void RectangularCutCubicMeshGenerator::loadMesh(RectangularCutCubicMesh* mesh,
GCMDispatcher* dispatcher, float h, int numX, int numY, int numZ,
int minX, int minY, int minZ,
int maxX, int maxY, int maxZ)
{
mesh->setNumX(numX);
mesh->setNumY(numY);
mesh->setNumZ(numZ);
static int startNumber = 0;
for( int k = 0; k <= numZ; k++ )
for( int j = 0; j <= numY; j++ )
for( int i = 0; i <= numX; i++ )
{
int n = i*(numY+1)*(numZ+1) + j*(numZ+1) + k + startNumber;
float x = i*h;
float y = j*h;
float z = k*h;
CalcNode* node = new CalcNode();//(n, x, y, z);
node->number = n;
node->coords[0] = x;
node->coords[1] = y;
node->coords[2] = z;
node->setPlacement(true);
mesh->addNode( *node );
}
mesh->setCutArea( AABB(minX*h, maxX*h, minY*h, maxY*h, minZ*h, maxZ*h) );
mesh->preProcess();
startNumber += 100000000;
}
void MshTetrFileReader::readFile(string file, TetrMeshFirstOrder* mesh, GCMDispatcher* dispatcher, int rank, bool ignoreDispatcher)
{
assert_true(mesh);
assert_true(dispatcher);
int tetrsCount = 0;
int fileVer;
string str;
int tmp_int;
float tmp_float;
int number_of_nodes;
int number_of_elements;
ifstream infile;
infile.open(file.c_str(), ifstream::in);
if(!infile.is_open())
THROW_INVALID_INPUT( "Can not open msh file" );
LOG_DEBUG("Reading msh file...");
infile >> str;
if(strcmp(str.c_str(),"$MeshFormat") != 0)
THROW_INVALID_INPUT("Wrong file format");
infile >> tmp_float >> tmp_int >> tmp_int;
fileVer = (int)(tmp_float*10);
infile >> str;
if(strcmp(str.c_str(),"$EndMeshFormat") != 0)
THROW_INVALID_INPUT("Wrong file format");
LOG_DEBUG("Header Ok");
infile >> str;
if(strcmp(str.c_str(),"$Nodes") != 0)
THROW_INVALID_INPUT("Wrong file format");
infile >> number_of_nodes;
LOG_DEBUG("File contains " << number_of_nodes << " nodes");
vector<CalcNode*>* nodes = new vector<CalcNode*>;
for(int i = 0; i < number_of_nodes; i++)
{
infile >> tmp_int;
if( tmp_int > 0 )
{
float coords[3];
infile >> coords[0] >> coords[1] >> coords[2];
if( ignoreDispatcher || dispatcher->isMine( coords, mesh->getBody()->getId() ) )
{
CalcNode* node = new CalcNode();
node->number = tmp_int - 1;
node->coords[0] = coords[0];
node->coords[1] = coords[1];
node->coords[2] = coords[2];
node->setPlacement(true);
nodes->push_back( node );
}
}
else
{
void TetrMeshSecondOrder::fillSecondOrderNode(CalcNode& newNode, int nodeIdx1, int nodeIdx2)
{
CalcNode& node1 = getNode(nodeIdx1);
CalcNode& node2 = getNode(nodeIdx2);
for (int i = 0; i < 3; i++)
newNode.coords[i] = (node1.coords[i] + node2.coords[i]) * 0.5;
for (int i = 0; i < 9; i++)
newNode.values[i] = (node1.values[i] + node2.values[i]) * 0.5;
newNode.setRho((node1.getRho() + node2.getRho()) * 0.5);
newNode.setMaterialId(node1.getMaterialId());
newNode.setPlacement(true);
newNode.setOrder(2);
}
void Vtu2TetrFileReader::readFile(string file, TetrMeshSecondOrder* mesh, GCMDispatcher* dispatcher, int rank, bool ignoreDispatcher)
{
vtkXMLUnstructuredGridReader *xgr = vtkXMLUnstructuredGridReader::New();
vtkUnstructuredGrid *g = vtkUnstructuredGrid::New();
xgr->SetFileName(const_cast<char*>(file.c_str()));
xgr->Update();
g = xgr->GetOutput();
if( ignoreDispatcher )
{
LOG_DEBUG("Reading file ignoring dispatcher");
}
else
{
LOG_DEBUG("Dispatcher zones:");
dispatcher->printZones();
}
LOG_DEBUG("Number of points: " << g->GetNumberOfPoints());
LOG_DEBUG("Number of cells: " << g->GetNumberOfCells());
double v[3];
vtkDoubleArray *vel = (vtkDoubleArray*) g->GetPointData()->GetArray("velocity");
vel->SetNumberOfComponents(3);
vtkDoubleArray *sxx = (vtkDoubleArray*) g->GetPointData()->GetArray("sxx");
vtkDoubleArray *sxy = (vtkDoubleArray*) g->GetPointData()->GetArray("sxy");
vtkDoubleArray *sxz = (vtkDoubleArray*) g->GetPointData()->GetArray("sxz");
vtkDoubleArray *syy = (vtkDoubleArray*) g->GetPointData()->GetArray("syy");
vtkDoubleArray *syz = (vtkDoubleArray*) g->GetPointData()->GetArray("syz");
vtkDoubleArray *szz = (vtkDoubleArray*) g->GetPointData()->GetArray("szz");
vtkIntArray *matId = (vtkIntArray*) g->GetPointData()->GetArray("materialID");
vtkDoubleArray *rho = (vtkDoubleArray*) g->GetPointData()->GetArray("rho");
vtkIntArray *nodeNumber = (vtkIntArray*) g->GetPointData ()->GetArray("nodeNumber");
vtkIntArray *publicFlags = (vtkIntArray*) g->GetPointData ()->GetArray("publicFlags");
vtkIntArray *privateFlags = (vtkIntArray*) g->GetPointData ()->GetArray("privateFlags");
vtkIntArray *nodeBorderConditionId = (vtkIntArray*) g->GetPointData ()->GetArray("borderConditionId");
vector<CalcNode*>* nodes = new vector<CalcNode*>;
for( int i = 0; i < g->GetNumberOfPoints(); i++ )
{
double* dp = g->GetPoint(i);
if( ignoreDispatcher || dispatcher->isMine( dp, mesh->getBody()->getId() ) )
{
CalcNode* node = new CalcNode();
node->number = nodeNumber->GetValue(i);
node->coords[0] = dp[0];
node->coords[1] = dp[1];
node->coords[2] = dp[2];
vel->GetTupleValue(i, v);
node->vx = v[0];
node->vy = v[1];
node->vz = v[2];
node->sxx = sxx->GetValue(i);
node->sxy = sxy->GetValue(i);
node->sxz = sxz->GetValue(i);
node->syy = syy->GetValue(i);
node->syz = syz->GetValue(i);
node->szz = szz->GetValue(i);
node->setMaterialId( matId->GetValue(i) );
node->setRho( rho->GetValue(i) );
node->setPublicFlags( publicFlags->GetValue(i) );
node->setPrivateFlags( privateFlags->GetValue(i) );
node->setBorderConditionId( nodeBorderConditionId->GetValue(i) );
if( !ignoreDispatcher )
node->setPlacement(true);
nodes->push_back( node );
}
}
LOG_DEBUG("Finished reading nodes");
LOG_DEBUG("There are " << nodes->size() << " local nodes");
mesh->createNodes( nodes->size() );
for(unsigned int i = 0; i < nodes->size(); i++)
{
mesh->addNode( *nodes->at(i) );
}
for(unsigned int i = 0; i < nodes->size(); i++)
{
delete( nodes->at(i));
}
nodes->clear();
delete nodes;
vtkIntArray* tetr2ndOrderNodes = (vtkIntArray*) g->GetCellData ()->GetArray ("tetr2ndOrderNodes");
assert_eq(tetr2ndOrderNodes->GetNumberOfComponents (), 6);
vtkIntArray* tetr1stOrderNodes = (vtkIntArray*) g->GetCellData ()->GetArray ("tetr1stOrderNodes");
vtkIntArray* tetrNumber = (vtkIntArray*) g->GetCellData ()->GetArray ("tetrNumber");
assert_eq(tetr1stOrderNodes->GetNumberOfComponents (), 4);
vector<TetrSecondOrder*>* tetrs = new vector<TetrSecondOrder*>;
TetrSecondOrder new_tetr;
for( int i = 0; i < g->GetNumberOfCells(); i++ )
{
new_tetr.number = tetrNumber->GetValue(i);
tetr1stOrderNodes->GetTupleValue (i, new_tetr.verts);
tetr2ndOrderNodes->GetTupleValue (i, new_tetr.addVerts);
/*vtkTetra *vt = (vtkTetra*) g->GetCell(i);
int vert[4];
vert[0] = vt->GetPointId(0);
vert[1] = vt->GetPointId(1);
vert[2] = vt->GetPointId(2);
vert[3] = vt->GetPointId(3);*/
if( mesh->hasNode(new_tetr.verts[0])
|| mesh->hasNode(new_tetr.verts[1])
|| mesh->hasNode(new_tetr.verts[2])
|| mesh->hasNode(new_tetr.verts[3]) )
tetrs->push_back( new TetrSecondOrder( new_tetr.number, new_tetr.verts, new_tetr.addVerts ) );
}
LOG_DEBUG("File contains " << g->GetNumberOfCells() << " tetrs");
LOG_DEBUG("There are " << tetrs->size() << " local tetrs");
map<int,int> remoteNodes;
mesh->createTetrs( tetrs->size() );
for(unsigned int i = 0; i < tetrs->size(); i++)
{
TetrSecondOrder* tetr = tetrs->at(i);
mesh->addTetr2( *tetr );
for(int j = 0; j < 4; j++)
if( ! mesh->hasNode( tetr->verts[j] ) )
remoteNodes[tetr->verts[j]] = i;
for(int j = 0; j < 6; j++)
if( ! mesh->hasNode( tetr->addVerts[j] ) )
remoteNodes[tetr->addVerts[j]] = i;
}
for(unsigned int i = 0; i < tetrs->size(); i++)
{
delete( tetrs->at(i) );
}
tetrs->clear();
delete tetrs;
LOG_DEBUG("Finished reading elements");
LOG_DEBUG("Reading required remote nodes");
LOG_DEBUG("We expect " << remoteNodes.size() << " nodes" );
int remoteNodesCount = 0;
CalcNode tmpNode;
for( int i = 0; i < g->GetNumberOfPoints(); i++ )
{
if( remoteNodes.find( nodeNumber->GetValue(i) ) != remoteNodes.end() )
{
double* dp = g->GetPoint(i);
tmpNode.number = nodeNumber->GetValue(i);
tmpNode.coords[0] = dp[0];
tmpNode.coords[1] = dp[1];
tmpNode.coords[2] = dp[2];
vel->GetTupleValue(i, v);
tmpNode.vx = v[0];
tmpNode.vy = v[1];
tmpNode.vz = v[2];
tmpNode.sxx = sxx->GetValue(i);
tmpNode.sxy = sxy->GetValue(i);
tmpNode.sxz = sxz->GetValue(i);
tmpNode.syy = syy->GetValue(i);
tmpNode.syz = syz->GetValue(i);
tmpNode.szz = szz->GetValue(i);
tmpNode.setMaterialId( matId->GetValue(i) );
tmpNode.setRho( rho->GetValue(i) );
tmpNode.setPublicFlags( publicFlags->GetValue(i) );
tmpNode.setPrivateFlags( privateFlags->GetValue(i) );
tmpNode.setBorderConditionId( nodeBorderConditionId->GetValue(i) );
tmpNode.setPlacement(false);
mesh->addNode(tmpNode);
remoteNodesCount++;
}
}
LOG_DEBUG("Read " << remoteNodesCount << " remote nodes");
LOG_DEBUG("Finished reading nodes");
LOG_DEBUG("File successfylly read.");
LOG_DEBUG("There are " << mesh->getNodesNumber() << " nodes is the mesh");
LOG_DEBUG("Checking tetrs and nodes");
for( int i = 0; i < mesh->getTetrsNumber(); i++ )
{
TetrSecondOrder& tetr = mesh->getTetr2ByLocalIndex(i);
for (int j = 0; j < 4; j++)
if ( ! mesh->hasNode(tetr.verts[j]) )
{
LOG_ERROR("Can not find node " << tetr.verts[j] << " required by local tetr " << i);
THROW_BAD_MESH("Missed node");
}
for (int j = 0; j < 6; j++)
if ( ! mesh->hasNode(tetr.addVerts[j]) )
{
LOG_ERROR("Can not find node " << tetr.addVerts[j] << " required by local tetr " << i);
THROW_BAD_MESH("Missed node");
}
}
//xgr->Delete();
//g->Delete();
}
void VtuTetrFileReader::readFile(string file, TetrMeshFirstOrder* mesh, GCMDispatcher* dispatcher, int rank)
{
vtkXMLUnstructuredGridReader *xgr = vtkXMLUnstructuredGridReader::New();
vtkUnstructuredGrid *g = vtkUnstructuredGrid::New();
xgr->SetFileName(const_cast<char*>(file.c_str()));
xgr->Update();
g = xgr->GetOutput();
LOG_DEBUG("Number of points: " << g->GetNumberOfPoints());
LOG_DEBUG("Number of cells: " << g->GetNumberOfCells());
double v[3];
vtkDoubleArray *vel = (vtkDoubleArray*) g->GetPointData()->GetArray("velocity");
vel->SetNumberOfComponents(3);
vtkDoubleArray *sxx = (vtkDoubleArray*) g->GetPointData()->GetArray("sxx");
vtkDoubleArray *sxy = (vtkDoubleArray*) g->GetPointData()->GetArray("sxy");
vtkDoubleArray *sxz = (vtkDoubleArray*) g->GetPointData()->GetArray("sxz");
vtkDoubleArray *syy = (vtkDoubleArray*) g->GetPointData()->GetArray("syy");
vtkDoubleArray *syz = (vtkDoubleArray*) g->GetPointData()->GetArray("syz");
vtkDoubleArray *szz = (vtkDoubleArray*) g->GetPointData()->GetArray("szz");
vtkIntArray *matId = (vtkIntArray*) g->GetPointData()->GetArray("materialID");
vtkDoubleArray *rho = (vtkDoubleArray*) g->GetPointData()->GetArray("rho");
vtkIntArray *publicFlags = (vtkIntArray*) g->GetPointData ()->GetArray("publicFlags");
vtkIntArray *privateFlags = (vtkIntArray*) g->GetPointData ()->GetArray("privateFlags");
vector<CalcNode*>* nodes = new vector<CalcNode*>;
for( int i = 0; i < g->GetNumberOfPoints(); i++ )
{
double* dp = g->GetPoint(i);
if( dispatcher->isMine( dp, mesh->getBody()->getId() ) )
{
CalcNode* node = new CalcNode();
node->number = i;
node->coords[0] = dp[0];
node->coords[1] = dp[1];
node->coords[2] = dp[2];
vel->GetTupleValue(i, v);
node->vx = v[0];
node->vy = v[1];
node->vz = v[2];
node->sxx = sxx->GetValue(i);
node->sxy = sxy->GetValue(i);
node->sxz = sxz->GetValue(i);
node->syy = syy->GetValue(i);
node->syz = syz->GetValue(i);
node->szz = szz->GetValue(i);
node->setMaterialId( matId->GetValue(i) );
node->setRho( rho->GetValue(i) );
node->setPublicFlags( publicFlags->GetValue(i) );
node->setPrivateFlags( privateFlags->GetValue(i) );
node->setPlacement(true);
nodes->push_back( node );
}
}
LOG_DEBUG("Finished reading nodes");
LOG_DEBUG("There are " << nodes->size() << " local nodes");
mesh->createNodes( nodes->size() );
for(unsigned int i = 0; i < nodes->size(); i++)
{
mesh->addNode( *nodes->at(i) );
}
nodes->clear();
delete nodes;
vector<TetrFirstOrder*>* tetrs = new vector<TetrFirstOrder*>;
for( int i = 0; i < g->GetNumberOfCells(); i++ )
{
int number = tetrs->size();
vtkTetra *vt = (vtkTetra*) g->GetCell(i);
int vert[4];
vert[0] = vt->GetPointId(0);
vert[1] = vt->GetPointId(1);
vert[2] = vt->GetPointId(2);
vert[3] = vt->GetPointId(3);
if( mesh->hasNode(vert[0])
|| mesh->hasNode(vert[1])
|| mesh->hasNode(vert[2])
|| mesh->hasNode(vert[3]) )
tetrs->push_back( new TetrFirstOrder( number, vert ) );
}
LOG_DEBUG("File contains " << g->GetNumberOfCells() << " tetrs");
LOG_DEBUG("There are " << tetrs->size() << " local tetrs");
map<int,int> remoteNodes;
mesh->createTetrs( tetrs->size() );
for(unsigned int i = 0; i < tetrs->size(); i++)
{
TetrFirstOrder* tetr = tetrs->at(i);
mesh->addTetr( *tetr );
for(int j = 0; j < 4; j++)
if( ! mesh->hasNode( tetr->verts[j] ) )
remoteNodes[tetr->verts[j]] = i;
}
tetrs->clear();
delete tetrs;
LOG_DEBUG("Finished reading elements");
LOG_DEBUG("Reading required remote nodes");
LOG_DEBUG("We expect " << remoteNodes.size() << " nodes" );
int remoteNodesCount = 0;
CalcNode tmpNode;
for( int i = 0; i < g->GetNumberOfPoints(); i++ )
{
if( remoteNodes.find( i ) != remoteNodes.end() )
{
double* dp = g->GetPoint(i);
tmpNode.number = i;
tmpNode.coords[0] = dp[0];
tmpNode.coords[1] = dp[1];
tmpNode.coords[2] = dp[2];
vel->GetTupleValue(i, v);
tmpNode.vx = v[0];
tmpNode.vy = v[1];
tmpNode.vz = v[2];
tmpNode.sxx = sxx->GetValue(i);
tmpNode.sxy = sxy->GetValue(i);
tmpNode.sxz = sxz->GetValue(i);
tmpNode.syy = syy->GetValue(i);
tmpNode.syz = syz->GetValue(i);
tmpNode.szz = szz->GetValue(i);
tmpNode.setMaterialId( matId->GetValue(i) );
tmpNode.setRho( rho->GetValue(i) );
tmpNode.setPublicFlags( publicFlags->GetValue(i) );
tmpNode.setPrivateFlags( privateFlags->GetValue(i) );
tmpNode.setPlacement(false);
mesh->addNode(tmpNode);
remoteNodesCount++;
}
}
LOG_DEBUG("Read " << remoteNodesCount << " remote nodes");
LOG_DEBUG("Finished reading nodes");
LOG_DEBUG("File successfylly read.");
LOG_DEBUG("There are " << mesh->getNodesNumber() << " nodes is the mesh");
}