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Nektar::Utilities::ProcessTetSplit Class Reference

This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian. More...

#include <ProcessTetSplit.h>

Inheritance diagram for Nektar::Utilities::ProcessTetSplit:
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Public Member Functions

 ProcessTetSplit (MeshSharedPtr m)
virtual ~ProcessTetSplit ()
virtual void Process ()
 Write mesh to output file.
- Public Member Functions inherited from Nektar::Utilities::ProcessModule
 ProcessModule ()
 ProcessModule (FieldSharedPtr p_f)
 ProcessModule (MeshSharedPtr p_m)
- Public Member Functions inherited from Nektar::Utilities::Module
 Module (FieldSharedPtr p_f)
virtual void Process (po::variables_map &vm)=0
void RegisterConfig (string key, string value)
 Register a configuration option with a module.
void PrintConfig ()
 Print out all configuration options for a module.
void SetDefaults ()
 Sets default configuration options for those which have not been set.
bool GetRequireEquiSpaced (void)
void SetRequireEquiSpaced (bool pVal)
void EvaluateTriFieldAtEquiSpacedPts (LocalRegions::ExpansionSharedPtr &exp, const Array< OneD, const NekDouble > &infield, Array< OneD, NekDouble > &outfield)
 Module (MeshSharedPtr p_m)
void RegisterConfig (string key, string value)
void PrintConfig ()
void SetDefaults ()
MeshSharedPtr GetMesh ()
virtual void ProcessVertices ()
 Extract element vertices.

Static Public Member Functions

static boost::shared_ptr< Module > create (MeshSharedPtr m)
 Creates an instance of this class.

Static Public Attributes

static ModuleKey className

Additional Inherited Members

- Protected Member Functions inherited from Nektar::Utilities::Module
 Module ()
virtual void ProcessEdges (bool ReprocessEdges=true)
 Extract element edges.
virtual void ProcessFaces (bool ReprocessFaces=true)
 Extract element faces.
virtual void ProcessElements ()
 Generate element IDs.
virtual void ProcessComposites ()
 Generate composites.
void ReorderPrisms (PerMap &perFaces)
 Reorder node IDs so that prisms and tetrahedra are aligned correctly.
void PrismLines (int prism, PerMap &perFaces, set< int > &prismsDone, vector< ElementSharedPtr > &line)
- Protected Attributes inherited from Nektar::Utilities::Module
FieldSharedPtr m_f
 Field object.
map< string, ConfigOption > m_config
 List of configuration values.
bool m_requireEquiSpaced
MeshSharedPtr m_mesh
 Mesh object.

Detailed Description

This processing module calculates the Jacobian of elements using SpatialDomains::GeomFactors and the Element::GetGeom method. For now it simply prints a list of elements which have negative Jacobian.

Definition at line 51 of file ProcessTetSplit.h.

Constructor & Destructor Documentation

Nektar::Utilities::ProcessTetSplit::ProcessTetSplit ( MeshSharedPtr  m)

Definition at line 61 of file ProcessTetSplit.cpp.

References Nektar::Utilities::Module::m_config.

: ProcessModule(m)
{
m_config["nq"] = ConfigOption(false, "3",
"Number of points in high order elements.");
}
Nektar::Utilities::ProcessTetSplit::~ProcessTetSplit ( )
virtual

Definition at line 67 of file ProcessTetSplit.cpp.

{
}

Member Function Documentation

static boost::shared_ptr<Module> Nektar::Utilities::ProcessTetSplit::create ( MeshSharedPtr  m)
inlinestatic

Creates an instance of this class.

Definition at line 55 of file ProcessTetSplit.h.

{
return MemoryManager<ProcessTetSplit>::AllocateSharedPtr(m);
}
void Nektar::Utilities::ProcessTetSplit::Process ( )
virtual

Write mesh to output file.

Implements Nektar::Utilities::Module.

Definition at line 72 of file ProcessTetSplit.cpp.

References Nektar::LibUtilities::eGaussLobattoLegendre, Nektar::LibUtilities::eGaussRadauMAlpha1Beta0, Nektar::LibUtilities::eModified_A, Nektar::LibUtilities::eModified_B, Nektar::LibUtilities::eNodalPrismEvenlySpaced, Nektar::LibUtilities::eNodalTriEvenlySpaced, Nektar::LibUtilities::eOrtho_A, Nektar::LibUtilities::eOrtho_B, Nektar::LibUtilities::ePolyEvenlySpaced, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::eTetrahedron, Nektar::LibUtilities::eTriangle, Nektar::Utilities::GetElementFactory(), Nektar::iterator, Nektar::Utilities::Module::m_config, Nektar::Utilities::Module::m_mesh, Nektar::LibUtilities::PointsManager(), Nektar::Utilities::Module::ProcessComposites(), Nektar::Utilities::Module::ProcessEdges(), Nektar::Utilities::Module::ProcessElements(), Nektar::Utilities::Module::ProcessFaces(), and Nektar::Utilities::Module::ProcessVertices().

{
int nodeId = m_mesh->m_vertexSet.size();
// Set up map which identifies edges (as pairs of vertex ids)
// including their vertices to the offset/stride in the 3d array of
// collapsed co-ordinates. Note that this map also includes the
// diagonal edges along quadrilateral faces which will be used to
// add high-order information to the split tetrahedra.
map<ipair, ipair> edgeMap;
map<ipair, ipair>::iterator it;
int nq = m_config["nq"].as<int>();
int ne = nq-2; // Edge interior
int nft = (ne-1)*ne/2; // Face interior (triangle)
int nfq = ne*ne; // Face interior (quad)
int o = 6;
// Standard prismatic edges (0->8)
edgeMap[ipair(0,1)] = ipair(o, 1);
edgeMap[ipair(1,2)] = ipair(o + 1*ne, 1);
edgeMap[ipair(3,2)] = ipair(o + 2*ne, 1);
edgeMap[ipair(0,3)] = ipair(o + 3*ne, 1);
edgeMap[ipair(0,4)] = ipair(o + 4*ne, 1);
edgeMap[ipair(1,4)] = ipair(o + 5*ne, 1);
edgeMap[ipair(2,5)] = ipair(o + 6*ne, 1);
edgeMap[ipair(3,5)] = ipair(o + 7*ne, 1);
edgeMap[ipair(4,5)] = ipair(o + 8*ne, 1);
// Face 0 diagonals
o += 9 * ne;
edgeMap[ipair(0,2)] = ipair(o, ne+1);
edgeMap[ipair(1,3)] = ipair(o+ne-1, ne-1);
// Face 2 diagonals
o += nfq + nft;
edgeMap[ipair(1,5)] = ipair(o, ne+1);
edgeMap[ipair(2,4)] = ipair(o+ne-1, ne-1);
// Face 4 diagonals
o += nfq + nft;
edgeMap[ipair(0,5)] = ipair(o, ne+1);
edgeMap[ipair(3,4)] = ipair(o+ne-1, ne-1);
// Default PointsType.
LibUtilities::PointsType pt = LibUtilities::ePolyEvenlySpaced;
/*
* Split all element types into tetrahedra. This is based on the
* algorithm found in:
*
* "How to Subdivide Pyramids, Prisms and Hexahedra into
* Tetrahedra", J. Dompierre et al.
*/
// Denotes a set of indices inside m_mesh->m_element[m_mesh->m_expDim-1] which are
// to be removed. These are precisely the quadrilateral boundary
// faces which will be replaced by two triangular faces.
set<int> toRemove;
// Represents table 2 of paper; each row i represents a rotation of
// the prism nodes such that vertex i is placed at position 0.
static int indir[6][6] = {
{0,1,2,3,4,5},
{1,2,0,4,5,3},
{2,0,1,5,3,4},
{3,5,4,0,2,1},
{4,3,5,1,0,2},
{5,4,3,2,1,0}
};
// Represents table 3 of paper; the first three rows are the three
// tetrahedra if the first condition is met; the latter three rows
// are the three tetrahedra if the second condition is met.
static int prismTet[6][4] = {
{0,1,2,5},
{0,1,5,4},
{0,4,5,3},
{0,1,2,4},
{0,4,2,5},
{0,4,5,3}
};
// Represents the order of tetrahedral edges (in Nektar++ ordering).
static int tetEdges[6][2] = {
{0,1}, {1,2},
{0,2}, {0,3},
{1,3}, {2,3}};
// A tetrahedron nodes -> faces map.
static int tetFaceNodes[4][3] = {
{0,1,2},{0,1,3},{1,2,3},{0,2,3}};
static NodeSharedPtr stdPrismNodes[6] = {
NodeSharedPtr(new Node(0,-1,-1,-1)),
NodeSharedPtr(new Node(1, 1,-1,-1)),
NodeSharedPtr(new Node(2, 1, 1,-1)),
NodeSharedPtr(new Node(3,-1, 1,-1)),
NodeSharedPtr(new Node(4,-1,-1, 1)),
NodeSharedPtr(new Node(5,-1, 1, 1))
};
// Generate equally spaced nodal points on triangle.
Array<OneD, NekDouble> rp(nq*(nq+1)/2), sp(nq*(nq+1)/2);
LibUtilities::PointsKey elec(nq, LibUtilities::eNodalTriEvenlySpaced);
LibUtilities::PointsManager()[elec]->GetPoints(rp,sp);
// Make a copy of the element list.
vector<ElementSharedPtr> el = m_mesh->m_element[m_mesh->m_expDim];
m_mesh->m_element[m_mesh->m_expDim].clear();
for (int i = 0; i < el.size(); ++i)
{
if (el[i]->GetConf().m_e != LibUtilities::ePrism)
{
m_mesh->m_element[m_mesh->m_expDim].push_back(el[i]);
continue;
}
vector<NodeSharedPtr> nodeList(6);
// Map Nektar++ ordering (vertices 0,1,2,3 are base quad) to
// paper ordering (vertices 0,1,2 are first triangular face).
int mapPrism[6] = {0,1,4,3,2,5};
for (int j = 0; j < 6; ++j)
{
nodeList[j] = el[i]->GetVertex(mapPrism[j]);
}
// Determine minimum ID of the nodes in this prism.
int minElId = nodeList[0]->m_id;
int minId = 0;
for (int j = 1; j < 6; ++j)
{
int curId = nodeList[j]->m_id;
if (curId < minElId)
{
minElId = curId;
minId = j;
}
}
int offset;
// Split prism using paper criterion.
int id1 = min(nodeList[indir[minId][1]]->m_id,
nodeList[indir[minId][5]]->m_id);
int id2 = min(nodeList[indir[minId][2]]->m_id,
nodeList[indir[minId][4]]->m_id);
if (id1 < id2)
{
offset = 0;
}
else if (id1 > id2)
{
offset = 3;
}
else
{
cerr << "Connectivity issue with prism->tet splitting."
<< endl;
abort();
}
// Create local prismatic region so that co-ordinates of the
// mapped element can be read from.
SpatialDomains::PrismGeomSharedPtr geomLayer =
boost::dynamic_pointer_cast<SpatialDomains::PrismGeom>(
el[i]->GetGeom(m_mesh->m_spaceDim));
LibUtilities::BasisKey B0(
LibUtilities::eOrtho_A, nq,
LibUtilities::PointsKey(
nq, LibUtilities::eGaussLobattoLegendre));
LibUtilities::BasisKey B1(
LibUtilities::eOrtho_B, nq,
LibUtilities::PointsKey(
nq, LibUtilities::eGaussRadauMAlpha1Beta0));
LocalRegions::PrismExpSharedPtr qs =
MemoryManager<LocalRegions::PrismExp>::AllocateSharedPtr(
B0, B0, B1, geomLayer);
// Get the coordinates of the high order prismatic element.
Array<OneD, NekDouble> wsp(3*nq*nq*nq);
Array<OneD, Array<OneD, NekDouble> > x(3);
x[0] = wsp;
x[1] = wsp + 1*nq*nq*nq;
x[2] = wsp + 2*nq*nq*nq;
qs->GetCoords(x[0], x[1], x[2]);
LibUtilities::BasisKey NB0(LibUtilities::eModified_A, nq,
LibUtilities::PointsKey(nq,pt));
LibUtilities::BasisKey NB1(LibUtilities::eModified_B, nq,
LibUtilities::PointsKey(nq,pt));
// Process face data. Initially put coordinates into equally
// spaced nodal distribution.
StdRegions::StdNodalPrismExpSharedPtr nodalPrism =
MemoryManager<StdRegions::StdNodalPrismExp>
::AllocateSharedPtr(
B0, B0, B1, LibUtilities::eNodalPrismEvenlySpaced);
int nCoeffs = nodalPrism->GetNcoeffs();
Array<OneD, NekDouble> wsp2(3*nCoeffs);
Array<OneD, Array<OneD, NekDouble> > xn(3);
xn[0] = wsp2;
xn[1] = wsp2 + 1*nCoeffs;
xn[2] = wsp2 + 2*nCoeffs;
for (int j = 0; j < 3; ++j)
{
Array<OneD, NekDouble> tmp(nodalPrism->GetNcoeffs());
qs ->FwdTrans (x[j], tmp);
nodalPrism->ModalToNodal(tmp, xn[j]);
}
// Store map of nodes.
map<int, int> prismVerts;
for (int j = 0; j < 6; ++j)
{
prismVerts[el[i]->GetVertex(j)->m_id] = j;
}
for (int j = 0; j < 3; ++j)
{
vector<NodeSharedPtr> tetNodes(4);
// Extract vertices for tetrahedron.
for (int k = 0; k < 4; ++k)
{
tetNodes[k] = nodeList[indir[minId][prismTet[j+offset][k]]];
}
// Add high order information to tetrahedral edges.
for (int k = 0; k < 6; ++k)
{
// Determine prismatic nodes which correspond with this
// edge. Apply prism map to this to get Nektar++
// ordering (this works since as a permutation,
// prismMap^2 = id).
int n1 = mapPrism[
indir[minId][prismTet[j+offset][tetEdges[k][0]]]];
int n2 = mapPrism[
indir[minId][prismTet[j+offset][tetEdges[k][1]]]];
// Find offset/stride
it = edgeMap.find(pair<int,int>(n1,n2));
if (it == edgeMap.end())
{
it = edgeMap.find(pair<int,int>(n2,n1));
if (it == edgeMap.end())
{
cerr << "Couldn't find prism edges " << n1
<< " " << n2 << endl;
abort();
}
// Extract vertices -- reverse order.
for (int l = ne-1; l >= 0; --l)
{
int pos = it->second.first + l*it->second.second;
tetNodes.push_back(
NodeSharedPtr(
new Node(nodeId++, xn[0][pos], xn[1][pos], xn[2][pos])));
}
}
else
{
// Extract vertices -- forwards order.
for (int l = 0; l < ne; ++l)
{
int pos = it->second.first + l*it->second.second;
tetNodes.push_back(
NodeSharedPtr(
new Node(nodeId++, xn[0][pos], xn[1][pos], xn[2][pos])));
}
}
}
// Create new tetrahedron with edge curvature.
vector<int> tags = el[i]->GetTagList();
ElmtConfig conf(LibUtilities::eTetrahedron, nq-1, false, false);
ElementSharedPtr elmt = GetElementFactory().
CreateInstance(LibUtilities::eTetrahedron,conf,tetNodes,tags);
// Extract interior face data.
for (int k = 0; k < 4; ++k)
{
// First determine which nodes of prism are being used
// for this face.
FaceSharedPtr face = elmt->GetFace(k);
vector<NodeSharedPtr> triNodes(3);
for (int l = 0; l < 3; ++l)
{
NodeSharedPtr v = face->m_vertexList[l];
triNodes[l] =
stdPrismNodes[prismVerts[v->m_id]];
}
// Create a triangle with the standard nodes of the
// prism.
vector<int> tags;
ElmtConfig conf(LibUtilities::eTriangle, 1, false, false);
ElementSharedPtr elmt = GetElementFactory().
CreateInstance(LibUtilities::eTriangle,conf,triNodes,tags);
SpatialDomains::GeometrySharedPtr triGeom =
elmt->GetGeom(3);
triGeom->FillGeom();
o = 3 + 3*ne;
face->m_curveType = LibUtilities::eNodalTriEvenlySpaced;
for (int l = 0; l < nft; ++l)
{
Array<OneD, NekDouble> tmp1(2), tmp2(3);
tmp1[0] = rp[o + l];
tmp1[1] = sp[o + l];
tmp2[0] = triGeom->GetCoord(0, tmp1);
tmp2[1] = triGeom->GetCoord(1, tmp1);
tmp2[2] = triGeom->GetCoord(2, tmp1);
// PhysEvaluate on prism geometry.
NekDouble xc = geomLayer->GetCoord(0, tmp2);
NekDouble yc = geomLayer->GetCoord(1, tmp2);
NekDouble zc = geomLayer->GetCoord(2, tmp2);
face->m_faceNodes.push_back(
NodeSharedPtr(new Node(nodeId++, xc, yc, zc)));
}
}
m_mesh->m_element[m_mesh->m_expDim].push_back(elmt);
}
// Now check to see if this one of the quadrilateral faces is
// associated with a boundary condition. If it is, we split the
// face into two triangles and mark the existing face for
// removal.
//
// Note that this algorithm has significant room for improvement
// and is likely one of the least optimal approachs - however
// implementation is simple.
for (int fid = 0; fid < 5; fid += 2)
{
int bl = el[i]->GetBoundaryLink(fid);
if (bl == -1)
{
continue;
}
vector<NodeSharedPtr> triNodeList(3);
vector<int> faceNodes (3);
vector<int> tmp;
vector<int> tagBE;
ElmtConfig bconf(LibUtilities::eTriangle, 1, true, true);
ElementSharedPtr elmt;
// Mark existing boundary face for removal.
toRemove.insert(bl);
tagBE = m_mesh->m_element[m_mesh->m_expDim-1][bl]->GetTagList();
// First loop over tets.
for (int j = 0; j < 3; ++j)
{
// Now loop over faces.
for (int k = 0; k < 4; ++k)
{
// Finally determine Nektar++ local node numbers for
// this face.
for (int l = 0; l < 3; ++l)
{
faceNodes[l] = mapPrism[indir[minId][prismTet[j+offset][tetFaceNodes[k][l]]]];
}
tmp = faceNodes;
sort(faceNodes.begin(), faceNodes.end());
// If this face matches a triple denoting a split
// quad face, add the face to the expansion list.
if ((fid == 0 && (
(faceNodes[0] == 0 && faceNodes[1] == 1 && faceNodes[2] == 2) ||
(faceNodes[0] == 0 && faceNodes[1] == 2 && faceNodes[2] == 3) ||
(faceNodes[0] == 0 && faceNodes[1] == 1 && faceNodes[2] == 3) ||
(faceNodes[0] == 1 && faceNodes[1] == 2 && faceNodes[2] == 3))) ||
(fid == 2 && (
(faceNodes[0] == 1 && faceNodes[1] == 2 && faceNodes[2] == 5) ||
(faceNodes[0] == 1 && faceNodes[1] == 4 && faceNodes[2] == 5) ||
(faceNodes[0] == 1 && faceNodes[1] == 2 && faceNodes[2] == 4) ||
(faceNodes[0] == 2 && faceNodes[1] == 4 && faceNodes[2] == 5))) ||
(fid == 4 && (
(faceNodes[0] == 0 && faceNodes[1] == 3 && faceNodes[2] == 5) ||
(faceNodes[0] == 0 && faceNodes[1] == 4 && faceNodes[2] == 5) ||
(faceNodes[0] == 0 && faceNodes[1] == 3 && faceNodes[2] == 4) ||
(faceNodes[0] == 3 && faceNodes[1] == 4 && faceNodes[2] == 5))))
{
triNodeList[0] = nodeList[mapPrism[tmp[0]]];
triNodeList[1] = nodeList[mapPrism[tmp[1]]];
triNodeList[2] = nodeList[mapPrism[tmp[2]]];
elmt = GetElementFactory().
CreateInstance(LibUtilities::eTriangle,bconf,triNodeList,tagBE);
m_mesh->m_element[m_mesh->m_expDim-1].push_back(elmt);
}
}
}
}
}
// Remove 2D elements.
vector<ElementSharedPtr> tmp;
for (int i = 0; i < m_mesh->m_element[m_mesh->m_expDim-1].size(); ++i)
{
set<int>::iterator it = toRemove.find(i);
if (it == toRemove.end())
{
tmp.push_back(m_mesh->m_element[m_mesh->m_expDim-1][i]);
}
}
m_mesh->m_element[m_mesh->m_expDim-1] = tmp;
// Re-process mesh to eliminate duplicate vertices and edges.
ProcessVertices();
ProcessEdges();
ProcessFaces();
ProcessElements();
ProcessComposites();
}

Member Data Documentation

ModuleKey Nektar::Utilities::ProcessTetSplit::className
static
Initial value:
GetModuleFactory().RegisterCreatorFunction(
ModuleKey(eProcessModule, "tetsplit"), ProcessTetSplit::create,
"Split prismatic elements to tetrahedra")

Definition at line 58 of file ProcessTetSplit.h.

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