// Constructor - creates the Epetra objects (maps and vectors)
ConvDiff_PDE::ConvDiff_PDE(
Epetra_Comm& Comm_ ,
double peclet_ ,
double radiation_ ,
double kappa_ ,
double bcWeight_ ,
double xmin_ ,
double xmax_ ,
double Tleft_ ,
double Tright_ ,
int NumGlobalUnknowns_ ,
std::string name_ ) :
GenericEpetraProblem(Comm_, NumGlobalUnknowns_, name_),
xmin ( xmin_ ) ,
xmax ( xmax_ ) ,
Tleft ( Tleft_ ) ,
Tright ( Tright_ ) ,
peclet ( peclet_ ) ,
radiation ( radiation_ ) ,
kappa ( kappa_ ) ,
bcWeight ( bcWeight_ ) ,
expandJacobian ( true ) ,
depProbPtr ( NULL )
{
// Create mesh and solution vectors
// We first initialize the mesh and then the solution since the latter can depend on the mesh.
xptr = Teuchos::rcp( new Epetra_Vector(*StandardMap) );
dx = (xmax - xmin) / ( (double) NumGlobalNodes - 1 );
for( int i = 0; i < NumMyNodes; ++i )
(*xptr)[i]=xmin + dx*((double) StandardMap->MinMyGID()+i);
// Create extra vector needed for transient problem interface
oldSolution = Teuchos::rcp( new Epetra_Vector(*StandardMap) );
// Create and initialize (using default provided) the solution vector
initialSolution = Teuchos::rcp(new Epetra_Vector(*StandardMap));
initializeSolution();
// Allocate the memory for a matrix dynamically (i.e. the graph is dynamic).
AA = Teuchos::rcp( new Epetra_CrsGraph(Copy, *StandardMap, 0) );
generateGraph();
#ifdef DEBUG
AA->Print(cout);
#endif
// Create a matrix using the graph just created - this creates a
// static graph so we can refill the new matirx after FillComplete()
// is called.
A = Teuchos::rcp(new Epetra_CrsMatrix (Copy, *AA));
A->FillComplete();
// Create the Importer needed for FD coloring
ColumnToOverlapImporter = Teuchos::rcp( new Epetra_Import(A->ColMap(),*OverlapMap) );
}
// Constructor - creates the Epetra objects (maps and vectors)
HMX_PDE::HMX_PDE(Epetra_Comm& comm,
double diffCoef_,
double Const_R_,
double Steric_C_,
double PreExp_A_,
double ActEnergy_,
map<string, double> SrcTermExponent_,
map<string, double> SrcTermWeight_,
int numGlobalNodes,
std::string name_) :
GenericEpetraProblem(comm, numGlobalNodes, name_),
xmin(0.0),
xmax(1.0),
dt(2.0e-1),
diffCoef(diffCoef_),
Const_R(Const_R_),
StericCoef(Steric_C_),
PreExp_A(PreExp_A_),
ActEnergy(ActEnergy_),
SrcTermExponent(SrcTermExponent_),
SrcTermWeight(SrcTermWeight_)
{
// Create mesh and solution vectors
// We first initialize the mesh and then the solution since the latter
// can depend on the mesh.
xptr = Teuchos::rcp( new Epetra_Vector(*StandardMap) );
double Length= xmax - xmin;
dx=Length/((double) NumGlobalNodes-1);
for (int i=0; i < NumMyNodes; i++) {
(*xptr)[i]=xmin + dx*((double) StandardMap->MinMyGID()+i);
}
// Create extra vector needed for this transient problem
oldSolution = new Epetra_Vector(*StandardMap);
// Next we create and initialize (using default provided) the solution vector
initialSolution = Teuchos::rcp(new Epetra_Vector(*StandardMap));
initializeSolution();
// Allocate the memory for a matrix dynamically (i.e. the graph is dynamic).
AA = Teuchos::rcp( new Epetra_CrsGraph(Copy, *StandardMap, 0) );
generateGraph();
#ifdef DEBUG
AA->Print(cout);
#endif
// Create a matrix using the graph just created - this creates a
// static graph so we can refill the new matirx after FillComplete()
// is called.
A = Teuchos::rcp(new Epetra_CrsMatrix (Copy, *AA));
A->FillComplete();
// Create the Importer needed for FD coloring
ColumnToOverlapImporter = new Epetra_Import(A->ColMap(),*OverlapMap);
}
void
MultiscaleModelFSI1D::setupModel()
{
#ifdef HAVE_LIFEV_DEBUG
debugStream ( 8130 ) << "MultiscaleModelFSI1D::setupModel() \n";
#endif
//FEspace
setupFESpace();
//Setup solution
M_solver->setupSolution ( *M_solution );
M_solver->setupSolution ( *M_solution_tn );
//Set default BC (has to be called after setting other BC)
M_bc->handler()->setDefaultBC();
M_bc->setPhysicalSolver ( M_solver );
M_bc->setSolution ( M_solution );
M_bc->setFluxSource ( M_flux, M_source );
//Post-processing
#ifdef HAVE_HDF5
M_exporter->setMeshProcId ( M_exporterMesh, M_comm->MyPID() );
DOF tmpDof ( *M_exporterMesh, M_feSpace->refFE() );
std::vector<Int> myGlobalElements ( tmpDof.globalElements ( *M_exporterMesh ) );
MapEpetra map ( -1, myGlobalElements.size(), &myGlobalElements[0], M_comm );
M_solver->setupSolution ( *M_exporterSolution, map, true );
M_exporter->addVariable ( IOData_Type::ScalarField, "Area ratio (fluid)", M_feSpace, (*M_exporterSolution) ["AoverA0minus1"], static_cast <UInt> ( 0 ) );
M_exporter->addVariable ( IOData_Type::ScalarField, "Flow rate (fluid)", M_feSpace, (*M_exporterSolution) ["Q"], static_cast <UInt> ( 0 ) );
//M_exporter->addVariable( IOData_Type::ScalarField, "W1", M_feSpace, (*M_exporterSolution)["W1"], static_cast <UInt> ( 0 ), M_feSpace->dof().numTotalDof() );
//M_exporter->addVariable( IOData_Type::ScalarField, "W2", M_feSpace, (*M_exporterSolution)["W2"], static_cast <UInt> ( 0 ), M_feSpace->dof().numTotalDof() );
M_exporter->addVariable ( IOData_Type::ScalarField, "Pressure (fluid)", M_feSpace, (*M_exporterSolution) ["P"], static_cast <UInt> ( 0 ) );
#endif
#ifdef HAVE_MATLAB_POSTPROCESSING
M_solver->resetOutput ( *M_exporterSolution );
#endif
//Setup solution
initializeSolution();
#ifdef JACOBIAN_WITH_FINITEDIFFERENCE
if ( M_couplings.size() > 0 )
{
createLinearBC();
updateLinearBC ( *M_solution );
setupLinearModel();
// Initialize the linear solution
copySolution ( *M_solution, *M_linearSolution );
}
#endif
}
// ===================================================
// Methods
// ===================================================
void ZeroDimensionalData::setup( const GetPot& dataFile,
bcPtr_Type bc,
const std::string & section )
{
if ( !M_time.get() )
M_time.reset( new time_Type( dataFile,
section + "/time_discretization" ) );
std::string circuirDataFile = dataFile( ( section + "/CircuitDataFile" ).data(),
"./inputFilexx.dat" );
GetPot dataFileCircuit( circuirDataFile );
std::string circuitFile = dataFileCircuit( "Files/InputFiles/CircuitFile",
"./circuitFilexx.dat" );
std::string folder = dataFileCircuit( "Files/OutputFiles/Folder",
"outputxx" );//TODO create folder output
std::string voltageFile = folder + "/" + dataFileCircuit( "Files/OutputFiles/VoltageFile",
"voltagexx.txt" );
std::string currentFile = folder + "/" + dataFileCircuit( "Files/OutputFiles/CurrentFile",
"currentxx.txt" );
std::string balanceFile = folder + "/" + dataFileCircuit( "Files/OutputFiles/BalanceCurrentinNode",
"balancexx.txt" );
M_voltageFileStream.open( voltageFile.c_str() );
M_currentFileStream.open( currentFile.c_str() );
M_balanceFileStream.open( balanceFile.c_str() );
//Build the Circuit
M_circuitData->buildCircuit( circuitFile.c_str(),
bc );
//assign varible index
assignVaribleIndex();
M_solverData.method = dataFile( ( section + "/Solver/method" ).data(), "IRK" );
M_solverData.numberTimeStep = dataFile( ( section + "/Solver/numberTimeStep" ).data(), 1 );
M_solverData.maxError = dataFile( ( section + "/Solver/maxError" ).data(), 1.0 );
M_solverData.reltol = dataFile( ( section + "/Solver/reltol" ).data(), 0.1 );
M_solverData.abstol = dataFile( ( section + "/Solver/abstol" ).data(), 1.0 );
M_solverData.maxOrder = dataFile( ( section + "/Solver/maxOrder" ).data(), 1 );
M_solverData.verbose = dataFile( ( section + "/Solver/verbose" ).data(), false );
M_solverData.verboseLevel = dataFile( ( section + "/Solver/verboseLevel" ).data(), 0 );
M_solverData.useNOX = dataFile( ( section + "/Solver/useNOX" ).data(), false );
M_solverData.fixTimeStep = dataFile( ( section + "/Solver/fixTimeStep" ).data(), true );
M_solverData.extraLSParamsFile = dataFile( ( section + "/Solver/extraLinearSolverParamsFile" ).data(), "./Extra_AztecOO_Params.xml" );
M_solverData.linearSolverParamsFile = dataFile( ( section + "/Solver/linearSolverParamsUsedFile" ).data(), "./lowsf.aztecoo.used.xml" );
//Set zero initial condition
// TODO: change to general initial condition
initializeSolution();
//Wrire Header OutputFiles
writeHeaders();
}
