QCAD::SchrodingerProblem::SchrodingerProblem( const Teuchos::RCP<Teuchos::ParameterList>& params_,
const Teuchos::RCP<ParamLib>& paramLib_,
const int numDim_,
Teuchos::RCP<const Teuchos::Comm<int> >& commT_):
Albany::AbstractProblem(params_, paramLib_, 1),
commT(commT_), havePotential(false),
numDim(numDim_)
{
havePotential = params->isSublist("Potential");
//Note: can't use get("ParamName" , <default>) form b/c non-const
energy_unit_in_eV = 1.0; //default eV
if(params->isType<double>("Energy Unit In Electron Volts"))
energy_unit_in_eV = params->get<double>("Energy Unit In Electron Volts");
*out << "Energy unit = " << energy_unit_in_eV << " eV" << std::endl;
length_unit_in_m = 1e-6; //default to um
if(params->isType<double>("Length Unit In Meters"))
length_unit_in_m = params->get<double>("Length Unit In Meters");
*out << "Length unit = " << length_unit_in_m << " meters" << std::endl;
mtrlDbFilename = "materials.xml";
if(params->isType<std::string>("MaterialDB Filename"))
mtrlDbFilename = params->get<std::string>("MaterialDB Filename");
bOnlySolveInQuantumBlocks = false;
if(params->isType<bool>("Only solve in quantum blocks"))
bOnlySolveInQuantumBlocks = params->get<bool>("Only solve in quantum blocks");
potentialFieldName = "V"; // name for potential at QPs field
potentialAuxIndex = -1; // if >= 0, index within workset's auxData multivector to import potential from
//Extract Aux index if necessary:
// Note: we can't do this from within SchrodingerPotential evaluator
// since it isn't created in the case of importing from an aux vector.
if(params->isSublist("Potential")) {
Teuchos::ParameterList& pList = params->sublist("Potential");
if(pList.isType<std::string>("Type")) {
if(pList.get<std::string>("Type") == "From Aux Data Vector") {
//do Potential list validation since SchrodingerPotential evaluator doesn't
// ** maybe we should allow other values from SchrodingerPotential as well? **
Teuchos::ParameterList validPL("Valid Schrodinger Potential Params");
validPL.set<std::string>("Type", "defaultType", "Switch between different potential types");
validPL.set<int>("Aux Index", 0, "Index of aux vector to import potential from.");
pList.validateParameters(validPL, 0);
potentialAuxIndex = pList.get<int>("Aux Index"); //error if doesn't exist
}
}
}
// Problem is transient
params->set<int>("Number Of Time Derivatives", 1);
TEUCHOS_TEST_FOR_EXCEPTION(params->isSublist("Source Functions"), Teuchos::Exceptions::InvalidParameter,
"\nError! Schrodinger problem does not parse Source Functions sublist\n"
<< "\tjust Potential sublist " << std::endl);
}
//================================================================
//================================================================
// RN_20091215: This needs to be called only once per time step
// in the beginning to set up the problem.
//================================================================
void FC_FUNC(inittrilinos,INITTRILINOS) (int& bandwidth, int& mySize,
int* myIndicies, double* myX, double* myY, double* myZ,
int* mpi_comm_f) {
// mpi_comm_f: CISM's fortran mpi communicator
#ifdef GLIMMER_MPI
// Make sure the MPI_Init in Fortran is recognized by C++.
// We used to call an extra MPI_Init if (!flag), but the behavior of doing so is uncertain,
// especially if CISM's MPI communicator is a subset of MPI_COMM_WORLD (as can be the case in CESM).
// Thus, for now, we die with an error message if C++ perceives MPI to be uninitialized.
// If this causes problems (e.g., if certain MPI implementations seem not to recognize
// that MPI has already been initialized), then we will revisit how to handle this.
int flag;
MPI_Initialized(&flag);
if (!flag) {
cout << "ERROR in inittrilinos: MPI not initialized according to C++ code" << endl;
exit(1);
}
MPI_Comm mpi_comm_c = MPI_Comm_f2c(*mpi_comm_f);
Epetra_MpiComm comm(mpi_comm_c);
Teuchos::MpiComm<int> tcomm(Teuchos::opaqueWrapper(mpi_comm_c));
#else
Epetra_SerialComm comm;
Teuchos::SerialComm<int> tcomm;
#endif
Teuchos::RCP<const Epetra_Map> rowMap =
Teuchos::rcp(new Epetra_Map(-1,mySize,myIndicies,1,comm) );
TEUCHOS_TEST_FOR_EXCEPTION(!rowMap->UniqueGIDs(), std::logic_error,
"Error: inittrilinos, myIndices array needs to have Unique entries"
<< " across all processor.");
// Diagnostic output for partitioning
int minSize, maxSize;
comm.MinAll(&mySize, &minSize, 1);
comm.MaxAll(&mySize, &maxSize, 1);
if (comm.MyPID()==0)
cout << "\nPartition Info in init_trilinos: Total nodes = " << rowMap->NumGlobalElements()
<< " Max = " << maxSize << " Min = " << minSize
<< " Ave = " << rowMap->NumGlobalElements() / comm.NumProc() << endl;
soln = Teuchos::rcp(new Epetra_Vector(*rowMap));
// Read parameter list once
try {
pl = Teuchos::rcp(new Teuchos::ParameterList("Trilinos Options"));
Teuchos::updateParametersFromXmlFileAndBroadcast("trilinosOptions.xml", pl.ptr(), tcomm);
Teuchos::ParameterList validPL("Valid List");;
validPL.sublist("Stratimikos"); validPL.sublist("Piro");
pl->validateParameters(validPL, 0);
}
catch (std::exception& e) {
cout << "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n"
<< e.what() << "\nExiting: Invalid trilinosOptions.xml file."
<< "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" << endl;
exit(1);
}
catch (...) {
cout << "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n"
<< "\nExiting: Invalid trilinosOptions.xml file."
<< "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" << endl;
exit(1);
}
try {
// Set the coordinate position of the nodes for ML for repartitioning (important for #procs > 100s)
if (pl->sublist("Stratimikos").isParameter("Preconditioner Type")) {
if ("ML" == pl->sublist("Stratimikos").get<string>("Preconditioner Type")) {
Teuchos::ParameterList& mlList =
pl->sublist("Stratimikos").sublist("Preconditioner Types").sublist("ML").sublist("ML Settings");
mlList.set("x-coordinates",myX);
mlList.set("y-coordinates",myY);
mlList.set("z-coordinates",myZ);
mlList.set("PDE equations", 1);
}
}
out = Teuchos::VerboseObjectBase::getDefaultOStream();
// Reset counters every time step: can remove these lines to have averages over entire run
linearSolveIters_total = 0;
linearSolveCount=0;
linearSolveSuccessCount = 0;
// Create an interface that holds a CrsMatrix instance and some useful methods.
interface = Teuchos::rcp(new TrilinosMatrix_Interface(rowMap, bandwidth, comm));
Stratimikos::DefaultLinearSolverBuilder linearSolverBuilder;
linearSolverBuilder.setParameterList(Teuchos::sublist(pl, "Stratimikos"));
lowsFactory = linearSolverBuilder.createLinearSolveStrategy("");
lowsFactory->setOStream(out);
lowsFactory->setVerbLevel(Teuchos::VERB_LOW);
lows=Teuchos::null;
thyraOper=Teuchos::null;
}
TEUCHOS_STANDARD_CATCH_STATEMENTS(true, std::cerr, success);
if (!success) exit(1);
}
