#include <InputNek5000.h>

Inheritance diagram for Nektar::Utilities::InputNek5000:

Collaboration diagram for Nektar::Utilities::InputNek5000:

Public Member Functions
	InputNek5000 (NekMeshUtils::MeshSharedPtr p_m)

virtual	~InputNek5000 ()

virtual void	Process ()
	Processes Nek5000 file format. More...

Public Member Functions inherited from Nektar::NekMeshUtils::InputModule
NEKMESHUTILS_EXPORT	InputModule (MeshSharedPtr p_m)

NEKMESHUTILS_EXPORT void	OpenStream ()
	Open a file for input. More...

Public Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT	Module (MeshSharedPtr p_m)

NEKMESHUTILS_EXPORT void	RegisterConfig (std::string key, std::string value)
	Register a configuration option with a module. More...

NEKMESHUTILS_EXPORT void	PrintConfig ()
	Print out all configuration options for a module. More...

NEKMESHUTILS_EXPORT void	SetDefaults ()
	Sets default configuration options for those which have not been set. More...

NEKMESHUTILS_EXPORT MeshSharedPtr	GetMesh ()

virtual NEKMESHUTILS_EXPORT void	ProcessVertices ()
	Extract element vertices. More...

virtual NEKMESHUTILS_EXPORT void	ProcessEdges (bool ReprocessEdges=true)
	Extract element edges. More...

virtual NEKMESHUTILS_EXPORT void	ProcessFaces (bool ReprocessFaces=true)
	Extract element faces. More...

virtual NEKMESHUTILS_EXPORT void	ProcessElements ()
	Generate element IDs. More...

virtual NEKMESHUTILS_EXPORT void	ProcessComposites ()
	Generate composites. More...

virtual NEKMESHUTILS_EXPORT void	ClearElementLinks ()

Static Public Member Functions
static NekMeshUtils::ModuleSharedPtr	create (NekMeshUtils::MeshSharedPtr m)
	Creates an instance of this class. More...

Static Public Attributes
static NekMeshUtils::ModuleKey	className
	ModuleKey for class. More...

Private Member Functions
void	LoadHOSurfaces ()

Additional Inherited Members
Protected Member Functions inherited from Nektar::NekMeshUtils::InputModule
NEKMESHUTILS_EXPORT void	PrintSummary ()
	Print summary of elements. More...

Protected Member Functions inherited from Nektar::NekMeshUtils::Module
NEKMESHUTILS_EXPORT void	ReorderPrisms (PerMap &perFaces)
	Reorder node IDs so that prisms and tetrahedra are aligned correctly. More...

NEKMESHUTILS_EXPORT void	PrismLines (int prism, PerMap &perFaces, std::set< int > &prismsDone, std::vector< ElementSharedPtr > &line)

Protected Attributes inherited from Nektar::NekMeshUtils::InputModule
io::filtering_istream	m_mshFile
	Input stream. More...

std::ifstream	m_mshFileStream
	Input stream. More...

Protected Attributes inherited from Nektar::NekMeshUtils::Module
MeshSharedPtr	m_mesh
	Mesh object. More...

std::map< std::string, ConfigOption >	m_config
	List of configuration values. More...

Detailed Description

Converter class for Nektar session files.

Definition at line 54 of file utilities/NekMesh/InputModules/InputNek5000.h.

Constructor & Destructor Documentation

Nektar::Utilities::InputNek5000::InputNek5000 ( NekMeshUtils::MeshSharedPtr p_m )

Definition at line 59 of file utilities/NekMesh/InputModules/InputNek5000.cpp.

                                           : InputModule(m)
 {
 }

Nektar::Utilities::InputNek5000::~InputNek5000 ( )

virtual

Definition at line 63 of file utilities/NekMesh/InputModules/InputNek5000.cpp.

64 {

65 }

Member Function Documentation

static NekMeshUtils::ModuleSharedPtr Nektar::Utilities::InputNek5000::create ( NekMeshUtils::MeshSharedPtr m )

inlinestatic

Creates an instance of this class.

Definition at line 62 of file utilities/NekMesh/InputModules/InputNek5000.h.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

     {
         return MemoryManager<InputNek5000>::AllocateSharedPtr(m);
     }

void Nektar::Utilities::InputNek5000::LoadHOSurfaces ( )

private

void Nektar::Utilities::InputNek5000::Process ( )

virtual

Processes Nek5000 file format.

Nek5000 sessions are defined by rea files, and contain sections defining a DNS simulation in a specific order. The converter only reads mesh information, curve information if it exists and boundary information. The format is similar to the rea format supported by #InputNek, but the layout is sufficiently different that this module is separate.

Implements Nektar::NekMeshUtils::Module.

Definition at line 76 of file utilities/NekMesh/InputModules/InputNek5000.cpp.

 {
     // Open the file stream.
     OpenStream();
 
     string line, word;
     int nParam, nElements, nCurves;
     int i, j, k, nodeCounter = 0;
     int nComposite           = 1;
     LibUtilities::ShapeType elType;
     double vertex[8][3];
 
     m_mesh->m_expDim   = 0;
     m_mesh->m_spaceDim = 0;
 
     if (m_mesh->m_verbose)
     {
         cout << "InputNek5000: Start reading file..." << endl;
     }
 
     // -- Read in parameters.
 
     // Ignore first 3 lines. 4th line contains number of parameters.
     for (i = 0; i < 4; ++i)
     {
         getline(m_mshFile, line);
     }
 
     stringstream s(line);
     s >> nParam;
 
     for (i = 0; i < nParam; ++i)
     {
         string tmp1, tmp2;
         getline(m_mshFile, line);
         s.str(line);
         s >> tmp1 >> tmp2;
     }
 
     // -- Read in passive scalars (ignore)
     getline(m_mshFile, line);
     s.clear();
     s.str(line);
     s >> j;
     for (i = 0; i < j; ++i)
     {
         getline(m_mshFile, line);
     }
 
     // -- Read in logical switches (ignore)
     getline(m_mshFile, line);
     s.clear();
     s.str(line);
     s >> j;
     for (i = 0; i < j; ++i)
     {
         getline(m_mshFile, line);
     }
 
     // -- Read in mesh data.
 
     // First hunt for MESH tag
     bool foundMesh = false;
     while (!m_mshFile.eof())
     {
         getline(m_mshFile, line);
         if (line.find("MESH") != string::npos)
         {
             foundMesh = true;
             break;
         }
     }
 
     if (!foundMesh)
     {
         cerr << "Couldn't find MESH tag inside file." << endl;
         abort();
     }
 
     // Now read in number of elements and space dimension.
     getline(m_mshFile, line);
     s.clear();
     s.str(line);
     s >> nElements >> m_mesh->m_expDim;
     m_mesh->m_spaceDim = m_mesh->m_expDim;
 
     // Set up field names.
     m_mesh->m_fields.push_back("u");
     m_mesh->m_fields.push_back("v");
     if (m_mesh->m_spaceDim > 2)
     {
         m_mesh->m_fields.push_back("w");
     }
     m_mesh->m_fields.push_back("p");
 
     // Loop over and create elements.
     for (i = 0; i < nElements; ++i)
     {
         int nNodes;
         getline(m_mshFile, line);
 
         if (m_mesh->m_expDim == 2)
         {
             // - quad: 2 lines with x-coords, y-coords
             elType = LibUtilities::eQuadrilateral;
             nNodes = 4;
             for (j = 0; j < 2; ++j)
             {
                 getline(m_mshFile, line);
                 s.clear();
                 s.str(line);
                 for (k = 0; k < 4; ++k)
                 {
                     s >> vertex[k][j];
                 }
             }
         }
         else
         {
             // - hex: 3 lines with x/y/z-coords for base 4 nodes, then 3 more
             //   for upper 4 nodes
             elType = LibUtilities::eHexahedron;
             nNodes = 8;
             for (j = 0; j < 6; ++j)
             {
                 getline(m_mshFile, line);
                 s.clear();
                 s.str(line);
                 int offset = j > 2 ? 4 : 0;
                 for (k = 0; k < 4; ++k)
                 {
                     s >> vertex[offset + k][j % 3];
                 }
             }
         }
 
         // Nek5000 meshes do not contain a unique list of nodes, so this block
         // constructs a unique set so that elements can be created with unique
         // nodes.
         vector<NodeSharedPtr> nodeList(nNodes);
         for (k = 0; k < nNodes; ++k)
         {
             nodeList[k] = boost::shared_ptr<Node>(
                 new Node(
                     0, vertex[k][0], vertex[k][1], vertex[k][2]));
             pair<NodeSet::iterator, bool> testIns =
                 m_mesh->m_vertexSet.insert(nodeList[k]);
 
             if (!testIns.second)
             {
                 nodeList[k] = *(testIns.first);
             }
             else
             {
                 nodeList[k]->m_id = nodeCounter++;
             }
         }
 
         vector<int> tags(1, 0);
         ElmtConfig conf(elType, 1, false, false);
         ElementSharedPtr E = GetElementFactory().CreateInstance(
             elType, conf, nodeList, tags);
         m_mesh->m_element[E->GetDim()].push_back(E);
     }
 
     // -- Read in curved data.
     getline(m_mshFile, line);
     if (line.find("CURVE") == string::npos)
     {
         cerr << "Cannot find curved side data." << endl;
         abort();
     }
 
     // Read number of curves.
     getline(m_mshFile, line);
     s.clear();
     s.str(line);
     s >> nCurves;
 
     Array<OneD, NekDouble> rp;
     int nq = 6;
     LibUtilities::PointsKey curveType(nq, LibUtilities::eGaussLobattoLegendre);
     LibUtilities::PointsManager()[curveType]->GetPoints(rp);
 
     // Map to reorder Nek5000 -> Nektar++ edge ordering. Nek5000 has the same
     // counter-clockwise ordering of edges/vertices; however the vertical
     // (i.e. t- or xi_3-direction) edges come last.
     int nek2nekedge[12] = {
         0, 1, 2, 3, 8, 9, 10, 11, 4, 5, 6, 7
     };
 
     // Map to reorder Nek5000 -> Nektar++ face ordering. Again we have the same
     // counter-clockwise ordering; however the 4 vertical faces of the hex are
     // first, followed by bottom face and then top face.
     int nek2nekface[6] = {
         1, 2, 3, 4, 0, 5
     };
 
     if (nCurves > 0)
     {
         for (i = 0; i < nCurves; ++i)
         {
             getline(m_mshFile, line);
 
             int elmt, side;
             NekDouble curveData[5];
             char curveType;
 
             if (nElements < 1000)
             {
                 // side in first 3 characters, elmt in next 3
                 s.str(line.substr(0, 3));
                 s >> side;
                 s.clear();
                 s.str(line.substr(3, 3));
                 s >> elmt;
                 line = line.substr(6);
             }
             else if (nElements < 1000000)
             {
                 // side in first 2 characters, elmt in next 6
                 s.str(line.substr(0, 2));
                 s >> side;
                 s.clear();
                 s.str(line.substr(2, 6));
                 s >> elmt;
                 line = line.substr(8);
             }
             else
             {
                 // side in first 2 characters, elmt in next 12
                 s.str(line.substr(0, 2));
                 s >> side;
                 s.clear();
                 s.str(line.substr(2, 12));
                 s >> elmt;
                 line = line.substr(14);
             }
 
             s.clear();
             s.str(line);
 
             for (j = 0; j < 5; ++j)
             {
                 s >> curveData[j];
             }
             s >> curveType;
 
             elmt--;
             side--;
             side = nek2nekedge[side];
 
             switch (curveType)
             {
                 case 'C':
                 {
                     // Apply circular curvature to edges. Nek5000 assumes that
                     // the curvature should be imposed in x-y planes and has no
                     // z-dependence. The following code is adapted from Semtex
                     // (src/mesh.C)
                     NekDouble radius = curveData[0];
                     int convexity = radius < 0 ? -1 : 1;
                     radius = fabs(radius);
 
                     ElementSharedPtr el =
                         m_mesh->m_element[m_mesh->m_expDim][elmt];
                     EdgeSharedPtr edge = el->GetEdge(side);
                     edge->m_curveType = LibUtilities::eGaussLobattoLegendre;
 
                     // Assume 2D projection
                     Node P1(*(edge->m_n1)), P2(*(edge->m_n2));
 
                     if (fabs(P1.m_z - P2.m_z) > 1e-8)
                     {
                         cout << "warning: detected non x-y edge." << endl;
                     }
                     P1.m_z = P2.m_z = 0.0;
 
                     Node unitNormal, link, centroid, centre;
                     Node midpoint = (P1 + P2)*0.5, dx = P2 - P1;
                     NekDouble l = sqrt(dx.abs2()), sign = 0.0, semiangle = 0.0;
 
                     unitNormal.m_x = -dx.m_y / l;
                     unitNormal.m_y = dx.m_x / l;
 
                     if (2.0 * radius < l)
                     {
                         cerr << "failure" << endl;
                     }
                     else
                     {
                         semiangle = asin (0.5 * l / radius);
                     }
 
                     // Calculate element centroid
                     vector<NodeSharedPtr> elNodes = el->GetVertexList();
                     int nNodes = elNodes.size();
 
                     for (int i = 0; i < nNodes; ++i)
                     {
                         // Assume 2D projection
                         Node tmp(*elNodes[i]);
                         tmp.m_z = 0.0;
                         centroid += tmp;
                     }
 
                     centroid /= (NekDouble)nNodes;
                     link      = centroid - midpoint;
                     sign      = link.dot(unitNormal);
                     sign      = convexity * sign / fabs(sign);
                     centre    = midpoint + unitNormal * (sign * cos(semiangle) *
                                                          radius);
 
                     NekDouble theta1, theta2, dtheta, phi;
                     theta1 = atan2 (P1.m_y - centre.m_y, P1.m_x - centre.m_x);
                     theta2 = atan2 (P2.m_y - centre.m_y, P2.m_x - centre.m_x);
                     dtheta = theta2 - theta1;
 
                     if (fabs(dtheta) > 2.0*semiangle + 1e-15)
                     {
                         dtheta += (dtheta < 0.0) ? 2.0*M_PI : -2.0*M_PI;
                     }
 
                     edge->m_edgeNodes.clear();
 
                     for (j = 1; j < nq-1; ++j) {
                         phi = theta1 + dtheta * 0.5 * (rp[j] + 1.0);
                         NodeSharedPtr asd(new Node(
                                               0,
                                               centre.m_x + radius * cos(phi),
                                               centre.m_y + radius * sin(phi),
                                               edge->m_n1->m_z));
                         edge->m_edgeNodes.push_back(asd);
                     }
                     break;
                 }
                 case 's':
                 case 'S':
                 case 'm':
                 case 'M':
                     cerr << "Curve type '" << curveType << "' on side " << side
                          << " of element " << elmt << " is unsupported;"
                          << "will ignore." << endl;
                     break;
                 default:
                     cerr << "Unknown curve type '" << curveType << "' on side "
                          << side << " of element " << elmt << "; will ignore."
                          << endl;
                     break;
             }
         }
     }
 
     // Read boundary conditions.
     getline(m_mshFile, line);
     getline(m_mshFile, line);
     if (line.find("BOUNDARY") == string::npos)
     {
         cerr << "Cannot find boundary conditions." << endl;
         abort();
     }
 
     int nSurfaces = 0;
     boost::unordered_set<pair<int, int> > periodicIn;
     int periodicInId = -1, periodicOutId = -1;
 
     // Boundary conditions: should be precisely nElements * nFaces lines to
     // read.
     int lineCnt = 0;
     int perIn = 0, perOut = 0;
 
     while (m_mshFile.good())
     {
         getline(m_mshFile, line);
 
         // Found a new section. We don't support anything in the rea file beyond
         // this point so we'll just quit.
         if (line.find("*") != string::npos)
         {
             break;
         }
 
         ConditionSharedPtr c = MemoryManager<Condition>::AllocateSharedPtr();
         char bcType;
         int elmt, side;
         NekDouble data[5];
 
         // type in chars 0-3
         s.clear();
         s.str(line.substr(0, 4));
         s >> bcType;
 
         // Some lines have no boundary condition entries
         if (s.fail())
         {
             lineCnt++;
             continue;
         }
 
         if (nElements < 1000)
         {
             // elmt in chars 4-6, side in next 3
             s.clear();
             s.str(line.substr(4, 3));
             s >> elmt;
             s.clear();
             s.str(line.substr(7, 3));
             s >> side;
             line = line.substr(10);
         }
         else if (nElements < 100000)
         {
             // elmt in chars 4-8, side in next 1
             s.clear();
             s.str(line.substr(4, 5));
             s >> elmt;
             s.clear();
             s.str(line.substr(9, 1));
             s >> side;
             line = line.substr(10);
         }
         else if (nElements < 1000000)
         {
             // elmt in chars 4-9, no side
             s.clear();
             s.str(line.substr(4, 6));
             s >> elmt;
             side = lineCnt % (2 * m_mesh->m_expDim);
             line = line.substr(9);
         }
         else
         {
             // elmt in chars 4-15, no side
             s.clear();
             s.str(line.substr(4, 12));
             s >> elmt;
             side = lineCnt % (2 * m_mesh->m_expDim);
             line = line.substr(15);
         }
 
         s.clear();
         s.str(line);
 
         for (i = 0; i < 5; ++i)
         {
             s >> data[i];
         }
 
         // Our ordering starts from 0, not 1.
         --elmt;
         --side;
 
         // Increment lines read
         lineCnt++;
 
         ElementSharedPtr el = m_mesh->m_element[m_mesh->m_spaceDim][elmt];
 
         std::string fields[] = { "u", "v", "w", "p" };
 
         switch (bcType)
         {
             case 'E':
                 // Edge/face connectivity; ignore since we already have this, at
                 // least for conformal meshes.
                 continue;
 
             case 'W':
             {
                 for (i = 0; i < m_mesh->m_fields.size() - 1; ++i)
                 {
                     c->field.push_back(fields[i]);
                     c->value.push_back("0");
                     c->type.push_back(eDirichlet);
                 }
 
                 // Set high-order boundary condition for wall.
                 c->field.push_back(fields[3]);
                 c->value.push_back("0");
                 c->type.push_back(eHOPCondition);
                 break;
             }
 
             case 'P':
             {
                 // Determine periodic element and face.
                 int perElmt = (int)(data[0] + 0.5) - 1;
                 int perFace = (int)(data[1] + 0.5) - 1;
 
                 bool setup = false;
                 if (periodicInId == -1)
                 {
                     periodicInId = m_mesh->m_condition.size();
                     periodicOutId = m_mesh->m_condition.size()+1;
                     setup = true;
                 }
 
                 bool hasIn = periodicIn.find(make_pair(perElmt, perFace)) !=
                     periodicIn.end();
 
                 if (hasIn)
                 {
                     swap(periodicInId, periodicOutId);
                     perOut++;
                 }
                 else
                 {
                     periodicIn.insert(make_pair(elmt, side));
                     perIn++;
                 }
 
                 std::string periodicInStr = "[" +
                     boost::lexical_cast<string>(periodicInId) + "]";
                 std::string periodicOutStr = "[" +
                     boost::lexical_cast<string>(periodicOutId) + "]";
 
                 for (i = 0; i < m_mesh->m_fields.size() - 1; ++i)
                 {
                     c->field.push_back(fields[i]);
                     c->value.push_back(periodicOutStr);
                     c->type.push_back(ePeriodic);
                 }
 
                 c->field.push_back(fields[3]);
                 c->value.push_back(periodicOutStr);
                 c->type.push_back(ePeriodic);
 
                 if (setup)
                 {
                     ConditionSharedPtr c2 = MemoryManager<Condition>
                         ::AllocateSharedPtr();
 
                     c->m_composite.push_back(nComposite++);
                     c2->m_composite.push_back(nComposite++);
 
                     c2->field = c->field;
                     c2->type = c->type;
                     for (i = 0; i < c->type.size(); ++i)
                     {
                         c2->value.push_back(periodicInStr);
                     }
 
                     m_mesh->m_condition[periodicInId] = c;
                     m_mesh->m_condition[periodicOutId] = c2;
                 }
 
                 if (hasIn)
                 {
                     swap(periodicInId, periodicOutId);
                 }
 
                 break;
             }
 
             default:
                 continue;
         }
 
         int compTag, conditionId;
         ElementSharedPtr surfEl;
 
         // Create element for face (3D) or segment (2D).
         if (el->GetDim() == 3)
         {
             FaceSharedPtr f = el->GetFace(nek2nekface[side]);
             vector<NodeSharedPtr> nodeList;
             nodeList.insert(nodeList.begin(),
                             f->m_vertexList.begin(),
                             f->m_vertexList.end());
 
             vector<int> tags;
             ElmtConfig conf(
                 LibUtilities::eQuadrilateral, 1, true, true, false,
                 LibUtilities::eGaussLobattoLegendre);
             surfEl =
                 GetElementFactory().CreateInstance(LibUtilities::eQuadrilateral,
                                                    conf, nodeList, tags);
 
             // Copy high-order surface information from edges.
             for (int i = 0; i < f->m_vertexList.size(); ++i)
             {
                 surfEl->GetEdge(i)->m_edgeNodes = f->m_edgeList[i]->m_edgeNodes;
                 surfEl->GetEdge(i)->m_curveType = f->m_edgeList[i]->m_curveType;
             }
         }
         else
         {
             EdgeSharedPtr f = el->GetEdge(side);
 
             vector<NodeSharedPtr> nodeList;
             nodeList.push_back(f->m_n1);
             nodeList.push_back(f->m_n2);
 
             vector<int> tags;
 
             ElmtConfig conf(
                 LibUtilities::eSegment, 1, true, true, false,
                 LibUtilities::eGaussLobattoLegendre);
             surfEl = GetElementFactory().CreateInstance(
                 LibUtilities::eSegment, conf, nodeList, tags);
         }
 
         // Now attempt to find this boundary condition inside
         // m_mesh->condition. This is currently a linear search and should
         // probably be made faster!
         ConditionMap::iterator it;
         bool found = false;
         for (it = m_mesh->m_condition.begin(); it != m_mesh->m_condition.end();
              ++it)
         {
             if (c == it->second)
             {
                 found = true;
                 c = it->second;
                 break;
             }
         }
 
         if (!found)
         {
             conditionId = m_mesh->m_condition.size();
             compTag = nComposite;
             c->m_composite.push_back(compTag);
             m_mesh->m_condition[conditionId] = c;
         }
         else
         {
             compTag = c->m_composite[0];
         }
 
         // Insert composite tag into element and insert element into
         // mesh.
         vector<int> existingTags = surfEl->GetTagList();
 
         existingTags.insert(existingTags.begin(), compTag);
         surfEl->SetTagList(existingTags);
         surfEl->SetId(nSurfaces);
 
         m_mesh->m_element[surfEl->GetDim()].push_back(surfEl);
         nSurfaces++;
     }
 
     if (lineCnt != nElements * (m_mesh->m_expDim * 2))
     {
         cerr << "Warning: boundary conditions may not have been correctly read "
              << "from Nek5000 input file." << endl;
     }
 
     if (perIn != perOut)
     {
         cerr << "Warning: number of periodic faces does not match." << endl;
     }
 
     m_mshFile.reset();
 
     // -- Process rest of mesh.
     ProcessEdges();
     ProcessFaces();
     ProcessElements();
     ProcessComposites();
 
     // -- Set periodic composites to not be reordered.
     if (periodicInId != -1)
     {
         m_mesh->m_composite[m_mesh->m_condition[periodicInId]
                             ->m_composite[0]]->m_reorder = false;
         m_mesh->m_composite[m_mesh->m_condition[periodicOutId]
                             ->m_composite[0]]->m_reorder = false;
     }
 }

Member Data Documentation

ModuleKey Nektar::Utilities::InputNek5000::className

static

Initial value:

= GetModuleFactory().RegisterCreatorFunction(
    ModuleKey(eInputModule, "rea5000"),
    InputNek5000::create, "Reads Nektar rea file.")

ModuleKey for class.

Definition at line 67 of file utilities/NekMesh/InputModules/InputNek5000.h.

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

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