void
NetgenMeshReader::readElements( UnsMesh& mesh )
//******************************************************************************
// Read element connectivity
//! \param[in] mesh Unstructured mesh object
//! \author J. Bakosi
//******************************************************************************
{
int nel;
// Read in number of tetrahedra
m_inFile >> nel;
if (!m_inFile.eof()) {
ErrChk( nel > 0, "Number of tetrahedra (volume elements) must be greater "
"than zero in file " + m_filename );
std::string s;
getline( m_inFile, s ); // finish reading the last line
// Read in tetrahedra element tags and connectivity
for (int i=0; i<nel; ++i) {
int tag;
std::array< std::size_t, 4 > n;
// tag n[1-4]
m_inFile >> tag >> n[3] >> n[0] >> n[1] >> n[2];
mesh.tettag().push_back( { tag } );
mesh.tetinpoel().push_back( n[0] );
mesh.tetinpoel().push_back( n[1] );
mesh.tetinpoel().push_back( n[2] );
mesh.tetinpoel().push_back( n[3] );
}
// Shift node IDs to start from zero
shiftToZero( mesh.tetinpoel() );
}
void
NetgenMeshReader::readNodes( UnsMesh& mesh )
//******************************************************************************
// Read nodes
//! \param[in] mesh Unstructured mesh object
//! \author J. Bakosi
//******************************************************************************
{
int nnode;
m_inFile >> nnode;
ErrChk( nnode > 0,
"Number of nodes must be greater than zero in file " + m_filename );
// Read in node coordinates: x-coord y-coord z-coord
for (int i=0; i<nnode; ++i) {
tk::real x, y, z;
m_inFile >> x >> y >> z;
mesh.x().push_back( x );
mesh.y().push_back( y );
mesh.z().push_back( z );
}
std::string s;
getline( m_inFile, s ); // finish reading the last line
}
void
GmshMeshWriter::writeElements( const UnsMesh& mesh )
//******************************************************************************
// Write "$Elements--$EndElements" section
//! \param[in] mesh Unstructured mesh object
//! \author J. Bakosi
//******************************************************************************
{
m_outFile << "$Elements" << std::endl;
// Write out number of elements
m_outFile << mesh.lininpoel().size()/2 +
mesh.triinpoel().size()/3 +
mesh.tetinpoel().size()/4
<< std::endl;
// Write out line element ids, tags, and connectivity (node list)
writeElemBlock( 2, GmshElemType::LIN, mesh.lintag(), mesh.lininpoel() );
// Write out triangle element ids, tags, and connectivity (node list)
writeElemBlock( 3, GmshElemType::TRI, mesh.tritag(), mesh.triinpoel() );
// Write out terahedron element ids, tags, and connectivity (node list)
writeElemBlock( 4, GmshElemType::TET, mesh.tettag(), mesh.tetinpoel() );
if (isBinary()) m_outFile << std::endl;
m_outFile << "$EndElements" << std::endl;
}
void
HyperMeshReader::readNodes( const std::string& filename, UnsMesh& mesh ) const
// *****************************************************************************
// Read nodes
//! \param[in] filename Filename to read nodes from
//! \param[in] mesh Unstructured mesh object to put nodes coordinates
//! \note We throw away the node ID, which means the nodes must be in order.
//! \author J. Bakosi
// *****************************************************************************
{
// Read in node coordinates: x-coord y-coord z-coord
for (auto& line : tk::Reader(filename).lines()) {
std::stringstream ss(line);
int id;
tk::real x, y, z;
ss >> id >> x >> y >> z;
mesh.x().push_back( x );
mesh.y().push_back( y );
mesh.z().push_back( z );
}
}
void
HyperMeshReader::readElements( const std::string& filename, UnsMesh& mesh )
const
// *****************************************************************************
// Read element connectivity
//! \param[in] filename Filename to read nodes from
//! \param[in] mesh Unstructured mesh object to put element connectivity
//! \note We throw away the element ID.
//! \author J. Bakosi
// *****************************************************************************
{
for (auto& line : tk::Reader(filename).lines()) {
std::stringstream ss(line);
int id;
std::array< std::size_t, 4 > n;
ss >> id >> n[0] >> n[1] >> n[2] >> n[3];
mesh.tetinpoel().push_back( n[0] );
mesh.tetinpoel().push_back( n[1] );
mesh.tetinpoel().push_back( n[2] );
mesh.tetinpoel().push_back( n[3] );
}
}
std::vector< std::pair< std::string, tk::real > >
writeUnsMesh( const tk::Print& print,
const std::string& filename,
UnsMesh& mesh,
bool reorder )
// *****************************************************************************
// Write unstructured mesh to file
//! \param[in] print Pretty printer
//! \param[in] filename Filename to write mesh to
//! \param[in] mesh Unstructured mesh object to write from
//! \param[in] reorder Whether to also reorder mesh nodes
//! \return Vector of time stamps consisting of a timer label (a string), and a
//! time state (a tk::real in seconds) measuring the renumber and the mesh
//! write time
//! \author J. Bakosi
// *****************************************************************************
{
std::vector< std::pair< std::string, tk::real > > times;
tk::Timer t;
if (reorder) {
print.diagstart( "Reordering mesh nodes ..." );
auto& inpoel = mesh.tetinpoel();
const auto psup = tk::genPsup( inpoel, 4, tk::genEsup( inpoel, 4 ) );
std::vector< std::size_t > map, invmap;
std::tie( map, invmap ) = tk::renumber( psup );
tk::remap( inpoel, map );
print.diagend( "done" );
times.emplace_back( "Renumber mesh", t.dsec() );
t.zero();
}
print.diagstart( "Writing mesh to file ..." );
const auto meshtype = pickOutput( filename );
if (meshtype == MeshWriter::GMSH)
GmshMeshWriter( filename ).writeMesh( mesh );
else if (meshtype == MeshWriter::NETGEN)
NetgenMeshWriter( filename ).writeMesh( mesh );
else if (meshtype== MeshWriter::EXODUSII)
ExodusIIMeshWriter( filename, ExoWriter::CREATE ).writeMesh( mesh );
print.diagend( "done" );
times.emplace_back( "Write mesh to file", t.dsec() );
return times;
}
void
GmshMeshWriter::writeNodes( const UnsMesh& mesh )
//******************************************************************************
// Write "$Nodes--$EndNodes" section
//! \param[in] mesh Unstructured mesh object
//! \author J. Bakosi
//******************************************************************************
{
m_outFile << "$Nodes" << std::endl;
// Write out number of nodes
m_outFile << mesh.nnode() << std::endl;
// Write node ids and coordinates: node-number x-coord y-coord z-coord
if (isASCII()) {
for (std::size_t i=0; i<mesh.nnode(); ++i) {
m_outFile << i+1 << " " << std::setprecision(16)
<< mesh.x()[i] << " "
<< mesh.y()[i] << " "
<< mesh.z()[i] << std::endl;
}
} else {
for (std::size_t i=0; i<mesh.nnode(); ++i) {
// gmsh likes one-based node ids
int I = static_cast< int >( i+1 );
m_outFile.write(
reinterpret_cast<const char*>(&I), sizeof(int) );
m_outFile.write(
reinterpret_cast<const char*>(&mesh.x()[i]), sizeof(double) );
m_outFile.write(
reinterpret_cast<const char*>(&mesh.y()[i]), sizeof(double) );
m_outFile.write(
reinterpret_cast<const char*>(&mesh.z()[i]), sizeof(double) );
}
m_outFile << std::endl;
}
m_outFile << "$EndNodes" << std::endl;
}
