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Merge Pull Request #6518 from alanw0/Trilinos/stk_20191220
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Automatically Merged using Trilinos Pull Request AutoTester
PR Title: Stk 20191220
PR Author: alanw0
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@trilinos-autotester
trilinos-autotester authored Jan 3, 2020
2 parents 4b0fef0 + 725d6d8 commit c858b70
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Showing 126 changed files with 6,107 additions and 4,377 deletions.
14 changes: 8 additions & 6 deletions packages/panzer/adapters-stk/src/stk_interface/Panzer_STK_ExodusReaderFactory.cpp
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Expand Up @@ -355,7 +355,8 @@ void STK_ExodusReaderFactory::registerElementBlocks(STK_Interface & mesh,stk::io
const std::string & name = entity->name();

const stk::mesh::Part * part = femMetaData->get_part(name);
const CellTopologyData * ct = femMetaData->get_cell_topology(*part).getCellTopologyData();
shards::CellTopology cellTopo = stk::mesh::get_cell_topology(femMetaData->get_topology(*part));
const CellTopologyData * ct = cellTopo.getCellTopologyData();

TEUCHOS_ASSERT(ct!=0);
mesh.addElementBlock(part->name(),ct);
Expand Down Expand Up @@ -383,8 +384,8 @@ void STK_ExodusReaderFactory::registerSidesets(STK_Interface & mesh) const
for(partItr=parts.begin();partItr!=parts.end();++partItr) {
const stk::mesh::Part * part = *partItr;
const stk::mesh::PartVector & subsets = part->subsets();
// const CellTopologyData * ct = stk::mesh::get_cell_topology(*part).getCellTopologyData();
const CellTopologyData * ct = metaData->get_cell_topology(*part).getCellTopologyData();
shards::CellTopology cellTopo = stk::mesh::get_cell_topology(metaData->get_topology(*part));
const CellTopologyData * ct = cellTopo.getCellTopologyData();

// if a side part ==> this is a sideset: now storage is recursive
// on part contains all sub parts with consistent topology
Expand All @@ -395,8 +396,8 @@ void STK_ExodusReaderFactory::registerSidesets(STK_Interface & mesh) const

// grab cell topology and name of subset part
const stk::mesh::Part * ss_part = subsets[0];
// const CellTopologyData * ss_ct = stk::mesh::get_cell_topology(*ss_part).getCellTopologyData();
const CellTopologyData * ss_ct = metaData->get_cell_topology(*ss_part).getCellTopologyData();
shards::CellTopology ss_cellTopo = stk::mesh::get_cell_topology(metaData->get_topology(*ss_part));
const CellTopologyData * ss_ct = ss_cellTopo.getCellTopologyData();

// only add subset parts that have no topology
if(ss_ct!=0)
Expand All @@ -415,7 +416,8 @@ void STK_ExodusReaderFactory::registerNodesets(STK_Interface & mesh) const
stk::mesh::PartVector::const_iterator partItr;
for(partItr=parts.begin();partItr!=parts.end();++partItr) {
const stk::mesh::Part * part = *partItr;
const CellTopologyData * ct = metaData->get_cell_topology(*part).getCellTopologyData();
shards::CellTopology cellTopo = stk::mesh::get_cell_topology(metaData->get_topology(*part));
const CellTopologyData * ct = cellTopo.getCellTopologyData();

// if a side part ==> this is a sideset: now storage is recursive
// on part contains all sub parts with consistent topology
Expand Down
99 changes: 0 additions & 99 deletions packages/percept/src/adapt/Allocate.cpp
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This file was deleted.

4 changes: 2 additions & 2 deletions packages/percept/src/adapt/main/RunAdaptRun.hpp
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Expand Up @@ -614,8 +614,8 @@ static void copy_error_indicator(PerceptMesh& eMesh_no_ft,PerceptMesh& eMesh,

ErrorFieldType * from_error_field =
&eMesh_error.get_fem_meta_data()->declare_field<ErrorFieldType>(stk::topology::ELEMENT_RANK, rar.m_error_indicator_field);
stk::mesh::FieldTraits<ErrorFieldType>::data_type* init_np = nullptr; // gcc 4.8 hack
stk::mesh::put_field_on_mesh( *from_error_field , eMesh_error.get_fem_meta_data()->universal_part(), 1, init_np);
stk::mesh::FieldTraits<ErrorFieldType>::data_type* init_np2 = nullptr; // gcc 4.8 hack
stk::mesh::put_field_on_mesh( *from_error_field , eMesh_error.get_fem_meta_data()->universal_part(), 1, init_np2);

eMesh_error.add_input_field(from_error_field);

Expand Down
46 changes: 0 additions & 46 deletions packages/percept/src/percept/SameRankRelation.hpp
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This file was deleted.

9 changes: 6 additions & 3 deletions packages/percept/src/percept/eigen_verify/EigenVerify.cpp
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Expand Up @@ -18,6 +18,7 @@
#include <percept/function/FieldFunction.hpp>
#include <percept/norm/Norm.hpp>
#include <percept/FieldBLAS.hpp>
#include <percept/PerceptMesh.hpp>

namespace percept
{
Expand Down Expand Up @@ -82,12 +83,12 @@ void EigenVerify::create_fields(const int num_time_steps)
// allocate data for the eigenvectors (receiving)
xferFieldAll[m] = & (mesh_data[m]->meta_data().declare_field<stk::mesh::Field<double, stk::mesh::SimpleArrayTag, stk::mesh::Cartesian> >(stk::topology::NODE_RANK, xfer_field_name_all));

stk::mesh::FieldTraits<stk::mesh::Field<double>>::data_type* init_np = nullptr; // gcc 4.8 hack
stk::mesh::FieldTraits<stk::mesh::Field<double>>::data_type* init_np2 = nullptr; // gcc 4.8 hack
stk::mesh::put_field_on_mesh( *xferFieldAll[m],
mesh_data[m]->meta_data().universal_part(),
mesh_data[m]->meta_data().spatial_dimension(),
num_time_steps,
init_np);
init_np2);

// get eigenvector field
inputField[m] = mesh_data[m]->meta_data().get_field<stk::mesh::Field<double, stk::mesh::Cartesian> >(stk::topology::NODE_RANK, field_name);
Expand Down Expand Up @@ -309,7 +310,9 @@ void EigenVerify::run(int argc, char** argv)
FieldFunction errorFunc("error", errorField, &(mesh_data[1]->bulk_data()),
Dimensions(3), Dimensions(3));

Norm<2> norm(mesh_data[1]->bulk_data(), &mesh_data[1]->meta_data().universal_part());
stk::mesh::Selector element_selector = PerceptMesh::get_selector_of_rank(mesh_data[1]->meta_data(), stk::topology::ELEMENT_RANK);

Norm<2> norm(mesh_data[1]->bulk_data(), &element_selector);
ConstantFunction result(0.0, "result");

// TODO add as global var to Exo output
Expand Down
9 changes: 3 additions & 6 deletions packages/percept/src/percept/fixtures/QuadFixture.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,6 @@
// typedef Topology QuadOrTriTopo ;
enum { NodesPerElem = stk::topology_detail::topology_data<Topology>::num_nodes };

typedef stk::mesh::Field<Scalar, stk::mesh::Cartesian> CoordFieldType;
typedef stk::mesh::Field<Scalar*,stk::mesh::ElementNode> CoordGatherFieldType;

static std::vector<std::string> get_entity_rank_names(unsigned dim)
{
std::vector<std::string> names = stk::mesh::entity_rank_names();
Expand All @@ -89,7 +86,7 @@
: meta_data(2, get_entity_rank_names(2) ),
bulk_data( meta_data, pm ),
quad_part( meta_data.declare_part("block_1", stk::topology::ELEMENT_RANK ) ),
coord_field( meta_data.declare_field<CoordFieldType>(stk::topology::NODE_RANK, "coordinates") ),
coord_field( meta_data.declare_field<CoordinatesFieldType>(stk::topology::NODE_RANK, "coordinates") ),
NX( nx ),
NY( ny ),
generate_sidesets(generate_sidesets_in),
Expand All @@ -104,7 +101,7 @@
stk::io::put_io_part_attribute(quad_part);

//put coord-field on all nodes:
stk::mesh::FieldTraits<CoordFieldType>::data_type* init_np = nullptr; // gcc 4.8 hack
stk::mesh::FieldTraits<CoordinatesFieldType>::data_type* init_np = nullptr; // gcc 4.8 hack
put_field_on_mesh(
coord_field,
meta_data.universal_part(),
Expand Down Expand Up @@ -307,7 +304,7 @@
stk::mesh::MetaData meta_data ;
stk::mesh::BulkData bulk_data ;
stk::mesh::Part & quad_part ;
CoordFieldType & coord_field ;
CoordinatesFieldType & coord_field ;
const unsigned NX ;
const unsigned NY ;
stk::mesh::Part *side_parts[4];
Expand Down
17 changes: 0 additions & 17 deletions packages/percept/src/percept/fixtures/WedgeFixture.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,7 @@

// line2 mesh
SweepMesher& tp2 = m_sweepMesher;
//tp2 = SweepMesher();

//tp2.initNodes(coordsLine.begin(), n_nodes_x);
tp2.initNodes(&coordsLine[0], n_nodes_x);
tp2.initElems(shards_Line_2, &line2Elems[0], n_nodes_x - 1);
if(verbose) std::cout << "line2 mesh\n";
Expand All @@ -91,15 +89,11 @@

SweepMesher quadMeshCopy;
quadMeshCopy.CopyFromBasicMesh(tp2);
//tp2.stkMeshCreate(parallel_machine);
//tp2.writeSTKMesh("wedge-quad-0.e");

// break all of the quads into tris
tp2.breakAllElements<shards_Quadrilateral_4, shards_Triangle_3>();
if(verbose) std::cout << "after break quad to tri\n";
tp2.dump(verbose);
//tp2.stkMeshCreate(parallel_machine);
//tp2.writeSTKMesh("tp2-quad-tri.e");

// sweep again to make a wedge mesh
std::array<double, 3> dir1 = {{0,0,(zmax-zmin)/double(n_nodes_z - 1)}};
Expand All @@ -126,12 +120,10 @@

stk::mesh::MetaData *getMetaData() { return m_sweepMesher.getMetaData() ; }

//stk::mesh::BulkData*
void
createBulkAfterMetaCommit(stk::ParallelMachine parallel_machine)
{
m_sweepMesher.stkMeshCreateBulkAfterMetaCommit(parallel_machine);
//return m_sweepMesher.get_bulk_data();
}

void createFixedSizeMesh(stk::ParallelMachine parallel_machine, std::string output_filename)
Expand All @@ -142,10 +134,6 @@
{{0,0,0}}, {{1,0,0}}, {{2,0,0}}, {{3,0,0}}, {{4,0,0}}
};

// double coordsCPP[][3] = {
// {0,0,0}, {1,0,0}, {2,2,0}, {0,3,0},
// {0,0,1}, {1,0,1}, {2,2,1}, {0,3,1}
// };
unsigned numNodesLine = sizeof(coordsLine)/sizeof(coordsLine[0]);

unsigned line2Elems[] = {
Expand Down Expand Up @@ -183,17 +171,12 @@

SweepMesher quadMeshCopy;
quadMeshCopy.CopyFromBasicMesh(tp2);
//tp2.stkMeshCreate(parallel_machine);
//tp2.writeSTKMesh("wedge-quad-0.e");

// break all of the quads into tris
tp2.breakAllElements<shards_Quadrilateral_4, shards_Triangle_3>();
//verbose=true;
if(verbose) std::cout << "after break quad to tri\n";
tp2.dump(verbose);
tp2.dump();
//tp2.stkMeshCreate(parallel_machine);
//tp2.writeSTKMesh("tp2-quad-tri.e");

// sweep again to make a wedge mesh
std::array<double, 3> dir1 = {{0,0,2.345}};
Expand Down
4 changes: 4 additions & 0 deletions packages/percept/src/percept/function/internal/IntegratedOp.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,10 @@
const CellTopologyData * const cell_topo_data = stk::mesh::get_cell_topology(mybucket(bulkData, bucket_or_element).topology()).getCellTopologyData();
CellTopology cell_topo(cell_topo_data);

if (cell_topo_data->key == shards::Particle::key ||
cell_topo_data->key == shards::Beam<2>::key)
return false;

int cell_dimension = cell_topo.getDimension();
int meta_dimension = stk::mesh::MetaData::get(bulkData).spatial_dimension();

Expand Down
2 changes: 1 addition & 1 deletion packages/percept/src/percept/function/internal/STKSearcherDef.hpp
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Expand Up @@ -86,7 +86,7 @@
if (EXTRA_PRINT) std::cout << "STKSearcher::findElement: nboxes= " << m_boxes.size() << std::endl;

IdentProcRelation relation;
stk::search::coarse_search(points, m_boxes, stk::search::BOOST_RTREE, bulkData.parallel(), relation);
stk::search::coarse_search(points, m_boxes, stk::search::KDTREE, bulkData.parallel(), relation);

if (EXTRA_PRINT) std::cout << "STKSearcher::findElement: found " << relation.size() << " containing bboxes" << std::endl;

Expand Down
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