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Nektar::LibUtilities::MeshPartition Class Referenceabstract

#include <MeshPartition.h>

Inheritance diagram for Nektar::LibUtilities::MeshPartition:
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Classes

struct  GraphEdgeProperties
 
struct  GraphVertexProperties
 
struct  MeshComposite
 
struct  MeshCurved
 
struct  MeshElement
 
struct  MeshEntity
 
struct  MeshFace
 

Public Member Functions

 MeshPartition (const SessionReaderSharedPtr &pSession)
 
virtual ~MeshPartition ()
 
void PartitionMesh (int nParts, bool shared=false, bool overlapping=false)
 
void WriteLocalPartition (SessionReaderSharedPtr &pSession)
 
void WriteAllPartitions (SessionReaderSharedPtr &pSession)
 
void PrintPartInfo (std::ostream &out)
 
void GetCompositeOrdering (CompositeOrdering &composites)
 
void GetBndRegionOrdering (BndRegionOrdering &composites)
 
void GetElementIDs (const int procid, std::vector< unsigned int > &tmp)
 

Private Types

typedef std::pair< std::string,
int > 		MeshCurvedKey
 
typedef std::vector< unsigned int > MultiWeight
 
typedef boost::adjacency_list
< boost::setS, boost::vecS,
boost::undirectedS,
GraphVertexProperties,
boost::property
< boost::edge_index_t,
unsigned int,
GraphEdgeProperties > > 		BoostGraph
 
typedef boost::subgraph
< BoostGraph > 		BoostSubGraph
 
typedef boost::graph_traits
< BoostGraph >
::vertex_descriptor 		BoostVertex
 
typedef boost::graph_traits
< BoostGraph >
::edge_descriptor 		BoostEdge
 
typedef boost::graph_traits
< BoostGraph >::edge_iterator 		BoostEdgeIterator
 
typedef boost::graph_traits
< BoostGraph >
::vertex_iterator 		BoostVertexIterator
 
typedef boost::graph_traits
< BoostGraph >
::adjacency_iterator 		BoostAdjacencyIterator
 
typedef std::vector< unsigned int > NumModes
 
typedef std::map< std::string,
NumModes > 		NummodesPerField
 

Private Member Functions

void ReadExpansions (const SessionReaderSharedPtr &pSession)
 
void ReadGeometry (const SessionReaderSharedPtr &pSession)
 
void ReadConditions (const SessionReaderSharedPtr &pSession)
 
void WeightElements ()
 
void CreateGraph (BoostSubGraph &pGraph)
 
void PartitionGraph (BoostSubGraph &pGraph, int nParts, std::vector< BoostSubGraph > &pLocalPartition, bool overlapping=false)
 Partition the graph. More...
 
virtual void PartitionGraphImpl (int &nVerts, int &nVertConds, Nektar::Array< Nektar::OneD, int > &xadj, Nektar::Array< Nektar::OneD, int > &adjcy, Nektar::Array< Nektar::OneD, int > &vertWgt, Nektar::Array< Nektar::OneD, int > &vertSize, Nektar::Array< Nektar::OneD, int > &edgeWgt, int &nparts, int &volume, Nektar::Array< Nektar::OneD, int > &part)=0
 
void OutputPartition (SessionReaderSharedPtr &pSession, BoostSubGraph &pGraph, TiXmlElement *pGeometry)
 
void CheckPartitions (int nParts, Array< OneD, int > &pPart)
 
int CalculateElementWeight (char elmtType, bool bndWeight, int na, int nb, int nc)
 
int CalculateEdgeWeight (char elmtType, int na, int nb, int nc)
 

Private Attributes

bool m_isCompressed
 
int m_dim
 
int m_numFields
 
std::map< int, MeshVertex > m_meshVertices
 
std::map< int, MeshEntity > m_meshEdges
 
std::map< int, MeshEntity > m_meshFaces
 
std::map< int, MeshEntity > m_meshElements
 
std::map< MeshCurvedKey,
MeshCurved > 		m_meshCurved
 
std::map< int, MeshCurvedPts > m_meshCurvedPts
 
std::map< int, MeshEntity > m_meshComposites
 
std::vector< unsigned int > m_domain
 
std::map< std::string,
std::string > 		m_vertexAttributes
 
std::map< int, NummodesPerField > m_expansions
 
std::map< int, char > m_shape
 
std::map< std::string, int > m_fieldNameToId
 
std::map< int, MultiWeight > m_vertWeights
 
std::map< int, MultiWeight > m_vertBndWeights
 
std::map< int, MultiWeight > m_edgeWeights
 
BndRegionOrdering m_bndRegOrder
 
BoostSubGraph m_mesh
 
std::vector< BoostSubGraph > m_localPartition
 
CommSharedPtr m_comm
 
bool m_weightingRequired
 
bool m_weightBnd
 
bool m_weightDofs
 
bool m_shared
 

Detailed Description

Definition at line 62 of file MeshPartition.h.

Member Typedef Documentation

typedef boost::graph_traits< BoostGraph >::adjacency_iterator Nektar::LibUtilities::MeshPartition::BoostAdjacencyIterator
private

Definition at line 176 of file MeshPartition.h.

typedef boost::graph_traits< BoostGraph >::edge_descriptor Nektar::LibUtilities::MeshPartition::BoostEdge
private

Definition at line 167 of file MeshPartition.h.

typedef boost::graph_traits< BoostGraph >::edge_iterator Nektar::LibUtilities::MeshPartition::BoostEdgeIterator
private

Definition at line 170 of file MeshPartition.h.

typedef boost::adjacency_list< boost::setS, boost::vecS, boost::undirectedS, GraphVertexProperties, boost::property< boost::edge_index_t, unsigned int, GraphEdgeProperties > > Nektar::LibUtilities::MeshPartition::BoostGraph
private

Definition at line 157 of file MeshPartition.h.

typedef boost::subgraph< BoostGraph > Nektar::LibUtilities::MeshPartition::BoostSubGraph
private

Definition at line 160 of file MeshPartition.h.

typedef boost::graph_traits< BoostGraph >::vertex_descriptor Nektar::LibUtilities::MeshPartition::BoostVertex
private

Definition at line 164 of file MeshPartition.h.

typedef boost::graph_traits< BoostGraph >::vertex_iterator Nektar::LibUtilities::MeshPartition::BoostVertexIterator
private

Definition at line 173 of file MeshPartition.h.

typedef std::pair<std::string, int> Nektar::LibUtilities::MeshPartition::MeshCurvedKey
private

Definition at line 125 of file MeshPartition.h.

typedef std::vector<unsigned int> Nektar::LibUtilities::MeshPartition::MultiWeight
private

Definition at line 126 of file MeshPartition.h.

typedef std::vector<unsigned int> Nektar::LibUtilities::MeshPartition::NumModes
private

Definition at line 178 of file MeshPartition.h.

typedef std::map<std::string, NumModes> Nektar::LibUtilities::MeshPartition::NummodesPerField
private

Definition at line 179 of file MeshPartition.h.

Constructor & Destructor Documentation

Nektar::LibUtilities::MeshPartition::MeshPartition ( const SessionReaderSharedPtr &  pSession)

Definition at line 79 of file MeshPartition.cpp.

References ReadConditions(), ReadExpansions(), and ReadGeometry().

79  :
80  m_isCompressed(false),
81  m_numFields(0),
82  m_fieldNameToId(),
83  m_comm(pSession->GetComm()),
84  m_weightingRequired(false),
85  m_weightBnd(false),
86  m_weightDofs(false)
87  {
88  ReadConditions(pSession);
89  ReadGeometry(pSession);
90  ReadExpansions(pSession);
91  }
Nektar::LibUtilities::MeshPartition::ReadConditions
void ReadConditions(const SessionReaderSharedPtr &pSession)
Definition: MeshPartition.cpp:1099
Nektar::LibUtilities::MeshPartition::m_fieldNameToId
std::map< std::string, int > m_fieldNameToId
Definition: MeshPartition.h:201
Nektar::LibUtilities::MeshPartition::ReadExpansions
void ReadExpansions(const SessionReaderSharedPtr &pSession)
Definition: MeshPartition.cpp:192
Nektar::LibUtilities::MeshPartition::ReadGeometry
void ReadGeometry(const SessionReaderSharedPtr &pSession)
Definition: MeshPartition.cpp:407
Nektar::LibUtilities::MeshPartition::~MeshPartition ( )
virtual

Definition at line 93 of file MeshPartition.cpp.

94  {
95 
96  }

Member Function Documentation

int Nektar::LibUtilities::MeshPartition::CalculateEdgeWeight ( char  elmtType,
int  na,
int  nb,
int  nc 
)
private

Calculate the number of modes needed for communication when in partition boundary, to be used as weighting for edges. Since we do not know exactly which face this refers to, assume the max order and quad face (for prisms) as arbitrary choices

Definition at line 2378 of file MeshPartition.cpp.

References Nektar::LibUtilities::StdTriData::getNumberOfCoefficients(), and Nektar::LibUtilities::StdQuadData::getNumberOfCoefficients().

Referenced by WeightElements().

2383  {
2384  int weight = 0;
2385  int n = std::max ( na, std::max(nb, nc));
2386  switch (elmtType)
2387  {
2388  case 'A':
2389  weight =
2390  StdTriData ::getNumberOfCoefficients (n, n);
2391  break;
2392  case 'R':
2393  weight =
2394  StdQuadData ::getNumberOfCoefficients (n, n);
2395  break;
2396  case 'H':
2397  weight =
2398  StdQuadData ::getNumberOfCoefficients (n, n);
2399  break;
2400  case 'P':
2401  weight =
2402  StdQuadData ::getNumberOfCoefficients (n, n);
2403  break;
2404  case 'Q':
2405  case 'T':
2406  weight = n;
2407  break;
2408  case 'S':
2409  weight = 1;
2410  break;
2411  default:
2412  break;
2413  }
2414 
2415  return weight;
2416  }
Nektar::LibUtilities::StdTriData::getNumberOfCoefficients
int getNumberOfCoefficients(int Na, int Nb)
Definition: ShapeType.hpp:111
Nektar::LibUtilities::StdQuadData::getNumberOfCoefficients
int getNumberOfCoefficients(int Na, int Nb)
Definition: ShapeType.hpp:132
int Nektar::LibUtilities::MeshPartition::CalculateElementWeight ( char  elmtType,
bool  bndWeight,
int  na,
int  nb,
int  nc 
)
private

Definition at line 2316 of file MeshPartition.cpp.

References Nektar::LibUtilities::StdSegData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdTriData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdQuadData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdHexData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdTetData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdPyrData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdPrismData::getNumberOfBndCoefficients(), Nektar::LibUtilities::StdSegData::getNumberOfCoefficients(), Nektar::LibUtilities::StdTriData::getNumberOfCoefficients(), Nektar::LibUtilities::StdQuadData::getNumberOfCoefficients(), Nektar::LibUtilities::StdHexData::getNumberOfCoefficients(), Nektar::LibUtilities::StdTetData::getNumberOfCoefficients(), Nektar::LibUtilities::StdPyrData::getNumberOfCoefficients(), and Nektar::LibUtilities::StdPrismData::getNumberOfCoefficients().

Referenced by PrintPartInfo(), and WeightElements().

2322  {
2323  int weight = 0;
2324 
2325  switch (elmtType)
2326  {
2327  case 'A':
2328  weight = bndWeight ?
2329  StdTetData ::getNumberOfBndCoefficients(na, nb, nc) :
2330  StdTetData ::getNumberOfCoefficients (na, nb, nc);
2331  break;
2332  case 'R':
2333  weight = bndWeight ?
2334  StdPrismData::getNumberOfBndCoefficients(na, nb, nc) :
2335  StdPrismData::getNumberOfCoefficients (na, nb, nc);
2336  break;
2337  case 'H':
2338  weight = bndWeight ?
2339  StdHexData ::getNumberOfBndCoefficients(na, nb, nc) :
2340  StdHexData ::getNumberOfCoefficients (na, nb, nc);
2341  break;
2342  case 'P':
2343  weight = bndWeight ?
2344  StdPyrData ::getNumberOfBndCoefficients(na, nb, nc) :
2345  StdPyrData ::getNumberOfCoefficients (na, nb, nc);
2346  break;
2347  case 'Q':
2348  weight = bndWeight ?
2349  StdQuadData ::getNumberOfBndCoefficients(na, nb) :
2350  StdQuadData ::getNumberOfCoefficients (na, nb);
2351  break;
2352  case 'T':
2353  weight = bndWeight ?
2354  StdTriData ::getNumberOfBndCoefficients(na, nb) :
2355  StdTriData ::getNumberOfCoefficients (na, nb);
2356  break;
2357  case 'S':
2358  weight = bndWeight ?
2359  StdSegData ::getNumberOfBndCoefficients(na) :
2360  StdSegData ::getNumberOfCoefficients (na);
2361  break;
2362  case 'V':
2363  weight = 1;
2364  break;
2365  default:
2366  break;
2367  }
2368 
2369  return weight;
2370  }
Nektar::LibUtilities::StdTriData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb)
Definition: ShapeType.hpp:120
Nektar::LibUtilities::StdHexData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb, int Nc)
Definition: ShapeType.hpp:159
Nektar::LibUtilities::StdPyrData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb, int Nc)
Definition: ShapeType.hpp:266
Nektar::LibUtilities::StdQuadData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb)
Definition: ShapeType.hpp:139
Nektar::LibUtilities::StdPrismData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb, int Nc)
Definition: ShapeType.hpp:297
Nektar::LibUtilities::StdTetData::getNumberOfBndCoefficients
int getNumberOfBndCoefficients(int Na, int Nb, int Nc)
Definition: ShapeType.hpp:209
void Nektar::LibUtilities::MeshPartition::CheckPartitions ( int  nParts,
Array< OneD, int > &  pPart 
)
private

Definition at line 1443 of file MeshPartition.cpp.

Referenced by PartitionGraph().

1444  {
1445  unsigned int i = 0;
1446  unsigned int cnt = 0;
1447  bool valid = true;
1448 
1449  // Check that every process has at least one element assigned
1450  for (i = 0; i < nParts; ++i)
1451  {
1452  cnt = std::count(pPart.begin(), pPart.end(), i);
1453  if (cnt == 0)
1454  {
1455  valid = false;
1456  }
1457  }
1458 
1459  // If METIS produced an invalid partition, repartition naively.
1460  // Elements are assigned to processes in a round-robin fashion.
1461  // It is assumed that METIS failure only occurs when the number of
1462  // elements is approx. the number of processes, so this approach
1463  // should not be too inefficient communication-wise.
1464  if (!valid)
1465  {
1466  for (i = 0; i < pPart.num_elements(); ++i)
1467  {
1468  pPart[i] = i % nParts;
1469  }
1470  }
1471  }
void Nektar::LibUtilities::MeshPartition::CreateGraph ( BoostSubGraph &  pGraph)
private

Definition at line 1232 of file MeshPartition.cpp.

References Nektar::iterator, m_edgeWeights, m_meshElements, m_vertBndWeights, m_vertWeights, and m_weightingRequired.

Referenced by PartitionMesh().

1233  {
1234  // Maps edge/face to first mesh element id.
1235  // On locating second mesh element id, graph edge is created instead.
1236  std::map<int, int> vGraphEdges;
1237  std::map<int, MeshEntity>::iterator eIt;
1238  int vcnt = 0;
1239 
1240  for (eIt = m_meshElements.begin(); eIt != m_meshElements.end();
1241  ++eIt, ++vcnt)
1242  {
1243  BoostVertex v = boost::add_vertex(pGraph);
1244  pGraph[v].id = eIt->first;
1245  pGraph[v].partition = 0;
1246 
1247  if (m_weightingRequired)
1248  {
1249  pGraph[v].weight = m_vertWeights[eIt->first];
1250  pGraph[v].bndWeight = m_vertBndWeights[eIt->first];
1251  pGraph[v].edgeWeight = m_edgeWeights[eIt->first];
1252  }
1253 
1254  // Process element entries and add graph edges
1255  for (unsigned j = 0; j < eIt->second.list.size(); ++j)
1256  {
1257  int eId = eIt->second.list[j];
1258 
1259  // Look to see if we've examined this edge/face before
1260  // If so, we've got both graph vertices so add edge
1261  if (vGraphEdges.find(eId) != vGraphEdges.end())
1262  {
1263  BoostEdge e = boost::add_edge(vcnt, vGraphEdges[eId], pGraph).first;
1264  pGraph[e].id = vcnt;
1265  }
1266  else
1267  {
1268  vGraphEdges[eId] = vcnt;
1269  }
1270  }
1271  }
1272  }
Nektar::LibUtilities::MeshPartition::BoostVertex
boost::graph_traits< BoostGraph >::vertex_descriptor BoostVertex
Definition: MeshPartition.h:164
Nektar::LibUtilities::MeshPartition::m_vertBndWeights
std::map< int, MultiWeight > m_vertBndWeights
Definition: MeshPartition.h:203
Nektar::LibUtilities::MeshPartition::m_vertWeights
std::map< int, MultiWeight > m_vertWeights
Definition: MeshPartition.h:202
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::m_edgeWeights
std::map< int, MultiWeight > m_edgeWeights
Definition: MeshPartition.h:204
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
Nektar::LibUtilities::MeshPartition::BoostEdge
boost::graph_traits< BoostGraph >::edge_descriptor BoostEdge
Definition: MeshPartition.h:167
void Nektar::LibUtilities::MeshPartition::GetBndRegionOrdering ( BndRegionOrdering &  composites)

Definition at line 186 of file MeshPartition.cpp.

References m_bndRegOrder.

187  {
188  bndRegs = m_bndRegOrder;
189  }
void Nektar::LibUtilities::MeshPartition::GetCompositeOrdering ( CompositeOrdering &  composites)

Definition at line 176 of file MeshPartition.cpp.

References Nektar::iterator, and m_meshComposites.

177  {
178  std::map<int, MeshEntity>::iterator it;
179  for (it = m_meshComposites.begin();
180  it != m_meshComposites.end(); ++it)
181  {
182  composites[it->first] = it->second.list;
183  }
184  }
Nektar::LibUtilities::MeshPartition::m_meshComposites
std::map< int, MeshEntity > m_meshComposites
Definition: MeshPartition.h:190
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
void Nektar::LibUtilities::MeshPartition::GetElementIDs ( const int  procid,
std::vector< unsigned int > &  tmp 
)

Definition at line 2301 of file MeshPartition.cpp.

References ASSERTL0, m_localPartition, and m_meshElements.

2302  {
2303  BoostVertexIterator vertit, vertit_end;
2304 
2305  ASSERTL0(procid < m_localPartition.size(),"procid is less than the number of partitions");
2306 
2307  // Populate lists of elements, edges and vertices required.
2308  for ( boost::tie(vertit, vertit_end) = boost::vertices(m_localPartition[procid]);
2309  vertit != vertit_end;
2310  ++vertit)
2311  {
2312  elmtid.push_back(m_meshElements[m_localPartition[procid][*vertit].id].id);
2313  }
2314  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::m_localPartition
std::vector< BoostSubGraph > m_localPartition
Definition: MeshPartition.h:209
Nektar::LibUtilities::MeshPartition::BoostVertexIterator
boost::graph_traits< BoostGraph >::vertex_iterator BoostVertexIterator
Definition: MeshPartition.h:173
void Nektar::LibUtilities::MeshPartition::OutputPartition ( LibUtilities::SessionReaderSharedPtr &  pSession,
BoostSubGraph &  pGraph,
TiXmlElement *  pGeometry 
)
private

Definition at line 1474 of file MeshPartition.cpp.

References ASSERTL0, Nektar::LibUtilities::MeshPartition::MeshCurved::data, Nektar::LibUtilities::MeshTri::e, Nektar::LibUtilities::MeshQuad::e, Nektar::LibUtilities::MeshCurvedInfo::entityid, Nektar::LibUtilities::MeshPartition::MeshCurved::entityid, Nektar::LibUtilities::MeshPartition::MeshCurved::entitytype, Nektar::LibUtilities::MeshTet::f, Nektar::LibUtilities::MeshPyr::f, Nektar::LibUtilities::MeshPrism::f, Nektar::LibUtilities::MeshHex::f, Nektar::ParseUtils::GenerateSeqString(), Nektar::ParseUtils::GenerateSeqVector(), Nektar::LibUtilities::CompressData::GetBitSizeStr(), Nektar::LibUtilities::CompressData::GetCompressString(), Nektar::LibUtilities::MeshVertex::id, Nektar::LibUtilities::MeshEdge::id, Nektar::LibUtilities::MeshTri::id, Nektar::LibUtilities::MeshQuad::id, Nektar::LibUtilities::MeshTet::id, Nektar::LibUtilities::MeshPyr::id, Nektar::LibUtilities::MeshPrism::id, Nektar::LibUtilities::MeshHex::id, Nektar::LibUtilities::MeshPartition::MeshCurved::id, Nektar::LibUtilities::MeshCurvedInfo::id, Nektar::LibUtilities::MeshCurvedPts::id, Nektar::LibUtilities::MeshCurvedPts::index, Nektar::iterator, Nektar::LibUtilities::kPointsTypeStr, m_bndRegOrder, m_dim, m_domain, m_isCompressed, m_meshComposites, m_meshCurved, m_meshCurvedPts, m_meshEdges, m_meshElements, m_meshFaces, m_meshVertices, m_vertexAttributes, Nektar::LibUtilities::MeshCurvedInfo::npoints, Nektar::LibUtilities::MeshPartition::MeshCurved::npoints, CellMLToNektar.cellml_metadata::p, Nektar::LibUtilities::MeshCurvedInfo::ptid, Nektar::LibUtilities::MeshPartition::MeshCurved::ptid, Nektar::LibUtilities::MeshCurvedInfo::ptoffset, Nektar::LibUtilities::MeshPartition::MeshCurved::ptoffset, Nektar::LibUtilities::MeshCurvedPts::pts, Nektar::LibUtilities::MeshCurvedInfo::ptype, Nektar::LibUtilities::SIZE_PointsType, Nektar::LibUtilities::MeshPartition::MeshCurved::type, Nektar::LibUtilities::MeshEdge::v0, Nektar::LibUtilities::MeshEdge::v1, Nektar::LibUtilities::MeshVertex::x, Nektar::LibUtilities::MeshVertex::y, Nektar::LibUtilities::MeshVertex::z, and Nektar::LibUtilities::CompressData::ZlibEncodeToBase64Str().

Referenced by WriteAllPartitions(), and WriteLocalPartition().

1478  {
1479  // Write Geometry data
1480  std::string vDim = pSession->GetElement("Nektar/Geometry")->Attribute("DIM");
1481  std::string vSpace = pSession->GetElement("Nektar/Geometry")->Attribute("SPACE");
1482  std::string vPart = boost::lexical_cast<std::string>(pGraph[*boost::vertices(pGraph).first].partition);
1483  TiXmlElement* vElmtGeometry = new TiXmlElement("GEOMETRY");
1484  vElmtGeometry->SetAttribute("DIM", vDim);
1485  vElmtGeometry->SetAttribute("SPACE", vSpace);
1486  vElmtGeometry->SetAttribute("PARTITION", vPart);
1487 
1488  TiXmlElement *vVertex = new TiXmlElement("VERTEX");
1489  TiXmlElement *vEdge = new TiXmlElement("EDGE");
1490  TiXmlElement *vFace = new TiXmlElement("FACE");
1491  TiXmlElement *vElement = new TiXmlElement("ELEMENT");
1492  TiXmlElement *vCurved = new TiXmlElement("CURVED");
1493  TiXmlElement *vComposite = new TiXmlElement("COMPOSITE");
1494  TiXmlElement *vDomain = new TiXmlElement("DOMAIN");
1495 
1496  TiXmlElement *x;
1497  TiXmlText *y;
1498 
1499  BoostVertexIterator vertit, vertit_end;
1500  int id;
1501 
1502  std::map<int, MeshEntity> vComposites;
1503  std::map<int, MeshEntity> vElements;
1504  std::map<int, MeshEntity> vEdges;
1505  std::map<int, MeshEntity> vFaces;
1506  std::map<int, MeshVertex> vVertices;
1507  std::map<int, MeshEntity>::iterator vIt;
1508  std::map<int, MeshVertex>::iterator vVertIt;
1509  std::map<std::string, std::string>::iterator vAttrIt;
1510 
1511  std::vector<unsigned int> idxList;
1512 
1513  // Populate lists of elements, edges and vertices required.
1514  for (boost::tie(vertit, vertit_end) = boost::vertices(pGraph);
1515  vertit != vertit_end;
1516  ++vertit)
1517  {
1518  id = pGraph[*vertit].id;
1519  vElements[id] = m_meshElements[pGraph[*vertit].id];
1520  }
1521 
1522  std::map<int, MeshEntity> * vNext = &vElements;
1523  switch (m_dim)
1524  {
1525  case 3:
1526  {
1527  // Compile list of faces
1528  for (vIt = vNext->begin(); vIt != vNext->end(); vIt++)
1529  {
1530  for (unsigned int j = 0; j < vIt->second.list.size(); ++j)
1531  {
1532  id = vIt->second.list[j];
1533  vFaces[id] = m_meshFaces[id];
1534  }
1535  }
1536  vNext = &vFaces;
1537  }
1538  case 2:
1539  {
1540  // Compile list of edges
1541  for (vIt = vNext->begin(); vIt != vNext->end(); vIt++)
1542  {
1543  for (unsigned int j = 0; j < vIt->second.list.size(); ++j)
1544  {
1545  id = vIt->second.list[j];
1546  vEdges[id] = m_meshEdges[id];
1547  }
1548  }
1549  vNext = &vEdges;
1550  }
1551  case 1:
1552  {
1553  // Compile list of vertices
1554  for (vIt = vNext->begin(); vIt != vNext->end(); vIt++)
1555  {
1556  for (unsigned int j = 0; j < vIt->second.list.size(); ++j)
1557  {
1558  id = vIt->second.list[j];
1559  vVertices[id] = m_meshVertices[id];
1560  }
1561  }
1562  }
1563  }
1564 
1565  // Generate XML data for these mesh entities
1566  if(m_isCompressed)
1567  {
1568  std::vector<MeshVertex> vertInfo;
1569  for (vVertIt = vVertices.begin();
1570  vVertIt != vVertices.end(); vVertIt++)
1571  {
1572  MeshVertex v;
1573  v.id = vVertIt->first;
1574  v.x = vVertIt->second.x;
1575  v.y = vVertIt->second.y;
1576  v.z = vVertIt->second.z;
1577  vertInfo.push_back(v);
1578  }
1579  std::string vertStr;
1580  CompressData::ZlibEncodeToBase64Str(vertInfo,vertStr);
1581  vVertex->SetAttribute("COMPRESSED",
1582  CompressData::GetCompressString());
1583  vVertex->SetAttribute("BITSIZE",
1584  CompressData::GetBitSizeStr());
1585  vVertex->LinkEndChild(new TiXmlText(vertStr));
1586  }
1587  else
1588  {
1589  for (vVertIt = vVertices.begin(); vVertIt != vVertices.end(); vVertIt++)
1590  {
1591  x = new TiXmlElement("V");
1592  x->SetAttribute("ID", vVertIt->first);
1593  std::stringstream vCoords;
1594  vCoords.precision(12);
1595  vCoords << std::setw(15) << vVertIt->second.x << " "
1596  << std::setw(15) << vVertIt->second.y << " "
1597  << std::setw(15) << vVertIt->second.z << " ";
1598  y = new TiXmlText(vCoords.str());
1599  x->LinkEndChild(y);
1600  vVertex->LinkEndChild(x);
1601  }
1602  }
1603 
1604  // Apply transformation attributes to VERTEX section
1605  for (vAttrIt = m_vertexAttributes.begin();
1606  vAttrIt != m_vertexAttributes.end();
1607  ++ vAttrIt)
1608  {
1609  vVertex->SetAttribute(vAttrIt->first, vAttrIt->second);
1610  }
1611 
1612  if (m_dim >= 2)
1613  {
1614  if(m_isCompressed)
1615  {
1616  std::vector<MeshEdge> edgeInfo;
1617  for (vIt = vEdges.begin(); vIt != vEdges.end(); vIt++)
1618  {
1619  MeshEdge e;
1620  e.id = vIt->first;
1621  e.v0 = vIt->second.list[0];
1622  e.v1 = vIt->second.list[1];
1623  edgeInfo.push_back(e);
1624  }
1625  std::string edgeStr;
1626  CompressData::ZlibEncodeToBase64Str(edgeInfo,edgeStr);
1627  vEdge->SetAttribute("COMPRESSED",
1628  CompressData::GetCompressString());
1629  vEdge->SetAttribute("BITSIZE",
1630  CompressData::GetBitSizeStr());
1631  vEdge->LinkEndChild(new TiXmlText(edgeStr));
1632  }
1633  else
1634  {
1635  for (vIt = vEdges.begin(); vIt != vEdges.end(); vIt++)
1636  {
1637  x = new TiXmlElement("E");
1638  x->SetAttribute("ID", vIt->first);
1639  std::stringstream vVertices;
1640  vVertices << std::setw(10) << vIt->second.list[0]
1641  << std::setw(10) << vIt->second.list[1]
1642  << " ";
1643  y = new TiXmlText(vVertices.str());
1644  x->LinkEndChild(y);
1645  vEdge->LinkEndChild(x);
1646  }
1647  }
1648  }
1649 
1650  if (m_dim >= 3)
1651  {
1652 
1653  if(m_isCompressed)
1654  {
1655  std::vector<MeshTri> TriFaceInfo;
1656  std::vector<MeshQuad> QuadFaceInfo;
1657 
1658  for (vIt = vFaces.begin(); vIt != vFaces.end(); vIt++)
1659  {
1660  switch(vIt->second.list.size())
1661  {
1662  case 3:
1663  {
1664  MeshTri f;
1665  f.id = vIt->first;
1666  for(int i = 0; i < 3; ++i)
1667  {
1668  f.e[i] = vIt->second.list[i];
1669  }
1670  TriFaceInfo.push_back(f);
1671  }
1672  break;
1673  case 4:
1674  {
1675  MeshQuad f;
1676  f.id = vIt->first;
1677  for(int i = 0; i < 4; ++i)
1678  {
1679  f.e[i] = vIt->second.list[i];
1680  }
1681  QuadFaceInfo.push_back(f);
1682  }
1683  break;
1684  default:
1685  ASSERTL0(false,"Unknown face type.");
1686  }
1687  }
1688 
1689  if(TriFaceInfo.size())
1690  {
1691  std::string vType("T");
1692  x = new TiXmlElement(vType);
1693 
1694  std::string faceStr;
1695  CompressData::ZlibEncodeToBase64Str(TriFaceInfo,
1696  faceStr);
1697  x->SetAttribute("COMPRESSED",
1698  CompressData::GetCompressString());
1699  x->SetAttribute("BITSIZE",
1700  CompressData::GetBitSizeStr());
1701  x->LinkEndChild(new TiXmlText(faceStr));
1702  vFace->LinkEndChild(x);
1703  }
1704 
1705  if(QuadFaceInfo.size())
1706  {
1707  std::string vType("Q");
1708  x = new TiXmlElement(vType);
1709  std::string faceStr;
1710  CompressData::ZlibEncodeToBase64Str(QuadFaceInfo,
1711  faceStr);
1712  x->SetAttribute("COMPRESSED",
1713  CompressData::GetCompressString());
1714  x->SetAttribute("BITSIZE",
1715  CompressData::GetBitSizeStr());
1716  x->LinkEndChild(new TiXmlText(faceStr));
1717  vFace->LinkEndChild(x);
1718  }
1719  }
1720  else
1721  {
1722  for (vIt = vFaces.begin(); vIt != vFaces.end(); vIt++)
1723  {
1724  std::string vType("F");
1725  vType[0] = vIt->second.type;
1726  x = new TiXmlElement(vType);
1727  x->SetAttribute("ID", vIt->first);
1728  std::stringstream vListStr;
1729  for (unsigned int i = 0; i < vIt->second.list.size(); ++i)
1730  {
1731  vListStr << std::setw(10) << vIt->second.list[i];
1732  }
1733  vListStr << " ";
1734  y = new TiXmlText(vListStr.str());
1735  x->LinkEndChild(y);
1736  vFace->LinkEndChild(x);
1737  }
1738  }
1739  }
1740 
1741 
1742  if(m_isCompressed)
1743  {
1744  std::vector<MeshEdge> SegInfo;
1745  std::vector<MeshTri> TriInfo;
1746  std::vector<MeshQuad> QuadInfo;
1747  std::vector<MeshTet> TetInfo;
1748  std::vector<MeshPyr> PyrInfo;
1749  std::vector<MeshPrism> PrismInfo;
1750  std::vector<MeshHex> HexInfo;
1751 
1752  //gather elemements in groups.
1753  for (vIt = vElements.begin(); vIt != vElements.end(); vIt++)
1754  {
1755  switch(vIt->second.type)
1756  {
1757  case 'S':
1758  {
1759  MeshEdge e;
1760  e.id = vIt->first;
1761  e.v0 = vIt->second.list[0];
1762  e.v1 = vIt->second.list[1];
1763  SegInfo.push_back(e);
1764  }
1765  break;
1766  case 'T':
1767  {
1768  MeshTri f;
1769  f.id = vIt->first;
1770  for(int i = 0; i < 3; ++i)
1771  {
1772  f.e[i] = vIt->second.list[i];
1773  }
1774  TriInfo.push_back(f);
1775  }
1776  break;
1777  case 'Q':
1778  {
1779  MeshQuad f;
1780  f.id = vIt->first;
1781  for(int i = 0; i < 4; ++i)
1782  {
1783  f.e[i] = vIt->second.list[i];
1784  }
1785  QuadInfo.push_back(f);
1786  }
1787  break;
1788  case 'A':
1789  {
1790  MeshTet vol;
1791  vol.id = vIt->first;
1792  for(int i = 0; i < 4; ++i)
1793  {
1794  vol.f[i] = vIt->second.list[i];
1795  }
1796  TetInfo.push_back(vol);
1797  }
1798  break;
1799  case 'P':
1800  {
1801  MeshPyr vol;
1802  vol.id = vIt->first;
1803  for(int i = 0; i < 5; ++i)
1804  {
1805  vol.f[i] = vIt->second.list[i];
1806  }
1807  PyrInfo.push_back(vol);
1808  }
1809  break;
1810  case 'R':
1811  {
1812  MeshPrism vol;
1813  vol.id = vIt->first;
1814  for(int i = 0; i < 5; ++i)
1815  {
1816  vol.f[i] = vIt->second.list[i];
1817  }
1818  PrismInfo.push_back(vol);
1819  }
1820  break;
1821  case 'H':
1822  {
1823  MeshHex vol;
1824  vol.id = vIt->first;
1825  for(int i = 0; i < 6; ++i)
1826  {
1827  vol.f[i] = vIt->second.list[i];
1828  }
1829  HexInfo.push_back(vol);
1830  }
1831  break;
1832  default:
1833  ASSERTL0(false,"Unknown element type");
1834  }
1835  }
1836 
1837  if(SegInfo.size())
1838  {
1839  std::string vType("S");
1840  x = new TiXmlElement(vType);
1841 
1842  std::string segStr;
1843  CompressData::ZlibEncodeToBase64Str(SegInfo,segStr);
1844  x->SetAttribute("COMPRESSED",
1845  CompressData::GetCompressString());
1846  x->SetAttribute("BITSIZE",
1847  CompressData::GetBitSizeStr());
1848  x->LinkEndChild(new TiXmlText(segStr));
1849  vElement->LinkEndChild(x);
1850  }
1851 
1852  if(TriInfo.size())
1853  {
1854  std::string vType("T");
1855  x = new TiXmlElement(vType);
1856 
1857  std::string faceStr;
1858  CompressData::ZlibEncodeToBase64Str(TriInfo,faceStr);
1859  x->SetAttribute("COMPRESSED",
1860  CompressData::GetCompressString());
1861  x->SetAttribute("BITSIZE",
1862  CompressData::GetBitSizeStr());
1863  x->LinkEndChild(new TiXmlText(faceStr));
1864  vElement->LinkEndChild(x);
1865  }
1866 
1867  if(QuadInfo.size())
1868  {
1869  std::string vType("Q");
1870  x = new TiXmlElement(vType);
1871  std::string faceStr;
1872  CompressData::ZlibEncodeToBase64Str(QuadInfo,faceStr);
1873  x->SetAttribute("COMPRESSED",
1874  CompressData::GetCompressString());
1875  x->SetAttribute("BITSIZE",
1876  CompressData::GetBitSizeStr());
1877  x->LinkEndChild(new TiXmlText(faceStr));
1878  vElement->LinkEndChild(x);
1879  }
1880 
1881  if(TetInfo.size())
1882  {
1883  std::string vType("A");
1884  x = new TiXmlElement(vType);
1885  std::string volStr;
1886  CompressData::ZlibEncodeToBase64Str(TetInfo,volStr);
1887  x->SetAttribute("COMPRESSED",
1888  CompressData::GetCompressString());
1889  x->SetAttribute("BITSIZE",
1890  CompressData::GetBitSizeStr());
1891  x->LinkEndChild(new TiXmlText(volStr));
1892  vElement->LinkEndChild(x);
1893  }
1894 
1895  if(PyrInfo.size())
1896  {
1897  std::string vType("P");
1898  x = new TiXmlElement(vType);
1899  std::string volStr;
1900  CompressData::ZlibEncodeToBase64Str(PyrInfo,volStr);
1901  x->SetAttribute("COMPRESSED",
1902  CompressData::GetCompressString());
1903  x->SetAttribute("BITSIZE",
1904  CompressData::GetBitSizeStr());
1905  x->LinkEndChild(new TiXmlText(volStr));
1906  vElement->LinkEndChild(x);
1907  }
1908 
1909  if(PrismInfo.size())
1910  {
1911  std::string vType("R");
1912  x = new TiXmlElement(vType);
1913  std::string volStr;
1914  CompressData::ZlibEncodeToBase64Str(PrismInfo,volStr);
1915  x->SetAttribute("COMPRESSED",
1916  CompressData::GetCompressString());
1917  x->SetAttribute("BITSIZE",
1918  CompressData::GetBitSizeStr());
1919  x->LinkEndChild(new TiXmlText(volStr));
1920  vElement->LinkEndChild(x);
1921  }
1922 
1923  if(HexInfo.size())
1924  {
1925  std::string vType("H");
1926  x = new TiXmlElement(vType);
1927  std::string volStr;
1928  CompressData::ZlibEncodeToBase64Str(HexInfo,volStr);
1929  x->SetAttribute("COMPRESSED",
1930  CompressData::GetCompressString());
1931  x->SetAttribute("BITSIZE",
1932  CompressData::GetBitSizeStr());
1933  x->LinkEndChild(new TiXmlText(volStr));
1934  vElement->LinkEndChild(x);
1935  }
1936 
1937  }
1938  else
1939  {
1940  for (vIt = vElements.begin(); vIt != vElements.end(); vIt++)
1941  {
1942  std::string vType("T");
1943  vType[0] = vIt->second.type;
1944  x = new TiXmlElement(vType.c_str());
1945  x->SetAttribute("ID", vIt->first);
1946  std::stringstream vEdges;
1947  for (unsigned i = 0; i < vIt->second.list.size(); ++i)
1948  {
1949  vEdges << std::setw(10) << vIt->second.list[i];
1950  }
1951  vEdges << " ";
1952  y = new TiXmlText(vEdges.str());
1953  x->LinkEndChild(y);
1954  vElement->LinkEndChild(x);
1955  }
1956  }
1957 
1958  if (m_dim >= 2)
1959  {
1960  std::map<MeshCurvedKey, MeshCurved>::const_iterator vItCurve;
1961 
1962  if(m_isCompressed)
1963  {
1964  std::vector<MeshCurvedInfo> edgeinfo;
1965  std::vector<MeshCurvedInfo> faceinfo;
1966  MeshCurvedPts curvedpts;
1967  curvedpts.id = 0; // assume all points are going in here
1968  int ptoffset = 0;
1969  int newidx = 0;
1970  std::map<int,int> idxmap;
1971 
1972  for (vItCurve = m_meshCurved.begin();
1973  vItCurve != m_meshCurved.end();
1974  ++vItCurve)
1975  {
1976  MeshCurved c = vItCurve->second;
1977 
1978  bool IsEdge = boost::iequals(c.entitytype,"E");
1979  bool IsFace = boost::iequals(c.entitytype,"F");
1980 
1981  if((IsEdge&&vEdges.find(c.entityid) != vEdges.end())||
1982  (IsFace&&vFaces.find(c.entityid) != vFaces.end()))
1983  {
1984  MeshCurvedInfo cinfo;
1985  // add in
1986  cinfo.id = c.id;
1987  cinfo.entityid = c.entityid;
1988  cinfo.npoints = c.npoints;
1989  for(int i = 0; i < SIZE_PointsType; ++i)
1990  {
1991  if(c.type.compare(kPointsTypeStr[i]) == 0)
1992  {
1993  cinfo.ptype = (PointsType) i;
1994  break;
1995  }
1996  }
1997  cinfo.ptid = 0; // set to just one point set
1998  cinfo.ptoffset = ptoffset;
1999  ptoffset += c.npoints;
2000 
2001  if (IsEdge)
2002  {
2003  edgeinfo.push_back(cinfo);
2004  }
2005  else
2006  {
2007  faceinfo.push_back(cinfo);
2008  }
2009 
2010  // fill in points to list.
2011  for(int i =0; i < c.npoints; ++i)
2012  {
2013  // get index from full list;
2014  int idx = m_meshCurvedPts[c.ptid]
2015  .index[c.ptoffset+i];
2016 
2017  // if index is not already in curved
2018  // points add it or set index to location
2019  if(idxmap.count(idx) == 0)
2020  {
2021  idxmap[idx] = newidx;
2022  curvedpts.index.push_back(newidx);
2023  curvedpts.pts.push_back(
2024  m_meshCurvedPts[c.ptid].pts[idx]);
2025  newidx++;
2026  }
2027  else
2028  {
2029  curvedpts.index.push_back(idxmap[idx]);
2030  }
2031  }
2032  }
2033  }
2034 
2035  // add xml information
2036  if(edgeinfo.size())
2037  {
2038  vCurved->SetAttribute("COMPRESSED",
2039  CompressData::GetCompressString());
2040  vCurved->SetAttribute("BITSIZE",
2041  CompressData::GetBitSizeStr());
2042 
2043  x = new TiXmlElement("E");
2044  std::string dataStr;
2045  CompressData::ZlibEncodeToBase64Str(edgeinfo,dataStr);
2046  x->LinkEndChild(new TiXmlText(dataStr));
2047  vCurved->LinkEndChild(x);
2048  }
2049 
2050  if(faceinfo.size())
2051  {
2052  vCurved->SetAttribute("COMPRESSED",
2053  CompressData::GetCompressString());
2054  vCurved->SetAttribute("BITSIZE",
2055  CompressData::GetBitSizeStr());
2056 
2057  x = new TiXmlElement("F");
2058  std::string dataStr;
2059  CompressData::ZlibEncodeToBase64Str(faceinfo,dataStr);
2060  x->LinkEndChild(new TiXmlText(dataStr));
2061  vCurved->LinkEndChild(x);
2062  }
2063 
2064  if(edgeinfo.size()||faceinfo.size())
2065  {
2066  x = new TiXmlElement("DATAPOINTS");
2067  x->SetAttribute("ID", curvedpts.id);
2068 
2069  TiXmlElement *subx = new TiXmlElement("INDEX");
2070  std::string dataStr;
2071  CompressData::ZlibEncodeToBase64Str(curvedpts.index,
2072  dataStr);
2073  subx->LinkEndChild(new TiXmlText(dataStr));
2074  x->LinkEndChild(subx);
2075 
2076  subx = new TiXmlElement("POINTS");
2077  CompressData::ZlibEncodeToBase64Str(curvedpts.pts,
2078  dataStr);
2079  subx->LinkEndChild(new TiXmlText(dataStr));
2080  x->LinkEndChild(subx);
2081 
2082  vCurved->LinkEndChild(x);
2083  }
2084  }
2085  else
2086  {
2087  for (vItCurve = m_meshCurved.begin();
2088  vItCurve != m_meshCurved.end();
2089  ++vItCurve)
2090  {
2091  MeshCurved c = vItCurve->second;
2092 
2093  bool IsEdge = boost::iequals(c.entitytype,"E");
2094  bool IsFace = boost::iequals(c.entitytype,"F");
2095 
2096  if((IsEdge&&vEdges.find(c.entityid) != vEdges.end())||
2097  (IsFace&&vFaces.find(c.entityid) != vFaces.end()))
2098  {
2099  x = new TiXmlElement(c.entitytype);
2100  x->SetAttribute("ID", c.id);
2101  if (IsEdge)
2102  {
2103  x->SetAttribute("EDGEID", c.entityid);
2104  }
2105  else
2106  {
2107  x->SetAttribute("FACEID", c.entityid);
2108  }
2109  x->SetAttribute("TYPE", c.type);
2110  x->SetAttribute("NUMPOINTS", c.npoints);
2111  y = new TiXmlText(c.data);
2112  x->LinkEndChild(y);
2113  vCurved->LinkEndChild(x);
2114  }
2115  }
2116  }
2117  }
2118 
2119  // Generate composites section comprising only those mesh entities
2120  // which belong to this partition.
2121  for (vIt = m_meshComposites.begin(); vIt != m_meshComposites.end(); ++vIt)
2122  {
2123  idxList.clear();
2124 
2125  for (unsigned int j = 0; j < vIt->second.list.size(); ++j)
2126  {
2127  // Based on entity type, check if in this partition
2128  switch (vIt->second.type)
2129  {
2130  case 'V':
2131  if (vVertices.find(vIt->second.list[j]) == vVertices.end())
2132  {
2133  continue;
2134  }
2135  break;
2136  case 'E':
2137  if (vEdges.find(vIt->second.list[j]) == vEdges.end())
2138  {
2139  continue;
2140  }
2141  break;
2142  case 'F':
2143  if (vFaces.find(vIt->second.list[j]) == vFaces.end())
2144  {
2145  continue;
2146  }
2147  break;
2148  default:
2149  if (vElements.find(vIt->second.list[j]) == vElements.end())
2150  {
2151  continue;
2152  }
2153  break;
2154  }
2155 
2156  idxList.push_back(vIt->second.list[j]);
2157  }
2158 
2159  std::string vCompositeStr = ParseUtils::GenerateSeqString(idxList);
2160 
2161  if (vCompositeStr.length() > 0)
2162  {
2163  vComposites[vIt->first] = vIt->second;
2164  x = new TiXmlElement("C");
2165  x->SetAttribute("ID", vIt->first);
2166  vCompositeStr = "X[" + vCompositeStr + "]";
2167  vCompositeStr[0] = vIt->second.type;
2168  y = new TiXmlText(vCompositeStr.c_str());
2169  x->LinkEndChild(y);
2170  vComposite->LinkEndChild(x);
2171  }
2172  }
2173 
2174  idxList.clear();
2175  std::string vDomainListStr;
2176  for (unsigned int i = 0; i < m_domain.size(); ++i)
2177  {
2178  if (vComposites.find(m_domain[i]) != vComposites.end())
2179  {
2180  idxList.push_back(m_domain[i]);
2181  }
2182  }
2183  vDomainListStr = "C[" + ParseUtils::GenerateSeqString(idxList) + "]";
2184  TiXmlText* vDomainList = new TiXmlText(vDomainListStr);
2185  vDomain->LinkEndChild(vDomainList);
2186 
2187  vElmtGeometry->LinkEndChild(vVertex);
2188  if (m_dim >= 2)
2189  {
2190  vElmtGeometry->LinkEndChild(vEdge);
2191  }
2192  if (m_dim >= 3)
2193  {
2194  vElmtGeometry->LinkEndChild(vFace);
2195  }
2196  vElmtGeometry->LinkEndChild(vElement);
2197  if (m_dim >= 2)
2198  {
2199  vElmtGeometry->LinkEndChild(vCurved);
2200  }
2201  vElmtGeometry->LinkEndChild(vComposite);
2202  vElmtGeometry->LinkEndChild(vDomain);
2203 
2204  pNektar->LinkEndChild(vElmtGeometry);
2205 
2206  if (pSession->DefinesElement("Nektar/Conditions"))
2207  {
2208  std::set<int> vBndRegionIdList;
2209  TiXmlElement* vConditions = new TiXmlElement(*pSession->GetElement("Nektar/Conditions"));
2210  TiXmlElement* vBndRegions = vConditions->FirstChildElement("BOUNDARYREGIONS");
2211  TiXmlElement* vBndConditions = vConditions->FirstChildElement("BOUNDARYCONDITIONS");
2212  TiXmlElement* vItem;
2213 
2214  if (vBndRegions)
2215  {
2216  TiXmlElement* vNewBndRegions = new TiXmlElement("BOUNDARYREGIONS");
2217  vItem = vBndRegions->FirstChildElement();
2218  while (vItem)
2219  {
2220  std::string vSeqStr = vItem->FirstChild()->ToText()->Value();
2221  std::string::size_type indxBeg = vSeqStr.find_first_of('[') + 1;
2222  std::string::size_type indxEnd = vSeqStr.find_last_of(']') - 1;
2223  vSeqStr = vSeqStr.substr(indxBeg, indxEnd - indxBeg + 1);
2224  std::vector<unsigned int> vSeq;
2225  ParseUtils::GenerateSeqVector(vSeqStr.c_str(), vSeq);
2226 
2227  idxList.clear();
2228 
2229  for (unsigned int i = 0; i < vSeq.size(); ++i)
2230  {
2231  if (vComposites.find(vSeq[i]) != vComposites.end())
2232  {
2233  idxList.push_back(vSeq[i]);
2234  }
2235  }
2236  int p = atoi(vItem->Attribute("ID"));
2237 
2238  std::string vListStr = ParseUtils::GenerateSeqString(idxList);
2239 
2240  if (vListStr.length() == 0)
2241  {
2242  TiXmlElement* tmp = vItem;
2243  vItem = vItem->NextSiblingElement();
2244  vBndRegions->RemoveChild(tmp);
2245  }
2246  else
2247  {
2248  vListStr = "C[" + vListStr + "]";
2249  TiXmlText* vList = new TiXmlText(vListStr);
2250  TiXmlElement* vNewElement = new TiXmlElement("B");
2251  vNewElement->SetAttribute("ID", p);
2252  vNewElement->LinkEndChild(vList);
2253  vNewBndRegions->LinkEndChild(vNewElement);
2254  vBndRegionIdList.insert(p);
2255  vItem = vItem->NextSiblingElement();
2256  }
2257 
2258  // Store original order of boundary region.
2259  m_bndRegOrder[p] = vSeq;
2260 
2261  }
2262  vConditions->ReplaceChild(vBndRegions, *vNewBndRegions);
2263  }
2264 
2265  if (vBndConditions)
2266  {
2267  vItem = vBndConditions->FirstChildElement();
2268  while (vItem)
2269  {
2270  std::set<int>::iterator x;
2271  if ((x = vBndRegionIdList.find(atoi(vItem->Attribute("REF")))) != vBndRegionIdList.end())
2272  {
2273  vItem->SetAttribute("REF", *x);
2274  vItem = vItem->NextSiblingElement();
2275  }
2276  else
2277  {
2278  TiXmlElement* tmp = vItem;
2279  vItem = vItem->NextSiblingElement();
2280  vBndConditions->RemoveChild(tmp);
2281  }
2282  }
2283  }
2284  pNektar->LinkEndChild(vConditions);
2285  }
2286 
2287  // Distribute other sections of the XML to each process as is.
2288  TiXmlElement* vSrc = pSession->GetElement("Nektar")
2289  ->FirstChildElement();
2290  while (vSrc)
2291  {
2292  std::string vName = boost::to_upper_copy(vSrc->ValueStr());
2293  if (vName != "GEOMETRY" && vName != "CONDITIONS")
2294  {
2295  pNektar->LinkEndChild(new TiXmlElement(*vSrc));
2296  }
2297  vSrc = vSrc->NextSiblingElement();
2298  }
2299  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::m_vertexAttributes
std::map< std::string, std::string > m_vertexAttributes
Definition: MeshPartition.h:192
Nektar::LibUtilities::MeshPartition::m_meshComposites
std::map< int, MeshEntity > m_meshComposites
Definition: MeshPartition.h:190
Nektar::LibUtilities::kPointsTypeStr
const std::string kPointsTypeStr[]
Definition: Foundations.hpp:69
Nektar::LibUtilities::MeshPartition::m_meshVertices
std::map< int, MeshVertex > m_meshVertices
Definition: MeshPartition.h:184
Nektar::ParseUtils::GenerateSeqString
static std::string GenerateSeqString(const std::vector< unsigned int > &elmtids)
Definition: ParseUtils.hpp:159
Nektar::LibUtilities::MeshPartition::m_meshCurved
std::map< MeshCurvedKey, MeshCurved > m_meshCurved
Definition: MeshPartition.h:188
Nektar::ParseUtils::GenerateSeqVector
static bool GenerateSeqVector(const char *const str, std::vector< unsigned int > &vec)
Definition: ParseUtils.hpp:79
CellMLToNektar.cellml_metadata.p
tuple p
Definition: cellml_metadata.py:350
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::m_domain
std::vector< unsigned int > m_domain
Definition: MeshPartition.h:191
Nektar::LibUtilities::CompressData::ZlibEncodeToBase64Str
int ZlibEncodeToBase64Str(std::vector< T > &in, std::string &out64)
Definition: CompressData.h:151
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
Nektar::LibUtilities::MeshPartition::m_meshEdges
std::map< int, MeshEntity > m_meshEdges
Definition: MeshPartition.h:185
Nektar::LibUtilities::MeshPartition::m_meshFaces
std::map< int, MeshEntity > m_meshFaces
Definition: MeshPartition.h:186
Nektar::LibUtilities::MeshPartition::BoostVertexIterator
boost::graph_traits< BoostGraph >::vertex_iterator BoostVertexIterator
Definition: MeshPartition.h:173
Nektar::LibUtilities::MeshPartition::m_meshCurvedPts
std::map< int, MeshCurvedPts > m_meshCurvedPts
Definition: MeshPartition.h:189
void Nektar::LibUtilities::MeshPartition::PartitionGraph ( BoostSubGraph &  pGraph,
int  nParts,
std::vector< BoostSubGraph > &  pLocalPartition,
bool  overlapping = false 
)
private

Partition the graph.

This routine partitions the graph pGraph into nParts, producing subgraphs that are populated in pLocalPartition. If the overlapping option is set (which is used for post-processing purposes), the resulting partitions are extended to cover neighbouring elements by additional vertex on the dual graph, which produces overlapping partitions (i.e. the intersection of two connected partitions is non-empty).

Parameters
pGraphGraph to be partitioned.
nPartsNumber of partitions.
pLocalPartitionVector of sub-graphs representing each partition.
overlappingTrue if resulting partitions should overlap.

Definition at line 1291 of file MeshPartition.cpp.

References CheckPartitions(), ErrorUtil::efatal, m_comm, m_shared, m_weightBnd, m_weightDofs, m_weightingRequired, NEKERROR, and PartitionGraphImpl().

Referenced by PartitionMesh().

1295  {
1296  int i;
1297  int nGraphVerts = boost::num_vertices(pGraph);
1298  int nGraphEdges = boost::num_edges(pGraph);
1299 
1300  int ncon = 1;
1301  if (m_weightDofs && m_weightBnd)
1302  {
1303  ncon = 2;
1304  }
1305  // Convert boost graph into CSR format
1306  BoostVertexIterator vertit, vertit_end;
1307  BoostAdjacencyIterator adjvertit, adjvertit_end;
1308  Array<OneD, int> part(nGraphVerts,0);
1309 
1310  if (m_comm->GetRowComm()->TreatAsRankZero())
1311  {
1312  int acnt = 0;
1313  int vcnt = 0;
1314  int nWeight = ncon*nGraphVerts;
1315  Array<OneD, int> xadj(nGraphVerts+1,0);
1316  Array<OneD, int> adjncy(2*nGraphEdges);
1317  Array<OneD, int> adjwgt(2*nGraphEdges, 1);
1318  Array<OneD, int> vwgt(nWeight, 1);
1319  Array<OneD, int> vsize(nGraphVerts, 1);
1320 
1321  for ( boost::tie(vertit, vertit_end) = boost::vertices(pGraph);
1322  vertit != vertit_end;
1323  ++vertit)
1324  {
1325  for ( boost::tie(adjvertit, adjvertit_end) = boost::adjacent_vertices(*vertit,pGraph);
1326  adjvertit != adjvertit_end;
1327  ++adjvertit)
1328  {
1329  adjncy[acnt++] = *adjvertit;
1330  if (m_weightingRequired)
1331  {
1332  adjwgt[acnt-1] = pGraph[*vertit].edgeWeight[0];
1333  }
1334  }
1335 
1336  xadj[++vcnt] = acnt;
1337 
1338  if (m_weightingRequired)
1339  {
1340  int ccnt = 0;
1341  if (m_weightDofs)
1342  {
1343  vwgt[ncon*(vcnt-1)+ccnt] = pGraph[*vertit].weight[0];
1344  ccnt++;
1345  }
1346  if (m_weightBnd)
1347  {
1348  vwgt[ncon*(vcnt-1)+ccnt] = pGraph[*vertit].bndWeight[0];
1349  }
1350  }
1351  }
1352 
1353  // Call Metis and partition graph
1354  int vol = 0;
1355 
1356  try
1357  {
1358  //////////////////////////////////////////////////////
1359  // On a cartesian communicator do mesh partiotion just on the first column
1360  // so there is no doubt the partitions are all the same in all the columns
1361  if(m_comm->GetColumnComm()->GetRank() == 0)
1362  {
1363  // Attempt partitioning using METIS.
1364  PartitionGraphImpl(nGraphVerts, ncon, xadj, adjncy, vwgt, vsize, adjwgt, nParts, vol, part);
1365 
1366  // Check METIS produced a valid partition and fix if not.
1367  CheckPartitions(nParts, part);
1368  if (!m_shared)
1369  {
1370  // distribute among columns
1371  for (i = 1; i < m_comm->GetColumnComm()->GetSize(); ++i)
1372  {
1373  m_comm->GetColumnComm()->Send(i, part);
1374  }
1375  }
1376  }
1377  else
1378  {
1379  m_comm->GetColumnComm()->Recv(0, part);
1380  }
1381  if (!m_shared)
1382  {
1383  m_comm->GetColumnComm()->Block();
1384 
1385  //////////////////////////////////
1386  // distribute among rows
1387  for (i = 1; i < m_comm->GetRowComm()->GetSize(); ++i)
1388  {
1389  m_comm->GetRowComm()->Send(i, part);
1390  }
1391  }
1392  }
1393  catch (...)
1394  {
1395  NEKERROR(ErrorUtil::efatal,
1396  "Error in calling metis to partition graph.");
1397  }
1398  }
1399  else
1400  {
1401  m_comm->GetRowComm()->Recv(0, part);
1402  }
1403 
1404  // Create boost subgraph for this process's partitions
1405  int nCols = nParts;
1406  pLocalPartition.resize(nCols);
1407  for (i = 0; i < nCols; ++i)
1408  {
1409  pLocalPartition[i] = pGraph.create_subgraph();
1410  }
1411 
1412  // Populate subgraph
1413  i = 0;
1414  for ( boost::tie(vertit, vertit_end) = boost::vertices(pGraph);
1415  vertit != vertit_end;
1416  ++vertit, ++i)
1417  {
1418  pGraph[*vertit].partition = part[i];
1419  boost::add_vertex(i, pLocalPartition[part[i]]);
1420  }
1421 
1422  // If the overlapping option is set (for post-processing purposes),
1423  // add vertices that correspond to the neighbouring elements.
1424  if (overlapping)
1425  {
1426  for ( boost::tie(vertit, vertit_end) = boost::vertices(pGraph);
1427  vertit != vertit_end;
1428  ++vertit)
1429  {
1430  for (boost::tie(adjvertit, adjvertit_end) = boost::adjacent_vertices(*vertit,pGraph);
1431  adjvertit != adjvertit_end; ++adjvertit)
1432  {
1433  if(part[*adjvertit] != part[*vertit])
1434  {
1435  boost::add_vertex(*adjvertit, pLocalPartition[part[*vertit]]);
1436  }
1437  }
1438  }
1439  }
1440  }
NEKERROR
#define NEKERROR(type, msg)
Assert Level 0 – Fundamental assert which is used whether in FULLDEBUG, DEBUG or OPT compilation mod...
Definition: ErrorUtil.hpp:191
Nektar::LibUtilities::MeshPartition::CheckPartitions
void CheckPartitions(int nParts, Array< OneD, int > &pPart)
Definition: MeshPartition.cpp:1443
Nektar::LibUtilities::MeshPartition::PartitionGraphImpl
virtual void PartitionGraphImpl(int &nVerts, int &nVertConds, Nektar::Array< Nektar::OneD, int > &xadj, Nektar::Array< Nektar::OneD, int > &adjcy, Nektar::Array< Nektar::OneD, int > &vertWgt, Nektar::Array< Nektar::OneD, int > &vertSize, Nektar::Array< Nektar::OneD, int > &edgeWgt, int &nparts, int &volume, Nektar::Array< Nektar::OneD, int > &part)=0
Nektar::LibUtilities::MeshPartition::BoostAdjacencyIterator
boost::graph_traits< BoostGraph >::adjacency_iterator BoostAdjacencyIterator
Definition: MeshPartition.h:176
Nektar::LibUtilities::MeshPartition::BoostVertexIterator
boost::graph_traits< BoostGraph >::vertex_iterator BoostVertexIterator
Definition: MeshPartition.h:173
virtual void Nektar::LibUtilities::MeshPartition::PartitionGraphImpl ( int &  nVerts,
int &  nVertConds,
Nektar::Array< Nektar::OneD, int > &  xadj,
Nektar::Array< Nektar::OneD, int > &  adjcy,
Nektar::Array< Nektar::OneD, int > &  vertWgt,
Nektar::Array< Nektar::OneD, int > &  vertSize,
Nektar::Array< Nektar::OneD, int > &  edgeWgt,
int &  nparts,
int &  volume,
Nektar::Array< Nektar::OneD, int > &  part 
)
privatepure virtual

Implemented in Nektar::LibUtilities::MeshPartitionScotch, and Nektar::LibUtilities::MeshPartitionMetis.

Referenced by PartitionGraph().

void Nektar::LibUtilities::MeshPartition::PartitionMesh ( int  nParts,
bool  shared = false,
bool  overlapping = false 
)

Definition at line 98 of file MeshPartition.cpp.

References ASSERTL0, CreateGraph(), m_localPartition, m_mesh, m_meshElements, m_shared, m_weightingRequired, PartitionGraph(), and WeightElements().

100  {
101  ASSERTL0(m_meshElements.size() >= nParts,
102  "Too few elements for this many processes.");
103  m_shared = shared;
104 
105  if (m_weightingRequired)
106  {
107  WeightElements();
108  }
109  CreateGraph(m_mesh);
110  PartitionGraph(m_mesh, nParts, m_localPartition, overlapping);
111  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::CreateGraph
void CreateGraph(BoostSubGraph &pGraph)
Definition: MeshPartition.cpp:1232
Nektar::LibUtilities::MeshPartition::m_localPartition
std::vector< BoostSubGraph > m_localPartition
Definition: MeshPartition.h:209
Nektar::LibUtilities::MeshPartition::PartitionGraph
void PartitionGraph(BoostSubGraph &pGraph, int nParts, std::vector< BoostSubGraph > &pLocalPartition, bool overlapping=false)
Partition the graph.
Definition: MeshPartition.cpp:1291
void Nektar::LibUtilities::MeshPartition::PrintPartInfo ( std::ostream &  out)

Definition at line 1031 of file MeshPartition.cpp.

References ASSERTL0, CalculateElementWeight(), Nektar::iterator, m_dim, m_expansions, m_localPartition, m_mesh, and m_shape.

1032  {
1033  int nElmt = boost::num_vertices(m_mesh);
1034  int nPart = m_localPartition.size();
1035 
1036  out << "# Partition information:" << std::endl;
1037  out << "# No. elements : " << nElmt << std::endl;
1038  out << "# No. partitions: " << nPart << std::endl;
1039  out << "# ID nElmt nLocDof nBndDof" << std::endl;
1040 
1041  BoostVertexIterator vertit, vertit_end;
1042  std::vector<int> partElmtCount(nPart, 0);
1043  std::vector<int> partLocCount (nPart, 0);
1044  std::vector<int> partBndCount (nPart, 0);
1045 
1046  std::map<int, int> elmtSizes;
1047  std::map<int, int> elmtBndSizes;
1048 
1049  for (std::map<int, NummodesPerField>::iterator expIt =
1050  m_expansions.begin(); expIt != m_expansions.end(); ++expIt)
1051  {
1052  int elid = expIt->first;
1053  NummodesPerField npf = expIt->second;
1054 
1055  for (NummodesPerField::iterator it = npf.begin(); it != npf.end(); ++it)
1056  {
1057  ASSERTL0(it->second.size() == m_dim,
1058  " Number of directional" \
1059  " modes in expansion spec for element id = " +
1060  boost::lexical_cast<std::string>(elid) +
1061  " and field " +
1062  boost::lexical_cast<std::string>(it->first) +
1063  " does not correspond to mesh dimension");
1064 
1065  int na = it->second[0];
1066  int nb = 0;
1067  int nc = 0;
1068  if (m_dim >= 2)
1069  {
1070  nb = it->second[1];
1071  }
1072  if (m_dim == 3)
1073  {
1074  nc = it->second[2];
1075  }
1076 
1077  elmtSizes[elid] = CalculateElementWeight(
1078  m_shape[elid], false, na, nb, nc);
1079  elmtBndSizes[elid] = CalculateElementWeight(
1080  m_shape[elid], true, na, nb, nc);
1081  }
1082  }
1083 
1084  for (boost::tie(vertit, vertit_end) = boost::vertices(m_mesh);
1085  vertit != vertit_end; ++vertit)
1086  {
1087  int partId = m_mesh[*vertit].partition;
1088  partElmtCount[partId]++;
1089  partLocCount [partId] += elmtSizes[m_mesh[*vertit].id];
1090  partBndCount [partId] += elmtBndSizes[m_mesh[*vertit].id];
1091  }
1092 
1093  for (int i = 0; i < nPart; ++i)
1094  {
1095  out << i << " " << partElmtCount[i] << " " << partLocCount[i] << " " << partBndCount[i] << std::endl;
1096  }
1097  }
Nektar::LibUtilities::MeshPartition::CalculateElementWeight
int CalculateElementWeight(char elmtType, bool bndWeight, int na, int nb, int nc)
Definition: MeshPartition.cpp:2316
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::NummodesPerField
std::map< std::string, NumModes > NummodesPerField
Definition: MeshPartition.h:179
Nektar::LibUtilities::MeshPartition::m_expansions
std::map< int, NummodesPerField > m_expansions
Definition: MeshPartition.h:196
Nektar::LibUtilities::MeshPartition::m_localPartition
std::vector< BoostSubGraph > m_localPartition
Definition: MeshPartition.h:209
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
Nektar::LibUtilities::MeshPartition::BoostVertexIterator
boost::graph_traits< BoostGraph >::vertex_iterator BoostVertexIterator
Definition: MeshPartition.h:173
void Nektar::LibUtilities::MeshPartition::ReadConditions ( const SessionReaderSharedPtr &  pSession)
private

Definition at line 1099 of file MeshPartition.cpp.

References ASSERTL0, m_weightBnd, m_weightDofs, and m_weightingRequired.

Referenced by MeshPartition().

1100  {
1101  if (!pSession->DefinesElement("Nektar/Conditions/SolverInfo"))
1102  {
1103  // No SolverInfo = no change of default action to weight
1104  // mesh graph.
1105  return;
1106  }
1107 
1108  TiXmlElement* solverInfoElement =
1109  pSession->GetElement("Nektar/Conditions/SolverInfo");
1110 
1111  TiXmlElement* solverInfo =
1112  solverInfoElement->FirstChildElement("I");
1113  ASSERTL0(solverInfo, "Cannot read SolverInfo tags");
1114 
1115  while (solverInfo)
1116  {
1117  // read the property name
1118  ASSERTL0(solverInfo->Attribute("PROPERTY"),
1119  "Missing PROPERTY attribute in solver info "
1120  "section. ");
1121  std::string solverProperty =
1122  solverInfo->Attribute("PROPERTY");
1123  ASSERTL0(!solverProperty.empty(),
1124  "Solver info properties must have a non-empty "
1125  "name. ");
1126  // make sure that solver property is capitalised
1127  std::string solverPropertyUpper =
1128  boost::to_upper_copy(solverProperty);
1129 
1130 
1131  // read the value
1132  ASSERTL0(solverInfo->Attribute("VALUE"),
1133  "Missing VALUE attribute in solver info section. ");
1134  std::string solverValue = solverInfo->Attribute("VALUE");
1135  ASSERTL0(!solverValue.empty(),
1136  "Solver info properties must have a non-empty value");
1137  // make sure that property value is capitalised
1138  std::string propertyValueUpper =
1139  boost::to_upper_copy(solverValue);
1140 
1141  if (solverPropertyUpper == "WEIGHTPARTITIONS")
1142  {
1143  if (propertyValueUpper == "DOF")
1144  {
1145  m_weightingRequired = true;
1146  m_weightDofs = true;
1147  }
1148  else if (propertyValueUpper == "BOUNDARY")
1149  {
1150  m_weightingRequired = true;
1151  m_weightBnd = true;
1152  }
1153  else if (propertyValueUpper == "BOTH")
1154  {
1155  m_weightingRequired = true;
1156  m_weightDofs = true;
1157  m_weightBnd = true;
1158  }
1159  return;
1160  }
1161  solverInfo = solverInfo->NextSiblingElement("I");
1162  }
1163  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
void Nektar::LibUtilities::MeshPartition::ReadExpansions ( const SessionReaderSharedPtr &  pSession)
private

Expansiontypes will contain plenty of data, where relevant at this stage are composite ID(s) that this expansion type describes, nummodes and a list of fields that this expansion relates to. If this does not exist the variable is only set to "DefaultVar".

Definition at line 192 of file MeshPartition.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::LibUtilities::eHexahedron, Nektar::LibUtilities::ePrism, Nektar::LibUtilities::ePyramid, Nektar::LibUtilities::eQuadrilateral, Nektar::LibUtilities::eSegment, Nektar::LibUtilities::eTetrahedron, Nektar::LibUtilities::eTriangle, Nektar::ParseUtils::GenerateOrderedStringVector(), Nektar::ParseUtils::GenerateOrderedVector(), Nektar::ParseUtils::GenerateSeqVector(), Nektar::LibUtilities::GetCommFactory(), Nektar::LibUtilities::GetFieldIOFactory(), Nektar::LibUtilities::FieldIO::GetFileType(), m_dim, m_expansions, m_fieldNameToId, m_meshComposites, m_numFields, and m_shape.

Referenced by MeshPartition().

193  {
194  // Find the Expansions tag
195  TiXmlElement *expansionTypes = pSession->GetElement("Nektar/Expansions");
196 
197  // Find the Expansion type
198  TiXmlElement *expansion = expansionTypes->FirstChildElement();
199  std::string expType = expansion->Value();
200 
201  /// Expansiontypes will contain plenty of data,
202  /// where relevant at this stage are composite
203  /// ID(s) that this expansion type describes,
204  /// nummodes and a list of fields that this
205  /// expansion relates to. If this does not exist
206  /// the variable is only set to "DefaultVar".
207 
208  if(expType == "E")
209  {
210  while (expansion)
211  {
212  std::vector<unsigned int> composite;
213  std::vector<unsigned int> nummodes;
214  std::vector<std::string> fieldName;
215 
216  const char *nModesStr = expansion->Attribute("NUMMODES");
217  ASSERTL0(nModesStr,"NUMMODES was not defined in EXPANSION section of input");
218  std::string numModesStr = nModesStr;
219  bool valid = ParseUtils::GenerateOrderedVector(numModesStr.c_str(), nummodes);
220  ASSERTL0(valid, "Unable to correctly parse the number of modes.");
221 
222  if (nummodes.size() == 1)
223  {
224  for (int i = 1; i < m_dim; i++)
225  {
226  nummodes.push_back( nummodes[0] );
227  }
228  }
229  ASSERTL0(nummodes.size() == m_dim,"Number of modes should match mesh dimension");
230 
231 
232  const char *fStr = expansion->Attribute("FIELDS");
233  if(fStr)
234  {
235  std::string fieldStr = fStr;
236  bool valid = ParseUtils::GenerateOrderedStringVector(fieldStr.c_str(),fieldName);
237  ASSERTL0(valid,"Unable to correctly parse the field string in ExpansionTypes.");
238 
239  for (int i = 0; i < fieldName.size(); ++i)
240  {
241  if (m_fieldNameToId.count(fieldName[i]) == 0)
242  {
243  int k = m_fieldNameToId.size();
244  m_fieldNameToId[ fieldName[i] ] = k;
245  m_numFields++;
246  }
247  }
248  }
249  else
250  {
251  fieldName.push_back("DefaultVar");
252  int k = m_fieldNameToId.size();
253 
254  if (m_fieldNameToId.count("DefaultVar") == 0)
255  {
256  ASSERTL0(k == 0,
257  "Omitting field variables and explicitly listing " \
258  "them in different ExpansionTypes is wrong practise");
259 
260  m_fieldNameToId[ "DefaultVar" ] = k;
261  m_numFields++;
262  }
263  }
264 
265  std::string compositeStr = expansion->Attribute("COMPOSITE");
266  ASSERTL0(compositeStr.length() > 3, "COMPOSITE must be specified in expansion definition");
267  int beg = compositeStr.find_first_of("[");
268  int end = compositeStr.find_first_of("]");
269  std::string compositeListStr = compositeStr.substr(beg+1,end-beg-1);
270  bool parseGood = ParseUtils::GenerateSeqVector(compositeListStr.c_str(), composite);
271  ASSERTL0(parseGood && !composite.empty(),
272  (std::string("Unable to read composite index range: ") + compositeListStr).c_str());
273 
274 
275  // construct mapping (elmt id, field name) -> nummodes
276  for (int i = 0; i < composite.size(); ++i)
277  {
278  for (int j = 0; j < fieldName.size(); j++)
279  {
280  for (unsigned int k = 0; k < m_meshComposites[composite[i]].list.size(); ++k)
281  {
282  int elid = m_meshComposites[composite[i]].list[k];
283  m_expansions[elid][fieldName[j]] = nummodes;
284  m_shape[elid] = m_meshComposites[composite[i]].type;
285  }
286  }
287  }
288 
289  expansion = expansion->NextSiblingElement("E");
290  }
291  }
292  else if(expType == "F")
293  {
294  ASSERTL0(expansion->Attribute("FILE"),
295  "Attribute FILE expected for type F expansion");
296  std::string filenameStr = expansion->Attribute("FILE");
297  ASSERTL0(!filenameStr.empty(),
298  "A filename must be specified for the FILE "
299  "attribute of expansion");
300 
301  // Create fieldIO object to load file
302  // need a serial communicator to avoid problems with
303  // shared file system
304  CommSharedPtr comm=
305  GetCommFactory().CreateInstance("Serial", 0, 0);
306  std::string iofmt = FieldIO::GetFileType(
307  filenameStr, comm);
308  FieldIOSharedPtr f = GetFieldIOFactory().CreateInstance(
309  iofmt,
310  comm,
311  pSession->GetSharedFilesystem());
312  // Load field definitions from file
313  std::vector<LibUtilities::FieldDefinitionsSharedPtr> fielddefs;
314  f->Import(filenameStr, fielddefs);
315 
316  // Parse field definitions
317  for (int i = 0; i < fielddefs.size(); ++i)
318  {
319  // Name of fields
320  for (int j = 0; j < fielddefs[i]->m_fields.size(); ++j)
321  {
322  std::string fieldName = fielddefs[i]->m_fields[j];
323  if (m_fieldNameToId.count(fieldName) == 0)
324  {
325  int k = m_fieldNameToId.size();
326  m_fieldNameToId[ fieldName ] = k;
327  m_numFields++;
328  }
329  }
330  // Number of modes and shape for each element
331  int numHomoDir = fielddefs[i]->m_numHomogeneousDir;
332  int cnt = 0;
333  for (int j = 0; j < fielddefs[i]->m_elementIDs.size(); ++j)
334  {
335  int elid = fielddefs[i]->m_elementIDs[j];
336  std::vector<unsigned int> nummodes;
337  for (int k = 0; k < m_dim; k++)
338  {
339  nummodes.push_back(fielddefs[i]->m_numModes[cnt++]);
340  }
341  if (fielddefs[i]->m_uniOrder)
342  {
343  cnt = 0;
344  }
345  else
346  {
347  cnt += numHomoDir;
348  }
349  for (int k = 0; k < fielddefs[i]->m_fields.size(); k++)
350  {
351  std::string fieldName = fielddefs[i]->m_fields[k];
352  m_expansions[elid][fieldName] = nummodes;
353  }
354  switch (fielddefs[i]->m_shapeType)
355  {
356  case eSegment:
357  {
358  m_shape[elid] = 'S';
359  break;
360  }
361  case eTriangle:
362  {
363  m_shape[elid] = 'T';
364  break;
365  }
366  case eQuadrilateral:
367  {
368  m_shape[elid] = 'Q';
369  break;
370  }
371  case eTetrahedron:
372  {
373  m_shape[elid] = 'A';
374  break;
375  }
376  case ePyramid:
377  {
378  m_shape[elid] = 'R';
379  break;
380  }
381  case ePrism:
382  {
383  m_shape[elid] = 'P';
384  break;
385  }
386  case eHexahedron:
387  {
388  m_shape[elid] = 'H';
389  break;
390  }
391  default:
392  ASSERTL0 (false, "Shape not recognized.");
393  break;
394  }
395  }
396  }
397  }
398  else
399  {
400  ASSERTL0(false,"Expansion type not defined or not supported at the moment");
401  }
402  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::ParseUtils::GenerateOrderedStringVector
static bool GenerateOrderedStringVector(const char *const str, std::vector< std::string > &vec)
Definition: ParseUtils.hpp:143
Nektar::ParseUtils::GenerateOrderedVector
static bool GenerateOrderedVector(const char *const str, std::vector< unsigned int > &vec)
Definition: ParseUtils.hpp:97
Nektar::LibUtilities::NekFactory::CreateInstance
tBaseSharedPtr CreateInstance(tKey idKey BOOST_PP_COMMA_IF(MAX_PARAM) BOOST_PP_ENUM_BINARY_PARAMS(MAX_PARAM, tParam, x))
Create an instance of the class referred to by idKey.
Definition: NekFactory.hpp:162
Nektar::LibUtilities::MeshPartition::m_meshComposites
std::map< int, MeshEntity > m_meshComposites
Definition: MeshPartition.h:190
Nektar::LibUtilities::GetFieldIOFactory
FieldIOFactory & GetFieldIOFactory()
Returns the FieldIO factory.
Definition: FieldIO.cpp:74
Nektar::ParseUtils::GenerateSeqVector
static bool GenerateSeqVector(const char *const str, std::vector< unsigned int > &vec)
Definition: ParseUtils.hpp:79
Nektar::LibUtilities::GetCommFactory
CommFactory & GetCommFactory()
Definition: Comm.cpp:61
Nektar::LibUtilities::MeshPartition::m_fieldNameToId
std::map< std::string, int > m_fieldNameToId
Definition: MeshPartition.h:201
Nektar::LibUtilities::MeshPartition::m_expansions
std::map< int, NummodesPerField > m_expansions
Definition: MeshPartition.h:196
Nektar::LibUtilities::CommSharedPtr
boost::shared_ptr< Comm > CommSharedPtr
Pointer to a Communicator object.
Definition: Comm.h:55
Nektar::LibUtilities::FieldIO::GetFileType
static const std::string GetFileType(const std::string &filename, CommSharedPtr comm)
Determine file type of given input file.
Definition: FieldIO.cpp:101
Nektar::LibUtilities::FieldIOSharedPtr
boost::shared_ptr< FieldIO > FieldIOSharedPtr
Definition: FieldIO.h:309
void Nektar::LibUtilities::MeshPartition::ReadGeometry ( const SessionReaderSharedPtr &  pSession)
private

Definition at line 407 of file MeshPartition.cpp.

References ASSERTL0, Nektar::LibUtilities::MeshPartition::MeshCurved::data, Nektar::LibUtilities::MeshPartition::MeshCurved::entityid, Nektar::LibUtilities::MeshPartition::MeshCurved::entitytype, Nektar::ParseUtils::GenerateSeqVector(), Nektar::LibUtilities::CompressData::GetCompressString(), Nektar::LibUtilities::MeshVertex::id, Nektar::LibUtilities::MeshPartition::MeshEntity::id, Nektar::LibUtilities::MeshPartition::MeshCurved::id, Nektar::LibUtilities::MeshCurvedPts::id, Nektar::LibUtilities::MeshCurvedPts::index, Nektar::LibUtilities::kPointsTypeStr, Nektar::LibUtilities::MeshPartition::MeshEntity::list, m_dim, m_domain, m_isCompressed, m_meshComposites, m_meshCurved, m_meshCurvedPts, m_meshEdges, m_meshElements, m_meshFaces, m_meshVertices, m_vertexAttributes, Nektar::LibUtilities::MeshPartition::MeshCurved::npoints, Nektar::LibUtilities::MeshPartition::MeshCurved::ptid, Nektar::LibUtilities::MeshPartition::MeshCurved::ptoffset, Nektar::LibUtilities::MeshCurvedPts::pts, Nektar::LibUtilities::MeshPartition::MeshEntity::type, Nektar::LibUtilities::MeshPartition::MeshCurved::type, Nektar::LibUtilities::MeshVertex::x, Nektar::LibUtilities::MeshVertex::y, Nektar::LibUtilities::MeshVertex::z, and Nektar::LibUtilities::CompressData::ZlibDecodeFromBase64Str().

Referenced by MeshPartition().

408  {
409  TiXmlElement* x;
410  TiXmlElement *vGeometry, *vSubElement;
411 
412  vGeometry = pSession->GetElement("Nektar/Geometry");
413  m_dim = atoi(vGeometry->Attribute("DIM"));
414 
415  // Read mesh vertices
416  vSubElement = pSession->GetElement("Nektar/Geometry/Vertex");
417 
418  // Retrieve any VERTEX attributes specifying mesh transforms
419  std::string attr[] = {"XSCALE", "YSCALE", "ZSCALE",
420  "XMOVE", "YMOVE", "ZMOVE" };
421  for (int i = 0; i < 6; ++i)
422  {
423  const char *val = vSubElement->Attribute(attr[i].c_str());
424  if (val)
425  {
426  m_vertexAttributes[attr[i]] = std::string(val);
427  }
428  }
429 
430  // check to see if compressed
431  std::string IsCompressed;
432  vSubElement->QueryStringAttribute("COMPRESSED",&IsCompressed);
433 
434  if(IsCompressed.size())
435  {
436  ASSERTL0(boost::iequals(IsCompressed,
437  CompressData::GetCompressString()),
438  "Compressed formats do not match. Expected :"
439  + CompressData::GetCompressString()
440  + "but got "+ std::string(IsCompressed));
441 
442  m_isCompressed = true;
443 
444  // Extract the vertex body
445  TiXmlNode* vertexChild = vSubElement->FirstChild();
446  ASSERTL0(vertexChild, "Unable to extract the data "
447  "from the compressed vertex tag.");
448 
449  std::string vertexStr;
450  if (vertexChild->Type() == TiXmlNode::TINYXML_TEXT)
451  {
452  vertexStr += vertexChild->ToText()->ValueStr();
453  }
454 
455  std::vector<MeshVertex> vertData;
456  CompressData::ZlibDecodeFromBase64Str(vertexStr,vertData);
457 
458  for(int i = 0; i < vertData.size(); ++i)
459  {
460  m_meshVertices[vertData[i].id] = vertData[i];
461  }
462  }
463  else
464  {
465  x = vSubElement->FirstChildElement();
466 
467  while(x)
468  {
469  TiXmlAttribute* y = x->FirstAttribute();
470  ASSERTL0(y, "Failed to get attribute.");
471  MeshVertex v;
472  v.id = y->IntValue();
473  std::vector<std::string> vCoords;
474  std::string vCoordStr = x->FirstChild()->ToText()->Value();
475  boost::split(vCoords, vCoordStr, boost::is_any_of("\t "));
476  v.x = atof(vCoords[0].c_str());
477  v.y = atof(vCoords[1].c_str());
478  v.z = atof(vCoords[2].c_str());
479  m_meshVertices[v.id] = v;
480  x = x->NextSiblingElement();
481  }
482  }
483 
484  // Read mesh edges
485  if (m_dim >= 2)
486  {
487  vSubElement = pSession->GetElement("Nektar/Geometry/Edge");
488  ASSERTL0(vSubElement, "Cannot read edges");
489 
490  // check to see if compressed
491  std::string IsCompressed;
492  vSubElement->QueryStringAttribute("COMPRESSED",&IsCompressed);
493 
494  if(IsCompressed.size())
495  {
496  ASSERTL0(boost::iequals(IsCompressed,
497  CompressData::GetCompressString()),
498  "Compressed formats do not match. Expected :"
499  + CompressData::GetCompressString()
500  + " but got "
501  + boost::lexical_cast<std::string>(IsCompressed));
502 
503  m_isCompressed = true;
504 
505  // Extract the edge body
506  TiXmlNode* edgeChild = vSubElement->FirstChild();
507  ASSERTL0(edgeChild,
508  "Unable to extract the data from the compressed "
509  "edge tag.");
510 
511  std::string edgeStr;
512 
513  if (edgeChild->Type() == TiXmlNode::TINYXML_TEXT)
514  {
515  edgeStr += edgeChild->ToText()->ValueStr();
516  }
517 
518  std::vector<MeshEdge> edgeData;
519  CompressData::ZlibDecodeFromBase64Str(edgeStr,edgeData);
520 
521  for(int i = 0; i < edgeData.size(); ++i)
522  {
523  MeshEntity e;
524  e.id = edgeData[i].id;
525  e.list.push_back(edgeData[i].v0);
526  e.list.push_back(edgeData[i].v1);
527  m_meshEdges[e.id] = e;
528  }
529  }
530  else
531  {
532  x = vSubElement->FirstChildElement();
533 
534  while(x)
535  {
536  TiXmlAttribute* y = x->FirstAttribute();
537  ASSERTL0(y, "Failed to get attribute.");
538  MeshEntity e;
539  e.id = y->IntValue();
540  e.type = 'E';
541  std::vector<std::string> vVertices;
542  std::string vVerticesString = x->FirstChild()->ToText()->Value();
543  boost::split(vVertices, vVerticesString, boost::is_any_of("\t "));
544  e.list.push_back(atoi(vVertices[0].c_str()));
545  e.list.push_back(atoi(vVertices[1].c_str()));
546  m_meshEdges[e.id] = e;
547  x = x->NextSiblingElement();
548  }
549  }
550  }
551 
552  // Read mesh faces
553  if (m_dim == 3)
554  {
555  vSubElement = pSession->GetElement("Nektar/Geometry/Face");
556  ASSERTL0(vSubElement, "Cannot read faces.");
557  x = vSubElement->FirstChildElement();
558 
559  while(x)
560  {
561  // check to see if compressed
562  std::string IsCompressed;
563  x->QueryStringAttribute("COMPRESSED",&IsCompressed);
564 
565  if(IsCompressed.size())
566  {
567  ASSERTL0(boost::iequals(IsCompressed,
568  CompressData::GetCompressString()),
569  "Compressed formats do not match. Expected :"
570  + CompressData::GetCompressString()
571  + " but got "
572  + boost::lexical_cast<std::string>(
573  IsCompressed));
574  m_isCompressed = true;
575 
576  // Extract the edge body
577  TiXmlNode* faceChild = x->FirstChild();
578  ASSERTL0(faceChild, "Unable to extract the data from "
579  "the compressed edge tag.");
580 
581  std::string faceStr;
582  if (faceChild->Type() == TiXmlNode::TINYXML_TEXT)
583  {
584  faceStr += faceChild->ToText()->ValueStr();
585  }
586 
587  // uncompress and fill in values.
588  const std::string val= x->Value();
589 
590  if(boost::iequals(val,"T")) // triangle
591  {
592  std::vector<MeshTri> faceData;
593  CompressData::ZlibDecodeFromBase64Str(faceStr,
594  faceData);
595 
596  for(int i= 0; i < faceData.size(); ++i)
597  {
598  MeshEntity f;
599 
600  f.id = faceData[i].id;
601  f.type = 'T';
602  for (int j = 0; j < 3; ++j)
603  {
604  f.list.push_back(faceData[i].e[j]);
605  }
606  m_meshFaces[f.id] = f;
607  }
608  }
609  else if (boost::iequals(val,"Q"))
610  {
611  std::vector<MeshQuad> faceData;
612  CompressData::ZlibDecodeFromBase64Str(faceStr,
613  faceData);
614 
615  for(int i= 0; i < faceData.size(); ++i)
616  {
617  MeshEntity f;
618 
619  f.id = faceData[i].id;
620  f.type = 'Q';
621  for (int j = 0; j < 4; ++j)
622  {
623  f.list.push_back(faceData[i].e[j]);
624  }
625  m_meshFaces[f.id] = f;
626  }
627  }
628  else
629  {
630  ASSERTL0(false,"Unrecognised face tag");
631  }
632  }
633  else
634  {
635  TiXmlAttribute* y = x->FirstAttribute();
636  ASSERTL0(y, "Failed to get attribute.");
637  MeshEntity f;
638  f.id = y->IntValue();
639  f.type = x->Value()[0];
640  std::vector<std::string> vEdges;
641  std::string vEdgeStr = x->FirstChild()->ToText()->Value();
642  boost::split(vEdges, vEdgeStr, boost::is_any_of("\t "));
643  for (int i = 0; i < vEdges.size(); ++i)
644  {
645  f.list.push_back(atoi(vEdges[i].c_str()));
646  }
647  m_meshFaces[f.id] = f;
648  }
649  x = x->NextSiblingElement();
650  }
651  }
652 
653  // Read mesh elements
654  vSubElement = pSession->GetElement("Nektar/Geometry/Element");
655  ASSERTL0(vSubElement, "Cannot read elements.");
656  x = vSubElement->FirstChildElement();
657  while(x)
658  {
659  // check to see if compressed
660  std::string IsCompressed;
661  x->QueryStringAttribute("COMPRESSED",&IsCompressed);
662 
663  if(IsCompressed.size())
664  {
665  ASSERTL0(boost::iequals(IsCompressed,
666  CompressData::GetCompressString()),
667  "Compressed formats do not match. Expected :"
668  + CompressData::GetCompressString()
669  + " but got "
670  + boost::lexical_cast<std::string>(IsCompressed));
671  m_isCompressed = true;
672 
673  // Extract the body
674  TiXmlNode* child = x->FirstChild();
675  ASSERTL0(child, "Unable to extract the data from the "
676  "compressed element tag.");
677 
678  std::string elmtStr;
679  if (child->Type() == TiXmlNode::TINYXML_TEXT)
680  {
681  elmtStr += child->ToText()->ValueStr();
682  }
683 
684  // uncompress and fill in values.
685  const std::string val= x->Value();
686 
687  switch(val[0])
688  {
689  case 'S': // segment
690  {
691  std::vector<MeshEdge> data;
692  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
693 
694  for(int i= 0; i < data.size(); ++i)
695  {
696  MeshEntity e;
697  e.id = data[i].id;
698  e.type = 'S';
699  e.list.push_back(data[i].v0);
700  e.list.push_back(data[i].v1);
701  m_meshElements[e.id] = e;
702  }
703  }
704  break;
705  case 'T': // triangle
706  {
707  std::vector<MeshTri> data;
708  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
709 
710  for(int i= 0; i < data.size(); ++i)
711  {
712  MeshEntity f;
713  f.id = data[i].id;
714  f.type = 'T';
715  for (int j = 0; j < 3; ++j)
716  {
717  f.list.push_back(data[i].e[j]);
718  }
719  m_meshElements[f.id] = f;
720  }
721  }
722  break;
723  case 'Q': // quadrilateral
724  {
725  std::vector<MeshQuad> data;
726  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
727 
728  for(int i= 0; i < data.size(); ++i)
729  {
730  MeshEntity f;
731  f.id = data[i].id;
732  f.type = 'Q';
733  for (int j = 0; j < 4; ++j)
734  {
735  f.list.push_back(data[i].e[j]);
736  }
737  m_meshElements[f.id] = f;
738  }
739  }
740  break;
741  case 'A': // tetrahedron
742  {
743  std::vector<MeshTet> data;
744  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
745 
746  for(int i= 0; i < data.size(); ++i)
747  {
748  MeshEntity f;
749  f.id = data[i].id;
750  f.type = 'A';
751  for (int j = 0; j < 4; ++j)
752  {
753  f.list.push_back(data[i].f[j]);
754  }
755  m_meshElements[f.id] = f;
756  }
757  }
758  break;
759  case 'P': // prism
760  {
761  std::vector<MeshPyr> data;
762  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
763 
764  for(int i= 0; i < data.size(); ++i)
765  {
766  MeshEntity f;
767  f.id = data[i].id;
768  f.type = 'P';
769  for (int j = 0; j < 5; ++j)
770  {
771  f.list.push_back(data[i].f[j]);
772  }
773  m_meshElements[f.id] = f;
774  }
775  }
776  break;
777  case 'R': // pyramid
778  {
779  std::vector<MeshPrism> data;
780  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
781 
782  for(int i= 0; i < data.size(); ++i)
783  {
784  MeshEntity f;
785  f.id = data[i].id;
786  f.type = 'R';
787  for (int j = 0; j < 5; ++j)
788  {
789  f.list.push_back(data[i].f[j]);
790  }
791  m_meshElements[f.id] = f;
792  }
793  }
794  break;
795  case 'H': // hexahedron
796  {
797  std::vector<MeshHex> data;
798  CompressData::ZlibDecodeFromBase64Str(elmtStr,data);
799 
800  for(int i= 0; i < data.size(); ++i)
801  {
802  MeshEntity f;
803  f.id = data[i].id;
804  f.type = 'H';
805  for (int j = 0; j < 6; ++j)
806  {
807  f.list.push_back(data[i].f[j]);
808  }
809  m_meshElements[f.id] = f;
810  }
811  }
812  break;
813  default:
814  ASSERTL0(false,"Unrecognised element tag");
815  }
816  }
817  else
818  {
819  TiXmlAttribute* y = x->FirstAttribute();
820  ASSERTL0(y, "Failed to get attribute.");
821  MeshEntity e;
822  e.id = y->IntValue();
823  std::vector<std::string> vItems;
824  std::string vItemStr = x->FirstChild()->ToText()->Value();
825  boost::split(vItems, vItemStr, boost::is_any_of("\t "));
826  for (int i = 0; i < vItems.size(); ++i)
827  {
828  e.list.push_back(atoi(vItems[i].c_str()));
829  }
830  e.type = x->Value()[0];
831  m_meshElements[e.id] = e;
832  }
833  x = x->NextSiblingElement();
834  }
835 
836  // Read mesh curves
837  if (pSession->DefinesElement("Nektar/Geometry/Curved"))
838  {
839  vSubElement = pSession->GetElement("Nektar/Geometry/Curved");
840 
841  // check to see if compressed
842  std::string IsCompressed;
843  vSubElement->QueryStringAttribute("COMPRESSED",&IsCompressed);
844 
845  x = vSubElement->FirstChildElement();
846  while(x)
847  {
848  if(IsCompressed.size())
849  {
850  ASSERTL0(boost::iequals(IsCompressed,
851  CompressData::GetCompressString()),
852  "Compressed formats do not match. Expected :"
853  + CompressData::GetCompressString()
854  + " but got "
855  + boost::lexical_cast<std::string>(
856  IsCompressed));
857 
858  m_isCompressed = true;
859 
860  const char *entitytype = x->Value();
861  // The compressed curved information is stored
862  // in two parts: MeshCurvedInfo and
863  // MeshCurvedPts. MeshCurvedPts is just a
864  // list of MeshVertex values of unique vertex
865  // values from which we can make edges and
866  // faces.
867  //
868  // Then there is a list of NekInt64 pieces of
869  // information which make a MeshCurvedInfo
870  // struct. This contains information such as
871  // the curve id, the entity id, the number of
872  // curved points and the offset of where these
873  // points are stored in the pts vector of
874  // MeshVertex values. Finally the point type
875  // is also stored but in NekInt64 format
876  // rather than an enum for binary stride
877  // compatibility.
878  if(boost::iequals(entitytype,"E")||
879  boost::iequals(entitytype,"F"))
880  {
881  // read in data
882  std::string elmtStr;
883  TiXmlNode* child = x->FirstChild();
884 
885  if (child->Type() == TiXmlNode::TINYXML_TEXT)
886  {
887  elmtStr = child->ToText()->ValueStr();
888  }
889 
890  std::vector<MeshCurvedInfo> cinfo;
891  CompressData::ZlibDecodeFromBase64Str(elmtStr,
892  cinfo);
893 
894  // unpack list of curved edge or faces
895  for(int i = 0; i < cinfo.size(); ++i)
896  {
897  MeshCurved c;
898  c.id = cinfo[i].id;
899  c.entitytype = entitytype[0];
900  c.entityid = cinfo[i].entityid;
901  c.npoints = cinfo[i].npoints;
902  c.type = kPointsTypeStr[cinfo[i].ptype];
903  c.ptid = cinfo[i].ptid;
904  c.ptoffset = cinfo[i].ptoffset;
905  m_meshCurved[std::make_pair(c.entitytype,
906  c.id)] = c;
907  }
908  }
909  else if(boost::iequals(entitytype,"DATAPOINTS"))
910  {
911  MeshCurvedPts cpts;
912  NekInt id;
913 
914  ASSERTL0(x->Attribute("ID", &id),
915  "Failed to get ID from PTS section");
916  cpts.id = id;
917 
918  // read in data
919  std::string elmtStr;
920 
921  TiXmlElement* DataIdx =
922  x->FirstChildElement("INDEX");
923  ASSERTL0(DataIdx,
924  "Cannot read data index tag in compressed "
925  "curved section");
926 
927  TiXmlNode* child = DataIdx->FirstChild();
928  if (child->Type() == TiXmlNode::TINYXML_TEXT)
929  {
930  elmtStr = child->ToText()->ValueStr();
931  }
932 
933  CompressData::ZlibDecodeFromBase64Str(elmtStr,
934  cpts.index);
935 
936  TiXmlElement* DataPts
937  = x->FirstChildElement("POINTS");
938  ASSERTL0(DataPts,
939  "Cannot read data pts tag in compressed "
940  "curved section");
941 
942  child = DataPts->FirstChild();
943  if (child->Type() == TiXmlNode::TINYXML_TEXT)
944  {
945  elmtStr = child->ToText()->ValueStr();
946  }
947 
948  CompressData::ZlibDecodeFromBase64Str(elmtStr,
949  cpts.pts);
950 
951  m_meshCurvedPts[cpts.id] = cpts;
952  }
953  else
954  {
955  ASSERTL0(false, "Unknown tag in curved section");
956  }
957 
958  x = x->NextSiblingElement();
959  }
960  else
961  {
962  MeshCurved c;
963  ASSERTL0(x->Attribute("ID", &c.id),
964  "Failed to get attribute ID");
965  c.type = std::string(x->Attribute("TYPE"));
966  ASSERTL0(!c.type.empty(),
967  "Failed to get attribute TYPE");
968  ASSERTL0(x->Attribute("NUMPOINTS", &c.npoints),
969  "Failed to get attribute NUMPOINTS");
970  c.data = x->FirstChild()->ToText()->Value();
971  c.entitytype = x->Value()[0];
972 
973  if (c.entitytype == "E")
974  {
975  ASSERTL0(x->Attribute("EDGEID", &c.entityid),
976  "Failed to get attribute EDGEID");
977  }
978  else if (c.entitytype == "F")
979  {
980  ASSERTL0(x->Attribute("FACEID", &c.entityid),
981  "Failed to get attribute FACEID");
982  }
983  else
984  {
985  ASSERTL0(false, "Unknown curve type.");
986  }
987 
988  m_meshCurved[std::make_pair(c.entitytype, c.id)] = c;
989  x = x->NextSiblingElement();
990  }
991  }
992  }
993 
994  // Read composites
995  vSubElement = pSession->GetElement("Nektar/Geometry/Composite");
996  ASSERTL0(vSubElement, "Cannot read composites.");
997  x = vSubElement->FirstChildElement();
998  while(x)
999  {
1000  TiXmlAttribute* y = x->FirstAttribute();
1001  ASSERTL0(y, "Failed to get attribute.");
1002  MeshEntity c;
1003  c.id = y->IntValue();
1004  std::string vSeqStr = x->FirstChild()->ToText()->Value();
1005  c.type = vSeqStr[0];
1006  std::string::size_type indxBeg = vSeqStr.find_first_of('[') + 1;
1007  std::string::size_type indxEnd = vSeqStr.find_last_of(']') - 1;
1008  vSeqStr = vSeqStr.substr(indxBeg, indxEnd - indxBeg + 1);
1009 
1010  std::vector<unsigned int> vSeq;
1011  ParseUtils::GenerateSeqVector(vSeqStr.c_str(), vSeq);
1012 
1013  for (int i = 0; i < vSeq.size(); ++i)
1014  {
1015  c.list.push_back(vSeq[i]);
1016  }
1017  m_meshComposites[c.id] = c;
1018  x = x->NextSiblingElement();
1019  }
1020 
1021  // Read Domain
1022  vSubElement = pSession->GetElement("Nektar/Geometry/Domain");
1023  ASSERTL0(vSubElement, "Cannot read domain");
1024  std::string vSeqStr = vSubElement->FirstChild()->ToText()->Value();
1025  std::string::size_type indxBeg = vSeqStr.find_first_of('[') + 1;
1026  std::string::size_type indxEnd = vSeqStr.find_last_of(']') - 1;
1027  vSeqStr = vSeqStr.substr(indxBeg, indxEnd - indxBeg + 1);
1028  ParseUtils::GenerateSeqVector(vSeqStr.c_str(), m_domain);
1029  }
Nektar::NekInt
boost::int32_t NekInt
Definition: NektarUnivTypeDefs.hpp:46
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::m_vertexAttributes
std::map< std::string, std::string > m_vertexAttributes
Definition: MeshPartition.h:192
Nektar::LibUtilities::MeshPartition::m_meshComposites
std::map< int, MeshEntity > m_meshComposites
Definition: MeshPartition.h:190
Nektar::LibUtilities::kPointsTypeStr
const std::string kPointsTypeStr[]
Definition: Foundations.hpp:69
Nektar::LibUtilities::MeshPartition::m_meshVertices
std::map< int, MeshVertex > m_meshVertices
Definition: MeshPartition.h:184
Nektar::LibUtilities::MeshPartition::m_meshCurved
std::map< MeshCurvedKey, MeshCurved > m_meshCurved
Definition: MeshPartition.h:188
Nektar::ParseUtils::GenerateSeqVector
static bool GenerateSeqVector(const char *const str, std::vector< unsigned int > &vec)
Definition: ParseUtils.hpp:79
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::m_domain
std::vector< unsigned int > m_domain
Definition: MeshPartition.h:191
Nektar::LibUtilities::MeshPartition::m_meshEdges
std::map< int, MeshEntity > m_meshEdges
Definition: MeshPartition.h:185
Nektar::LibUtilities::MeshPartition::m_meshFaces
std::map< int, MeshEntity > m_meshFaces
Definition: MeshPartition.h:186
Nektar::LibUtilities::MeshPartition::m_meshCurvedPts
std::map< int, MeshCurvedPts > m_meshCurvedPts
Definition: MeshPartition.h:189
Nektar::LibUtilities::CompressData::ZlibDecodeFromBase64Str
int ZlibDecodeFromBase64Str(std::string &in64, std::vector< T > &out)
Definition: CompressData.h:243
void Nektar::LibUtilities::MeshPartition::WeightElements ( )
private

Definition at line 1180 of file MeshPartition.cpp.

References ASSERTL0, CalculateEdgeWeight(), CalculateElementWeight(), Nektar::iterator, m_dim, m_edgeWeights, m_expansions, m_fieldNameToId, m_meshElements, m_numFields, m_shape, m_vertBndWeights, and m_vertWeights.

Referenced by PartitionMesh().

1181  {
1182  std::vector<unsigned int> weight(m_numFields, 1);
1183  std::map<int, MeshEntity>::iterator eIt;
1184  for (eIt = m_meshElements.begin(); eIt != m_meshElements.end(); ++eIt)
1185  {
1186  m_vertWeights[eIt->first] = weight;
1187  m_vertBndWeights[eIt->first] = weight;
1188  m_edgeWeights[eIt->first] = weight;
1189  }
1190 
1191  for (std::map<int, NummodesPerField>::iterator expIt =
1192  m_expansions.begin(); expIt != m_expansions.end(); ++expIt)
1193  {
1194  int elid = expIt->first;
1195  NummodesPerField npf = expIt->second;
1196 
1197  for (NummodesPerField::iterator it = npf.begin(); it != npf.end(); ++it)
1198  {
1199  ASSERTL0(it->second.size() == m_dim,
1200  " Number of directional" \
1201  " modes in expansion spec for element id = " +
1202  boost::lexical_cast<std::string>(elid) +
1203  " and field " +
1204  boost::lexical_cast<std::string>(it->first) +
1205  " does not correspond to mesh dimension");
1206 
1207  int na = it->second[0];
1208  int nb = 0;
1209  int nc = 0;
1210  if (m_dim >= 2)
1211  {
1212  nb = it->second[1];
1213  }
1214  if (m_dim == 3)
1215  {
1216  nc = it->second[2];
1217  }
1218 
1219  m_vertWeights[elid][m_fieldNameToId[it->first]] =
1220  CalculateElementWeight(m_shape[elid], false,
1221  na, nb, nc);
1222  m_vertBndWeights[elid][m_fieldNameToId[it->first]] =
1223  CalculateElementWeight(m_shape[elid], true,
1224  na, nb, nc);
1225  m_edgeWeights[elid][m_fieldNameToId[it->first]] =
1226  CalculateEdgeWeight(m_shape[elid],
1227  na, nb, nc);
1228  }
1229  } // for i
1230  }
Nektar::LibUtilities::MeshPartition::CalculateElementWeight
int CalculateElementWeight(char elmtType, bool bndWeight, int na, int nb, int nc)
Definition: MeshPartition.cpp:2316
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:198
Nektar::LibUtilities::MeshPartition::m_vertBndWeights
std::map< int, MultiWeight > m_vertBndWeights
Definition: MeshPartition.h:203
Nektar::LibUtilities::MeshPartition::m_vertWeights
std::map< int, MultiWeight > m_vertWeights
Definition: MeshPartition.h:202
Nektar::LibUtilities::MeshPartition::NummodesPerField
std::map< std::string, NumModes > NummodesPerField
Definition: MeshPartition.h:179
Nektar::LibUtilities::MeshPartition::m_fieldNameToId
std::map< std::string, int > m_fieldNameToId
Definition: MeshPartition.h:201
Nektar::LibUtilities::MeshPartition::m_expansions
std::map< int, NummodesPerField > m_expansions
Definition: MeshPartition.h:196
Nektar::LibUtilities::MeshPartition::m_meshElements
std::map< int, MeshEntity > m_meshElements
Definition: MeshPartition.h:187
Nektar::LibUtilities::MeshPartition::CalculateEdgeWeight
int CalculateEdgeWeight(char elmtType, int na, int nb, int nc)
Definition: MeshPartition.cpp:2378
Nektar::LibUtilities::MeshPartition::m_edgeWeights
std::map< int, MultiWeight > m_edgeWeights
Definition: MeshPartition.h:204
Nektar::iterator
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
Definition: MatrixOperations.cpp:96
void Nektar::LibUtilities::MeshPartition::WriteAllPartitions ( LibUtilities::SessionReaderSharedPtr &  pSession)

Definition at line 143 of file MeshPartition.cpp.

References CellMLToNektar.pycml::format, m_localPartition, OutputPartition(), and Nektar::LibUtilities::PortablePath().

144  {
145  for (int i = 0; i < m_localPartition.size(); ++i)
146  {
147  TiXmlDocument vNew;
148  TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
149  vNew.LinkEndChild(decl);
150 
151  TiXmlElement* vElmtNektar;
152  vElmtNektar = new TiXmlElement("NEKTAR");
153 
154  OutputPartition(pSession, m_localPartition[i], vElmtNektar);
155 
156  vNew.LinkEndChild(vElmtNektar);
157 
158  std::string dirname = pSession->GetSessionName() + "_xml";
159  fs::path pdirname(dirname);
160 
161  boost::format pad("P%1$07d.xml");
162  pad % i;
163  fs::path pFilename(pad.str());
164 
165  fs::path fullpath = pdirname / pFilename;
166 
167  if(!fs::is_directory(dirname))
168  {
169  fs::create_directory(dirname);
170  }
171 
172  vNew.SaveFile(PortablePath(fullpath));
173  }
174  }
Nektar::LibUtilities::MeshPartition::m_localPartition
std::vector< BoostSubGraph > m_localPartition
Definition: MeshPartition.h:209
Nektar::LibUtilities::PortablePath
std::string PortablePath(const boost::filesystem::path &path)
create portable path on different platforms for boost::filesystem path
Definition: FileSystem.cpp:41
Nektar::LibUtilities::MeshPartition::OutputPartition
void OutputPartition(SessionReaderSharedPtr &pSession, BoostSubGraph &pGraph, TiXmlElement *pGeometry)
Definition: MeshPartition.cpp:1474
void Nektar::LibUtilities::MeshPartition::WriteLocalPartition ( LibUtilities::SessionReaderSharedPtr &  pSession)

Definition at line 113 of file MeshPartition.cpp.

References CellMLToNektar.pycml::format, m_comm, m_localPartition, OutputPartition(), and Nektar::LibUtilities::PortablePath().

114  {
115  TiXmlDocument vNew;
116  TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
117  vNew.LinkEndChild(decl);
118 
119  TiXmlElement* vElmtNektar;
120  vElmtNektar = new TiXmlElement("NEKTAR");
121 
122  int rank = m_comm->GetRowComm()->GetRank();
123  OutputPartition(pSession, m_localPartition[rank], vElmtNektar);
124 
125  vNew.LinkEndChild(vElmtNektar);
126 
127  std::string dirname = pSession->GetSessionName() + "_xml";
128  fs::path pdirname(dirname);
129 
130  boost::format pad("P%1$07d.xml");
131  pad % rank;
132  fs::path pFilename(pad.str());
133 
134  if(!fs::is_directory(dirname))
135  {
136  fs::create_directory(dirname);
137  }
138 
139  fs::path fullpath = pdirname / pFilename;
140  vNew.SaveFile(PortablePath(fullpath));
141  }
Nektar::LibUtilities::MeshPartition::m_localPartition
std::vector< BoostSubGraph > m_localPartition
Definition: MeshPartition.h:209
Nektar::LibUtilities::PortablePath
std::string PortablePath(const boost::filesystem::path &path)
create portable path on different platforms for boost::filesystem path
Definition: FileSystem.cpp:41
Nektar::LibUtilities::MeshPartition::OutputPartition
void OutputPartition(SessionReaderSharedPtr &pSession, BoostSubGraph &pGraph, TiXmlElement *pGeometry)
Definition: MeshPartition.cpp:1474

Member Data Documentation

BndRegionOrdering Nektar::LibUtilities::MeshPartition::m_bndRegOrder
private

Definition at line 206 of file MeshPartition.h.

Referenced by GetBndRegionOrdering(), and OutputPartition().

CommSharedPtr Nektar::LibUtilities::MeshPartition::m_comm
private

Definition at line 211 of file MeshPartition.h.

Referenced by PartitionGraph(), and WriteLocalPartition().

int Nektar::LibUtilities::MeshPartition::m_dim
private

Definition at line 181 of file MeshPartition.h.

Referenced by OutputPartition(), PrintPartInfo(), ReadExpansions(), ReadGeometry(), and WeightElements().

std::vector<unsigned int> Nektar::LibUtilities::MeshPartition::m_domain
private

Definition at line 191 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MultiWeight> Nektar::LibUtilities::MeshPartition::m_edgeWeights
private

Definition at line 204 of file MeshPartition.h.

Referenced by CreateGraph(), and WeightElements().

std::map<int, NummodesPerField> Nektar::LibUtilities::MeshPartition::m_expansions
private

Definition at line 196 of file MeshPartition.h.

Referenced by PrintPartInfo(), ReadExpansions(), and WeightElements().

std::map<std::string, int> Nektar::LibUtilities::MeshPartition::m_fieldNameToId
private

Definition at line 201 of file MeshPartition.h.

Referenced by ReadExpansions(), and WeightElements().

bool Nektar::LibUtilities::MeshPartition::m_isCompressed
private

Definition at line 124 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::vector<BoostSubGraph> Nektar::LibUtilities::MeshPartition::m_localPartition
private

Definition at line 209 of file MeshPartition.h.

Referenced by GetElementIDs(), PartitionMesh(), PrintPartInfo(), WriteAllPartitions(), and WriteLocalPartition().

BoostSubGraph Nektar::LibUtilities::MeshPartition::m_mesh
private

Definition at line 208 of file MeshPartition.h.

Referenced by PartitionMesh(), and PrintPartInfo().

std::map<int, MeshEntity> Nektar::LibUtilities::MeshPartition::m_meshComposites
private

Definition at line 190 of file MeshPartition.h.

Referenced by GetCompositeOrdering(), OutputPartition(), ReadExpansions(), and ReadGeometry().

std::map<MeshCurvedKey, MeshCurved> Nektar::LibUtilities::MeshPartition::m_meshCurved
private

Definition at line 188 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MeshCurvedPts> Nektar::LibUtilities::MeshPartition::m_meshCurvedPts
private

Definition at line 189 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MeshEntity> Nektar::LibUtilities::MeshPartition::m_meshEdges
private

Definition at line 185 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MeshEntity> Nektar::LibUtilities::MeshPartition::m_meshElements
private

Definition at line 187 of file MeshPartition.h.

Referenced by CreateGraph(), GetElementIDs(), OutputPartition(), PartitionMesh(), ReadGeometry(), and WeightElements().

std::map<int, MeshEntity> Nektar::LibUtilities::MeshPartition::m_meshFaces
private

Definition at line 186 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MeshVertex> Nektar::LibUtilities::MeshPartition::m_meshVertices
private

Definition at line 184 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

int Nektar::LibUtilities::MeshPartition::m_numFields
private

Definition at line 182 of file MeshPartition.h.

Referenced by ReadExpansions(), and WeightElements().

std::map<int, char> Nektar::LibUtilities::MeshPartition::m_shape
private

Definition at line 199 of file MeshPartition.h.

Referenced by PrintPartInfo(), ReadExpansions(), and WeightElements().

bool Nektar::LibUtilities::MeshPartition::m_shared
private

Definition at line 216 of file MeshPartition.h.

Referenced by PartitionGraph(), and PartitionMesh().

std::map<int, MultiWeight> Nektar::LibUtilities::MeshPartition::m_vertBndWeights
private

Definition at line 203 of file MeshPartition.h.

Referenced by CreateGraph(), and WeightElements().

std::map<std::string, std::string> Nektar::LibUtilities::MeshPartition::m_vertexAttributes
private

Definition at line 192 of file MeshPartition.h.

Referenced by OutputPartition(), and ReadGeometry().

std::map<int, MultiWeight> Nektar::LibUtilities::MeshPartition::m_vertWeights
private

Definition at line 202 of file MeshPartition.h.

Referenced by CreateGraph(), and WeightElements().

bool Nektar::LibUtilities::MeshPartition::m_weightBnd
private

Definition at line 214 of file MeshPartition.h.

Referenced by PartitionGraph(), and ReadConditions().

bool Nektar::LibUtilities::MeshPartition::m_weightDofs
private

Definition at line 215 of file MeshPartition.h.

Referenced by PartitionGraph(), and ReadConditions().

bool Nektar::LibUtilities::MeshPartition::m_weightingRequired
private

Definition at line 213 of file MeshPartition.h.

Referenced by CreateGraph(), PartitionGraph(), PartitionMesh(), and ReadConditions().

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