void build_local_element_map(RegionVector &part_mesh,
std::vector<INT> &local_element_map)
{
size_t global = 0;
size_t offset = 0;
for (size_t p = 0; p < part_mesh.size(); p++) {
Ioss::ElementBlockContainer ebs = part_mesh[p]->get_element_blocks();
Ioss::ElementBlockContainer::const_iterator i = ebs.begin();
while (i != ebs.end()) {
Ioss::ElementBlock *eb = *i++;
size_t num_elem = eb->get_property("entity_count").get_int();
if (entity_is_omitted(eb)) {
// Fill local_element_map with -1 for the omitted elements.
for (size_t j = 0; j < num_elem; j++) {
local_element_map[offset+j] = -1;
}
} else {
for (size_t j = 0; j < num_elem; j++) {
local_element_map[offset+j] = global++;
}
}
offset += num_elem;
}
}
}
Block::Block(const Ioss::ElementBlock &other)
{
id = other.get_property("id").get_int();
elementCount = other.get_property("entity_count").get_int();
nodesPerElement = other.get_property("topology_node_count").get_int();
attributeCount = other.get_property("attribute_count").get_int();
offset_ = other.get_offset();
std::string el_type = other.get_property("topology_type").get_string();
if (other.property_exists("original_topology_type")) {
el_type = other.get_property("original_topology_type").get_string();
}
std::strncpy(elType, el_type.c_str(), MAX_STR_LENGTH);
elType[MAX_STR_LENGTH] = 0;
// Fixup an exodusII kludge. For triangular elements, the same
// name is used for 2D elements and 3D shell elements. Convert
// to unambiguous names for the IO Subsystem. The 2D name
// stays the same, the 3D name becomes 'trishell#'
// Here, we need to map back to the 'triangle' name...
if (std::strncmp(elType, "trishell", 8) == 0)
std::strncpy(elType, "triangle", 8);
std::string io_name = other.name();
std::strncpy(name, io_name.c_str(), MAX_STR_LENGTH);
name[MAX_STR_LENGTH] = 0;
}
// ========================================================================
void process_elementblocks(Ioss::Region ®ion, stk::mesh::BulkData &bulk)
{
const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();
for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
it != elem_blocks.end(); ++it) {
Ioss::ElementBlock *entity = *it;
if (stk::io::include_entity(entity)) {
const std::string &name = entity->name();
const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
stk::mesh::Part* const part = meta.get_part(name);
STKIORequire(part != NULL);
const stk::topology topo = part->topology();
if (topo == stk::topology::INVALID_TOPOLOGY) {
std::ostringstream msg ;
msg << " INTERNAL_ERROR: Part " << part->name() << " returned INVALID from get_topology()";
throw std::runtime_error( msg.str() );
}
std::vector<int> elem_ids ;
std::vector<int> connectivity ;
entity->get_field_data("ids", elem_ids);
entity->get_field_data("connectivity", connectivity);
size_t element_count = elem_ids.size();
int nodes_per_elem = topo.num_nodes();
stk::mesh::EntityIdVector connectivity2(nodes_per_elem);
std::vector<int>::const_iterator connBegin = connectivity.begin();
std::vector<stk::mesh::Entity> elements(element_count);
for(size_t i=0; i<element_count; ++i, connBegin += nodes_per_elem) {
std::copy(connBegin, connBegin + nodes_per_elem, connectivity2.begin());
elements[i] = stk::mesh::declare_element(bulk, *part, elem_ids[i], connectivity2);
}
// For this example, we are just taking all attribute fields
// found on the io database and populating fields on the
// corresponding mesh part. In practice, would probably be
// selective about which attributes to use...
Ioss::NameList names;
entity->field_describe(Ioss::Field::ATTRIBUTE, &names);
for (Ioss::NameList::const_iterator I = names.begin(); I != names.end(); ++I) {
if (*I == "attribute" && names.size() > 1)
continue;
stk::mesh::FieldBase *field = meta.get_field<stk::mesh::FieldBase>(stk::topology::ELEMENT_RANK, *I);
stk::io::field_data_from_ioss(bulk, field, elements, entity, *I);
}
}
}
}
AxisAlignedBoundingBox DatabaseIO::get_bounding_box(const Ioss::ElementBlock *eb) const
{
if (elementBlockBoundingBoxes.empty()) {
// Calculate the bounding boxes for all element blocks...
std::vector<double> coordinates;
Ioss::NodeBlock * nb = get_region()->get_node_blocks()[0];
nb->get_field_data("mesh_model_coordinates", coordinates);
ssize_t nnode = nb->get_property("entity_count").get_int();
ssize_t ndim = nb->get_property("component_degree").get_int();
Ioss::ElementBlockContainer element_blocks = get_region()->get_element_blocks();
size_t nblock = element_blocks.size();
std::vector<double> minmax;
minmax.reserve(6 * nblock);
for (auto &block : element_blocks) {
double xmin, ymin, zmin, xmax, ymax, zmax;
if (block->get_database()->int_byte_size_api() == 8) {
std::vector<int64_t> connectivity;
block->get_field_data("connectivity_raw", connectivity);
calc_bounding_box(ndim, nnode, coordinates, connectivity, xmin, ymin, zmin, xmax, ymax,
zmax);
}
else {
std::vector<int> connectivity;
block->get_field_data("connectivity_raw", connectivity);
calc_bounding_box(ndim, nnode, coordinates, connectivity, xmin, ymin, zmin, xmax, ymax,
zmax);
}
minmax.push_back(xmin);
minmax.push_back(ymin);
minmax.push_back(zmin);
minmax.push_back(-xmax);
minmax.push_back(-ymax);
minmax.push_back(-zmax);
}
util().global_array_minmax(minmax, Ioss::ParallelUtils::DO_MIN);
for (size_t i = 0; i < element_blocks.size(); i++) {
Ioss::ElementBlock * block = element_blocks[i];
const std::string & name = block->name();
AxisAlignedBoundingBox bbox(minmax[6 * i + 0], minmax[6 * i + 1], minmax[6 * i + 2],
-minmax[6 * i + 3], -minmax[6 * i + 4], -minmax[6 * i + 5]);
elementBlockBoundingBoxes[name] = bbox;
}
}
return elementBlockBoundingBoxes[eb->name()];
}
// ========================================================================
void process_elementblocks(Ioss::Region ®ion, stk::mesh::MetaData &meta)
{
const stk::mesh::EntityRank element_rank = stk::topology::ELEMENT_RANK;
const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();
stk::io::default_part_processing(elem_blocks, meta, element_rank);
// Parts were created above, now handle element block specific
// information (topology, attributes, ...);
for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
it != elem_blocks.end(); ++it) {
Ioss::ElementBlock *entity = *it;
if (stk::io::include_entity(entity)) {
stk::mesh::Part* const part = meta.get_part(entity->name());
STKIORequire(part != NULL);
const stk::mesh::EntityRank part_rank = part->primary_entity_rank();
// Element Block attributes (if any)...
/** \todo IMPLEMENT truly handle attribute fields... For this
* case we are just defining a field for each attribute field
* that is present in the mesh...
*/
stk::io::define_io_fields(entity, Ioss::Field::ATTRIBUTE,
*part,
part_rank);
/** \todo IMPLEMENT truly handle fields... For this case we
* are just defining a field for each transient field that is
* present in the mesh...
*/
stk::io::define_io_fields(entity, Ioss::Field::TRANSIENT,
*part,
part_rank);
}
}
}
void generate_element_ids(RegionVector &part_mesh,
const std::vector<INT> &local_element_map,
std::vector<INT> &global_element_map)
{
// Follow same logic as 'build_local_element_map' to ensure elements
// are processed in same order.
// Many models do not use the element number map at all, so they
// will have a 1..numel map. If all parts have that, then we don't
// want to do any fancy duplicate removal and other processing, just
// output a 1..numel map for the output mesh... We still generate
// the global_element_map, but check whether any of the part blocks
// have a non-1..numel map...
bool has_map = false;
size_t offset = 0;
for (size_t p = 0; p < part_mesh.size(); p++) {
Ioss::ElementBlockContainer ebs = part_mesh[p]->get_element_blocks();
Ioss::ElementBlockContainer::const_iterator i = ebs.begin();
while (i != ebs.end()) {
Ioss::ElementBlock *eb = *i++;
INT num_elem = eb->get_property("entity_count").get_int();
if (!entity_is_omitted(eb)) {
std::vector<INT> part_ids;
eb->get_field_data("ids", part_ids);
if (!has_map) {
INT eb_offset = eb->get_offset();
for (INT j = 0; j < num_elem; j++) {
if (part_ids[j] != eb_offset+j+1) {
has_map = true;
break;
}
}
}
for (INT j = 0; j < num_elem; j++) {
INT gpos = local_element_map[offset+j];
if (gpos >= 0)
global_element_map[gpos] = part_ids[j];
}
}
offset += num_elem;
}
}
// Check for duplicates...
// NOTE: Used to use an indexed sort here, but if there was a
// duplicate id, it didnt really care whether part 1 or part N's
// index came first which causes really screwy element maps.
// Instead, lets sort a vector containing pairs of <id, index> where
// the index will always? increase for increasing part numbers...
std::vector<std::pair<INT,INT> > index(global_element_map.size());
for (size_t i=0; i < index.size(); i++) {
index[i] = std::make_pair(global_element_map[i],(INT)i);
}
std::sort(index.begin(), index.end());
INT max_id = index[index.size()-1].first + 1;
size_t beg = 0;
for (size_t i=1; i < index.size(); i++) {
if (index[beg].first == index[i].first) {
// Duplicate found... Assign it a new id greater than any
// existing id... (What happens if we exceed INT_MAX?)
global_element_map[index[i].second] = max_id++;
// Keep 'beg' the same in case multiple duplicate of this value.
} else {
beg = i;
}
}
}
/// This function shows the basic calls needed to perform definition
/// and input of the mesh model and definition and periodic output
/// of a results database. The function is given the mesh filename
/// and the output filename and goes through all steps of
/// associating the filename with an Ioss::DatabaseIO object of the
/// correct type ("exodusII" in this example); creating an
/// Ioss::Region and then defining an stk::mesh corresponding to
/// this mesh. The function also provides an example of how
/// specific element blocks existing in the mesh database could be
/// omitted from the analysis model.
///
/// The example then shows how to define a results database
/// corresponding to the analysis model and periodically output the
/// results in an execute loop.
///
/// A true application would have to provide additional
/// functionality and robustness, but the example shows how the
/// basic functionality can be provided by an application.
///
/// Note that the paradigm illustrated here is different than the
/// mesh input and output paradigm provided in the current
/// framework. In this case, the application is responsible for the
/// majority of the IO behavior and the toolkit only provides some
/// helper functions to bridge between the Ioss and the stk::mesh.
/// It is hoped that this paradigm will result in more functionality
/// for the application with less complication and overhead.
void io_example( const std::string& in_filename,
const std::string& out_filename,
const std::string& decomp_method)
{
// Initialize IO system. Registers all element types and storage
// types and the exodusII default database type.
Ioss::Init::Initializer init_db;
std::cout << "========================================================================\n"
<< " Copy input mesh to output mesh. \n"
<< "========================================================================\n";
std::string dbtype("exodusII");
Ioss::PropertyManager properties;
if (!decomp_method.empty()) {
properties.add(Ioss::Property("DECOMPOSITION_METHOD", Ioss::Utils::uppercase(decomp_method)));
}
Ioss::DatabaseIO *dbi = Ioss::IOFactory::create(dbtype, in_filename, Ioss::READ_MODEL,
MPI_COMM_WORLD, properties);
if (dbi == NULL || !dbi->ok()) {
std::cerr << "ERROR: Could not open database '" << in_filename
<< "' of type '" << dbtype << "'\n";
std::exit(EXIT_FAILURE);
}
std::cout << "Reading input file: " << in_filename << "\n";
// NOTE: 'in_region' owns 'dbi' pointer at this time...
Ioss::Region in_region(dbi, "input_model");
// SUBSETTING PARSING/PREPROCESSING...
// Just an example of how application could control whether an
// entity is subsetted or not...
#if 0
// Example command line in current code corresponding to behavior below:
std::cout << "\nWhen processing file multi-block.g for use case 2, the blocks below will be omitted:\n";
std::cout << "\tOMIT BLOCK Cblock Eblock I1 I2\n\n";
Ioss::ElementBlock *eb = in_region.get_element_block("cblock");
if (eb != NULL)
eb->property_add(Ioss::Property(std::string("omitted"), 1));
eb = in_region.get_element_block("eblock");
if (eb != NULL)
eb->property_add(Ioss::Property(std::string("omitted"), 1));
eb = in_region.get_element_block("i1");
if (eb != NULL)
eb->property_add(Ioss::Property(std::string("omitted"), 1));
eb = in_region.get_element_block("i2");
if (eb != NULL)
eb->property_add(Ioss::Property(std::string("omitted"), 1));
#endif
#if 0
// Example for subsetting -- omit "odd" blocks
if (entity->type() == Ioss::ELEMENTBLOCK) {
int id = entity->get_property("id").get_int();
if (id % 2) {
entity->property_add(Ioss::Property(std::string("omitted"), 1));
std::cout << "Skipping " << entity->type_string() << ": " << entity->name() << "\n";
}
}
#endif
//----------------------------------
// Process Entity Types. Subsetting is possible.
static size_t spatial_dimension = in_region.get_property("spatial_dimension").get_int();
stk::mesh::MetaData fem_meta_data( spatial_dimension );
process_elementblocks(in_region, fem_meta_data);
process_nodeblocks(in_region, fem_meta_data);
process_sidesets(in_region, fem_meta_data);
process_nodesets(in_region, fem_meta_data);
//----------------------------------
// Done populating meta data, commit and create bulk data
fem_meta_data.commit();
//----------------------------------
// Process Bulkdata for all Entity Types. Subsetting is possible.
stk::mesh::BulkData bulk_data(fem_meta_data, MPI_COMM_WORLD);
bulk_data.modification_begin();
process_elementblocks(in_region, bulk_data);
process_nodeblocks(in_region, bulk_data);
process_sidesets(in_region, bulk_data);
process_nodesets(in_region, bulk_data);
bulk_data.modification_end();
//----------------------------------
// OUTPUT...Create the output "mesh" portion
std::cout << "Creating output file: " << out_filename << "\n";
Ioss::DatabaseIO *dbo = Ioss::IOFactory::create(dbtype, out_filename,
Ioss::WRITE_RESULTS,
MPI_COMM_WORLD);
if (dbo == NULL || !dbo->ok()) {
std::cerr << "ERROR: Could not open results database '" << out_filename
<< "' of type '" << dbtype << "'\n";
std::exit(EXIT_FAILURE);
}
#if 0
{
// Code to test the remove_io_part_attribute functionality.
// Hook this up to a command line option at some point to test nightly...
const stk::mesh::PartVector & all_parts = fem_meta_data.get_parts();
for ( stk::mesh::PartVector::const_iterator ip = all_parts.begin(); ip != all_parts.end(); ++ip ) {
stk::mesh::Part * const part = *ip;
const stk::mesh::EntityRank part_rank = part->primary_entity_rank();
if (stk::io::is_part_io_part(*part) && part_rank == 2) {
std::cout << "Removing part attribute from " << part->name() << "\n";
stk::io::remove_io_part_attribute(*part);
}
}
}
#endif
// NOTE: 'out_region' owns 'dbo' pointer at this time...
Ioss::Region out_region(dbo, "results_output");
stk::io::define_output_db(out_region, bulk_data, &in_region);
stk::io::write_output_db(out_region, bulk_data);
// ------------------------------------------------------------------------
/** \todo REFACTOR A real app would register a subset of the
* fields on the mesh database as fields that the app would want
* read at one or all or specified steps. In this example, all
* fields existing on the input mesh database are defined on the
* parts in the stk::mesh.
*
* The real app would also only register a subset of the stk::mesh
* fields as output fields and would probably have a mapping from
* the internally used name to some name picked by the user. In
* this example, all Ioss::Field::TRANSIENT fields defined on the stk::mesh are
* output to the results database and the internal stk::mesh field
* name is used as the name on the database....
*/
out_region.begin_mode(Ioss::STATE_DEFINE_TRANSIENT);
// Special processing for nodeblock (all nodes in model)...
stk::io::ioss_add_fields(fem_meta_data.universal_part(), stk::topology::NODE_RANK,
out_region.get_node_blocks()[0],
Ioss::Field::TRANSIENT);
const stk::mesh::PartVector & all_parts = fem_meta_data.get_parts();
for ( stk::mesh::PartVector::const_iterator
ip = all_parts.begin(); ip != all_parts.end(); ++ip ) {
stk::mesh::Part * const part = *ip;
const stk::mesh::EntityRank part_rank = part->primary_entity_rank();
// Check whether this part should be output to results database.
if (stk::io::is_part_io_part(*part)) {
// Get Ioss::GroupingEntity corresponding to this part...
Ioss::GroupingEntity *entity = out_region.get_entity(part->name());
if (entity != NULL) {
if (entity->type() == Ioss::SIDESET) {
Ioss::SideSet *sset = dynamic_cast<Ioss::SideSet*>(entity);
assert(sset != NULL);
int block_count = sset->block_count();
for (int i=0; i < block_count; i++) {
Ioss::SideBlock *fb = sset->get_block(i);
stk::io::ioss_add_fields(*part, part_rank,
fb, Ioss::Field::TRANSIENT);
}
} else {
stk::io::ioss_add_fields(*part, part_rank,
entity, Ioss::Field::TRANSIENT);
}
} else {
/// \todo IMPLEMENT handle error... Possibly an assert since
/// I think the corresponding entity should always exist...
}
}
}
out_region.end_mode(Ioss::STATE_DEFINE_TRANSIENT);
// ------------------------------------------------------------------------
// Read and Write transient fields...
out_region.begin_mode(Ioss::STATE_TRANSIENT);
int timestep_count = in_region.get_property("state_count").get_int();
for (int step = 1; step <= timestep_count; step++) {
double time = in_region.get_state_time(step);
// Read data from the io input mesh database into stk::mesh fields...
process_input_request(in_region, bulk_data, step);
// execute()
// Write data from the stk::mesh fields out to the output database.a
int out_step = out_region.add_state(time);
process_output_request(out_region, bulk_data, out_step);
}
out_region.end_mode(Ioss::STATE_TRANSIENT);
}
