mesh_counts(M, counts);
// max_id is no longer available from comm_mesh_stats.
// If we assume uniform numbering from 1.., then max_id
// should be equal to counts...
const stk::mesh::EntityId node_id_base = counts[ stk::topology::NODE_RANK ] + 1 ;
const stk::mesh::EntityId elem_id_base = counts[ element_rank ] + 1 ;
const unsigned long elem_id_gear_max =
m_angle_num * ( m_rad_num - 1 ) * ( m_z_num - 1 );
std::vector<stk::mesh::Part*> elem_parts ;
std::vector<stk::mesh::Part*> face_parts ;
std::vector<stk::mesh::Part*> node_parts ;
{
stk::mesh::Part * const p_gear = & m_gear ;
stk::mesh::Part * const p_surf = & m_surf ;
elem_parts.push_back( p_gear );
face_parts.push_back( p_surf );
}
for ( unsigned ia = 0 ; ia < m_angle_num ; ++ia ) {
for ( unsigned ir = 0 ; ir < m_rad_num - 1 ; ++ir ) {
for ( unsigned iz = 0 ; iz < m_z_num - 1 ; ++iz ) {
stk::mesh::EntityId elem_id_gear = identifier( m_z_num-1 , m_rad_num-1 , iz , ir , ia );
if ( ( ( elem_id_gear * p_size ) / elem_id_gear_max ) == p_rank ) {
stk::mesh::EntityId elem_id = elem_id_base + elem_id_gear ;
// Create the node and set the model_coordinates
const size_t ia_1 = ( ia + 1 ) % m_angle_num ;
const size_t ir_1 = ir + 1 ;
const size_t iz_1 = iz + 1 ;
stk::mesh::Entity node[8] ;
node[0] = create_node( node_parts, node_id_base, iz , ir , ia_1 );
node[1] = create_node( node_parts, node_id_base, iz_1, ir , ia_1 );
node[2] = create_node( node_parts, node_id_base, iz_1, ir , ia );
node[3] = create_node( node_parts, node_id_base, iz , ir , ia );
node[4] = create_node( node_parts, node_id_base, iz , ir_1, ia_1 );
node[5] = create_node( node_parts, node_id_base, iz_1, ir_1, ia_1 );
node[6] = create_node( node_parts, node_id_base, iz_1, ir_1, ia );
node[7] = create_node( node_parts, node_id_base, iz , ir_1, ia );
#if 0 /* VERIFY_CENTROID */
// Centroid of the element for verification
const double TWO_PI = 2.0 * acos( -1.0 );
const double angle = m_ang_inc * (0.5 + ia);
const double z = m_center[2] + m_z_min + m_z_inc * (0.5 + iz);
double c[3] = { 0 , 0 , 0 };
for ( size_t j = 0 ; j < 8 ; ++j ) {
double * const coord_data = field_data( m_model_coord , *node[j] );
c[0] += coord_data[0] ;
c[1] += coord_data[1] ;
c[2] += coord_data[2] ;
}
c[0] /= 8 ; c[1] /= 8 ; c[2] /= 8 ;
c[0] -= m_center[0] ;
c[1] -= m_center[1] ;
double val_a = atan2( c[1] , c[0] );
if ( val_a < 0 ) { val_a += TWO_PI ; }
const double err_a = angle - val_a ;
const double err_z = z - c[2] ;
const double eps = 100 * std::numeric_limits<double>::epsilon();
if ( err_z < - eps || eps < err_z ||
err_a < - eps || eps < err_a ) {
std::string msg ;
msg.append("problem setup element centroid error" );
throw std::logic_error( msg );
}
#endif
stk::mesh::Entity elem =
M.declare_entity( element_rank, elem_id, elem_parts );
for ( size_t j = 0 ; j < 8 ; ++j ) {
M.declare_relation( elem , node[j] ,
static_cast<unsigned>(j) );
}
}
}
}
}
// Array of faces on the surface
{
const size_t ir = m_rad_num - 1 ;
for ( size_t ia = 0 ; ia < m_angle_num ; ++ia ) {
for ( size_t iz = 0 ; iz < m_z_num - 1 ; ++iz ) {
stk::mesh::EntityId elem_id_gear =
identifier( m_z_num-1 , m_rad_num-1 , iz , ir-1 , ia );
if ( ( ( elem_id_gear * p_size ) / elem_id_gear_max ) == p_rank ) {
stk::mesh::EntityId elem_id = elem_id_base + elem_id_gear ;
unsigned face_ord = 5 ;
stk::mesh::EntityId face_id = elem_id * 10 + face_ord + 1;
stk::mesh::Entity node[4] ;
const size_t ia_1 = ( ia + 1 ) % m_angle_num ;
const size_t iz_1 = iz + 1 ;
node[0] = create_node( node_parts, node_id_base, iz , ir , ia_1 );
node[1] = create_node( node_parts, node_id_base, iz_1, ir , ia_1 );
node[2] = create_node( node_parts, node_id_base, iz_1, ir , ia );
node[3] = create_node( node_parts, node_id_base, iz , ir , ia );
stk::mesh::Entity face =
M.declare_entity( side_rank, face_id, face_parts );
for ( size_t j = 0 ; j < 4 ; ++j ) {
M.declare_relation( face , node[j] ,
static_cast<unsigned>(j) );
}
stk::mesh::Entity elem = M.get_entity(element_rank, elem_id);
M.declare_relation( elem , face , face_ord );
}
}
}
}
M.modification_begin();
}
void fixup_ghosted_to_shared_nodes(stk::mesh::BulkData & bulk)
{
stk::mesh::EntityVector ghosted_nodes_that_are_now_shared;
find_ghosted_nodes_that_need_to_be_shared(bulk, ghosted_nodes_that_are_now_shared);
stk::CommSparse comm(bulk.parallel());
for (int phase=0;phase<2;++phase)
{
for (size_t i = 0; i < ghosted_nodes_that_are_now_shared.size(); ++i)
{
stk::mesh::Entity node = ghosted_nodes_that_are_now_shared[i];
int proc = bulk.parallel_owner_rank(node);
comm.send_buffer(proc).pack<stk::mesh::EntityKey>(bulk.entity_key(node));
}
if (phase == 0 )
{
comm.allocate_buffers();
}
else
{
comm.communicate();
}
}
stk::mesh::EntityVector sharedNodes;
for (int process=0;process<bulk.parallel_size();++process)
{
while(comm.recv_buffer(process).remaining())
{
stk::mesh::EntityKey key;
comm.recv_buffer(process).unpack<stk::mesh::EntityKey>(key);
stk::mesh::Entity entity = bulk.get_entity(key);
if ( bulk.state(entity) != stk::mesh::Deleted && bulk.is_valid(entity) )
{
bulk.add_node_sharing(entity, process);
sharedNodes.push_back(entity);
}
}
}
/////////////////////////
stk::CommSparse commSecondStage(bulk.parallel());
for (int phase=0;phase<2;++phase)
{
for (size_t i=0;i<sharedNodes.size();++i)
{
std::vector<int> procs;
stk::mesh::EntityKey key = bulk.entity_key(sharedNodes[i]);
bulk.comm_shared_procs(key, procs);
for (size_t j=0;j<procs.size();++j)
{
if ( procs[j] != bulk.parallel_rank() )
{
commSecondStage.send_buffer(procs[j]).pack<int>(bulk.parallel_rank()).pack<stk::mesh::EntityKey>(key);
for (size_t k=0;k<procs.size();++k)
{
commSecondStage.send_buffer(procs[j]).pack<int>(procs[k]).pack<stk::mesh::EntityKey>(key);
}
}
}
}
if (phase == 0 )
{
commSecondStage.allocate_buffers();
}
else
{
commSecondStage.communicate();
}
}
for (int proc_that_sent_message=0;proc_that_sent_message<bulk.parallel_size();++proc_that_sent_message)
{
if ( proc_that_sent_message == bulk.parallel_rank() ) continue;
while(commSecondStage.recv_buffer(proc_that_sent_message).remaining())
{
stk::mesh::EntityKey key;
int sharingProc;
commSecondStage.recv_buffer(proc_that_sent_message).unpack<int>(sharingProc).unpack<stk::mesh::EntityKey>(key);
if ( sharingProc != bulk.parallel_rank() )
{
stk::mesh::Entity entity = bulk.get_entity(key);
if ( bulk.state(entity) != stk::mesh::Deleted && bulk.is_valid(entity) && !bulk.in_shared(key, sharingProc) )
{
bulk.add_node_sharing(entity, sharingProc);
}
}
}
}
}
inline
void setup2Block2HexMesh(stk::mesh::BulkData& bulk)
{
//
// proc 0 proc 1
// |
// block_1 | block_2
// |
// 8----7 | 7----12
// / /| | / / |
// 5----6 3 | 6----11 10
// | 1 |/ | | 2 | /
// 1----2 | 2----9
// |
// |
// |
//
//shared nodes 2, 3, 6, 7
//
if (bulk.parallel_size() > 2) {
return;
}
stk::mesh::MetaData& meta = bulk.mesh_meta_data();
stk::topology hex = stk::topology::HEX_8;
stk::mesh::Part& block_1 = meta.declare_part_with_topology("block_1", hex);
stk::mesh::Part& block_2 = meta.declare_part_with_topology("block_2", hex);
meta.commit();
bulk.modification_begin();
stk::mesh::EntityIdVector elem1_nodes {1, 2, 3, 4, 5, 6, 7, 8};
stk::mesh::EntityIdVector elem2_nodes {2, 9, 10, 3, 6, 11, 12, 7};
stk::mesh::EntityId elemId = 1;
if (bulk.parallel_rank() == 0) {
stk::mesh::declare_element(bulk, block_1, elemId, elem1_nodes);
}
if (bulk.parallel_rank() == 1 || bulk.parallel_size() == 1) {
elemId = 2;
stk::mesh::declare_element(bulk, block_2, elemId, elem2_nodes);
}
if(bulk.parallel_rank() == 0 && bulk.parallel_size() == 2)
{
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 2), 1);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 3), 1);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 6), 1);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 7), 1);
}
if(bulk.parallel_rank() == 1 && bulk.parallel_size() == 2)
{
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 2), 0);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 3), 0);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 6), 0);
bulk.add_node_sharing(bulk.get_entity(stk::topology::NODE_RANK , 7), 0);
}
bulk.modification_end();
}