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STK: Snapshot 05-06-22 13:38
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@tasmith4
tasmith4 committed May 6, 2022
1 parent 00f1cf4 commit c7da259
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Showing 13 changed files with 71 additions and 242 deletions.
11 changes: 6 additions & 5 deletions packages/krino/delete_small_elements/Akri_DeleteSmallElementsMain.cpp
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Expand Up @@ -11,6 +11,7 @@
#include <stk_io/StkMeshIoBroker.hpp>
#include <stk_mesh/base/BulkData.hpp>
#include <stk_mesh/base/MetaData.hpp>
#include <stk_mesh/base/MeshBuilder.hpp>
#include <stk_mesh/base/Selector.hpp>
#include <stk_util/command_line/CommandLineParser.hpp>
#include <stk_util/command_line/CommandLineParserParallel.hpp>
Expand Down Expand Up @@ -105,14 +106,14 @@ bool read_command_line( int argc, char *argv[], DeleteSmallElementsInputData & i
static bool delete_small_elements(const DeleteSmallElementsInputData& inputData,
const stk::ParallelMachine comm)
{
stk::mesh::MetaData meta;
stk::mesh::BulkData bulk(meta, comm);
std::shared_ptr<stk::mesh::BulkData> bulk = stk::mesh::MeshBuilder(comm).create();
stk::mesh::MetaData& meta = bulk->mesh_meta_data();

stk::io::fill_mesh_with_auto_decomp(inputData.meshIn, bulk);
stk::io::fill_mesh_with_auto_decomp(inputData.meshIn, *bulk);

// delete infinitesimal elements
double minEdgeLength, maxEdgeLength, minElementVolume, maxElementVolume;
compute_element_quality(bulk, minEdgeLength, maxEdgeLength, minElementVolume, maxElementVolume);
compute_element_quality(*bulk, minEdgeLength, maxEdgeLength, minElementVolume, maxElementVolume);
sierra::Env::outputP0() << "Overall mesh size results: minEdgeLength=" << minEdgeLength << ", maxEdgeLength=" << maxEdgeLength << ", minElementVolume=" << minElementVolume << ", maxElementVolume=" << maxElementVolume << std::endl;

stk::mesh::Selector blockSelector = meta.universal_part();
Expand All @@ -129,7 +130,7 @@ static bool delete_small_elements(const DeleteSmallElementsInputData& inputData,

const double minRetainedElementVolume = inputData.minNodalVolumeSpecified ? inputData.minNodalVolume : (inputData.minRelativeNodalVolume*maxElementVolume);
if (minElementVolume < minRetainedElementVolume)
delete_all_entities_using_nodes_with_nodal_volume_below_threshold(bulk, blockSelector, minRetainedElementVolume);
delete_all_entities_using_nodes_with_nodal_volume_below_threshold(*bulk, blockSelector, minRetainedElementVolume);
else
sierra::Env::outputP0() << "All nodes already have nodal volume larger than " << minRetainedElementVolume << "." << std::endl;

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184 changes: 0 additions & 184 deletions packages/percept/src/ngp/example.cpp
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This file was deleted.

2 changes: 1 addition & 1 deletion packages/percept/src/percept/FieldTypes.hpp
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Expand Up @@ -16,7 +16,7 @@

namespace percept {

typedef stk::mesh::Field<double, stk::mesh::SimpleArrayTag> GenericFieldType;
typedef stk::mesh::Field<double> GenericFieldType;

typedef stk::mesh::Field<double> ScalarFieldType ;
typedef stk::mesh::Field<int> ScalarIntFieldType ;
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35 changes: 13 additions & 22 deletions packages/percept/src/percept/PerceptMesh.cpp
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Expand Up @@ -80,6 +80,7 @@
#include <stk_mesh/base/BoundaryAnalysis.hpp>
#include <stk_mesh/base/BulkModification.hpp>
#include <stk_mesh/base/MeshUtils.hpp>
#include <stk_mesh/base/MeshBuilder.hpp>


// FIXME
Expand Down Expand Up @@ -115,7 +116,6 @@
m_isOpen(false),
m_isInitialized(false),
m_isAdopted(false),
m_needsDelete(false),
m_dontCheckState(false),
m_outputActiveChildrenOnly(false),
m_filename(),
Expand Down Expand Up @@ -192,9 +192,10 @@
entity_rank_names.push_back("FAMILY_TREE");
#endif

m_metaData = new stk::mesh::MetaData();
stk::mesh::MeshBuilder builder(m_comm);
m_bulkData = builder.create();
m_metaData = std::shared_ptr<stk::mesh::MetaData>(&m_bulkData->mesh_meta_data(),[](auto ptrWeWontDelete){});
m_metaData->initialize(m_spatialDim, entity_rank_names);
m_bulkData = new stk::mesh::BulkData(*m_metaData, m_comm);

const unsigned p_rank = stk::parallel_machine_rank( m_comm );

Expand All @@ -217,7 +218,6 @@
}
m_isOpen = true;
m_filename = "";
m_needsDelete = true;
}

void PerceptMesh::
Expand Down Expand Up @@ -291,8 +291,6 @@
setProperty("in_filename", in_filename);
setProperty("file_type", type);

m_needsDelete = false;

if (m_isOpen)
{
throw std::runtime_error("percept::Mesh::open: mesh is already opened. Please close() before trying open, or use reopen().");
Expand Down Expand Up @@ -1776,8 +1774,8 @@

// ctor constructor
PerceptMesh::PerceptMesh(const stk::mesh::MetaData* metaData, stk::mesh::BulkData* bulkData, bool isCommitted) :
m_metaData(const_cast<stk::mesh::MetaData *>(metaData)),
m_bulkData(bulkData),
m_metaData(std::shared_ptr<stk::mesh::MetaData>(const_cast<stk::mesh::MetaData*>(metaData),[](auto ptrWeWontDelete){})),
m_bulkData(std::shared_ptr<stk::mesh::BulkData>(bulkData,[](auto ptrWeWontDelete){})),
m_output_file_index(0),
m_iossMeshDataDidPopulate(false),
m_sync_io_regions(false),
Expand All @@ -1789,7 +1787,6 @@
m_isOpen(true),
m_isInitialized(true),
m_isAdopted(true),
m_needsDelete(false),
m_dontCheckState(false),
m_outputActiveChildrenOnly(false),
m_filename(),
Expand Down Expand Up @@ -1842,7 +1839,7 @@

void PerceptMesh::set_bulk_data(stk::mesh::BulkData *bulkData)
{
m_bulkData = bulkData;
m_bulkData = std::shared_ptr<stk::mesh::BulkData>(bulkData,[](auto ptrWeWontDelete){});
m_comm = bulkData->parallel();
if (!Teuchos::is_null(m_iossMeshData) && m_iossMeshData->is_bulk_data_null())
m_iossMeshData->set_bulk_data(*bulkData);
Expand Down Expand Up @@ -1896,13 +1893,8 @@
m_geometry_parts = 0;
m_iossMeshData = Teuchos::null;
m_iossMeshDataOut = Teuchos::null;
if (m_needsDelete)
{
if (m_bulkData) delete m_bulkData;
if (m_metaData) delete m_metaData;
m_metaData = 0;
m_bulkData = 0;
}
m_bulkData.reset();
m_metaData.reset();
}

PerceptMesh::~PerceptMesh()
Expand Down Expand Up @@ -2365,13 +2357,13 @@
switch (m_searchType)
{
case FieldFunction::SIMPLE_SEARCH:
m_searcher = new SimpleSearcher(m_bulkData);
m_searcher = new SimpleSearcher(m_bulkData.get());
break;
case FieldFunction::STK_SEARCH:
{
//int spDim = last_dimension(input_phy_points);
if (get_spatial_dim() == 3)
m_searcher = new STKSearcher(m_bulkData);
m_searcher = new STKSearcher(m_bulkData.get());
else
{
//m_searcher = new STKSearcher<2>(this);
Expand Down Expand Up @@ -2460,7 +2452,7 @@
// The coordinates field will be set to the correct dimension.
// this call creates the MetaData
mesh_data->create_input_mesh();
m_metaData = &mesh_data->meta_data();
m_metaData = mesh_data->meta_data_ptr();

// This defines all fields found on the input mesh as stk fields
if (!m_avoid_add_all_mesh_fields_as_input_fields)
Expand Down Expand Up @@ -2594,7 +2586,6 @@

//----------------------------------
// Process Bulkdata for all Entity Types. Subsetting is possible.
//stk::mesh::BulkData bulk_data(meta_data, comm);

// Read the model (topology, coordinates, attributes, etc)
// from the mesh-file into the mesh bulk data.
Expand All @@ -2603,7 +2594,7 @@
{
mesh_data->populate_bulk_data();
m_iossMeshDataDidPopulate = true;
m_bulkData = &mesh_data->bulk_data();
m_bulkData = mesh_data->bulk_data_ptr();
}

int timestep_count = mesh_data->get_input_io_region()->get_property("state_count").get_int();
Expand Down
10 changes: 4 additions & 6 deletions packages/percept/src/percept/PerceptMesh.hpp
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Expand Up @@ -278,10 +278,10 @@
void dump_elements_compact(const std::string& partName = "", bool include_family_tree=false);

/// get the low-level bulk data pointer from stk_mesh
inline stk::mesh::BulkData * get_bulk_data() { return m_bulkData; }
inline stk::mesh::BulkData * get_bulk_data() { return m_bulkData.get(); }

/// get the low-level meta data pointer from stk_mesh
inline stk::mesh::MetaData * get_fem_meta_data() { return m_metaData; }
inline stk::mesh::MetaData * get_fem_meta_data() { return m_metaData.get(); }

/// get a pointer to a stk_mesh Part with the given name - if @param partial_string_match_ok, allow a
/// partial match of the part_name with any part found, in the sense that @param part_name can
Expand Down Expand Up @@ -1093,9 +1093,8 @@
Teuchos::RCP<stk::io::StkMeshIoBroker> get_ioss_mesh_data_output() { return m_iossMeshDataOut; }
size_t get_output_file_index() { return m_output_file_index;}
private:
//stk::mesh::MetaData * m_fem_meta_data;
stk::mesh::MetaData * m_metaData;
stk::mesh::BulkData * m_bulkData;
std::shared_ptr<stk::mesh::MetaData> m_metaData;
std::shared_ptr<stk::mesh::BulkData> m_bulkData;
Teuchos::RCP<stk::io::StkMeshIoBroker> m_iossMeshData;
Teuchos::RCP<stk::io::StkMeshIoBroker> m_iossMeshDataOut;

Expand All @@ -1114,7 +1113,6 @@
bool m_isOpen;
bool m_isInitialized;
bool m_isAdopted;
bool m_needsDelete;
bool m_dontCheckState;
bool m_outputActiveChildrenOnly;
std::string m_filename;
Expand Down
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