void Bidomain::DoOdeRhs(
const Array<OneD, const Array<OneD, NekDouble> >&inarray,
Array<OneD, Array<OneD, NekDouble> >&outarray,
const NekDouble time)
{
int nq = m_fields[0]->GetNpoints();
m_cell->TimeIntegrate(inarray, outarray, time);
if (m_stimDuration > 0 && time < m_stimDuration)
{
Array<OneD,NekDouble> x0(nq);
Array<OneD,NekDouble> x1(nq);
Array<OneD,NekDouble> x2(nq);
Array<OneD,NekDouble> result(nq);
// get the coordinates
m_fields[0]->GetCoords(x0,x1,x2);
LibUtilities::EquationSharedPtr ifunc
= m_session->GetFunction("Stimulus", "u");
ifunc->Evaluate(x0,x1,x2,time, result);
Vmath::Vadd(nq, outarray[0], 1, result, 1, outarray[0], 1);
}
Vmath::Smul(nq, 1.0/m_capMembrane, outarray[0], 1, outarray[0], 1);
}
void Forcing::EvaluateFunction(
Array<OneD, MultiRegions::ExpListSharedPtr> pFields,
LibUtilities::SessionReaderSharedPtr pSession,
std::string pFieldName,
Array<OneD, NekDouble>& pArray,
const std::string& pFunctionName,
NekDouble pTime)
{
ASSERTL0(pSession->DefinesFunction(pFunctionName),
"Function '" + pFunctionName + "' does not exist.");
unsigned int nq = pFields[0]->GetNpoints();
if (pArray.num_elements() != nq)
{
pArray = Array<OneD, NekDouble> (nq);
}
LibUtilities::FunctionType vType;
vType = pSession->GetFunctionType(pFunctionName, pFieldName);
if (vType == LibUtilities::eFunctionTypeExpression)
{
Array<OneD, NekDouble> x0(nq);
Array<OneD, NekDouble> x1(nq);
Array<OneD, NekDouble> x2(nq);
pFields[0]->GetCoords(x0, x1, x2);
LibUtilities::EquationSharedPtr ffunc =
pSession->GetFunction(pFunctionName, pFieldName);
ffunc->Evaluate(x0, x1, x2, pTime, pArray);
}
else if (vType == LibUtilities::eFunctionTypeFile)
{
std::string filename = pSession->GetFunctionFilename(
pFunctionName,
pFieldName);
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef;
std::vector<std::vector<NekDouble> > FieldData;
Array<OneD, NekDouble> vCoeffs(pFields[0]->GetNcoeffs());
Vmath::Zero(vCoeffs.num_elements(), vCoeffs, 1);
LibUtilities::FieldIOSharedPtr fld =
MemoryManager<LibUtilities::FieldIO>::AllocateSharedPtr(m_session->GetComm());
fld->Import(filename, FieldDef, FieldData);
int idx = -1;
for (int i = 0; i < FieldDef.size(); ++i)
{
for (int j = 0; j < FieldDef[i]->m_fields.size(); ++j)
{
if (FieldDef[i]->m_fields[j] == pFieldName)
{
idx = j;
}
}
if (idx >= 0)
{
pFields[0]->ExtractDataToCoeffs(
FieldDef[i],
FieldData[i],
FieldDef[i]->m_fields[idx],
vCoeffs);
}
else
{
cout << "Field " + pFieldName + " not found." << endl;
}
}
pFields[0]->BwdTrans_IterPerExp(vCoeffs, pArray);
}
}
void VelocityCorrectionScheme::v_InitObject()
{
int n;
IncNavierStokes::v_InitObject();
m_explicitDiffusion = false;
// Set m_pressure to point to last field of m_fields;
if (boost::iequals(m_session->GetVariable(m_fields.num_elements()-1), "p"))
{
m_nConvectiveFields = m_fields.num_elements()-1;
m_pressure = m_fields[m_nConvectiveFields];
}
else
{
ASSERTL0(false,"Need to set up pressure field definition");
}
// Determine equations on which SVV is activated
m_useSpecVanVisc = Array<OneD, bool> (m_nConvectiveFields, false);
m_sVVCutoffRatio = Array<OneD, NekDouble> (m_nConvectiveFields, 0.75);
m_sVVDiffCoeff = Array<OneD, NekDouble> (m_nConvectiveFields, 0.1);
m_useHomo1DSpecVanVisc = Array<OneD, bool> (m_nConvectiveFields, false);
// Determine diffusion coefficients for each field
m_diffCoeff = Array<OneD, NekDouble> (m_nConvectiveFields, m_kinvis);
for (n = 0; n < m_nConvectiveFields; ++n)
{
std::string varName = m_session->GetVariable(n);
if ( m_session->DefinesFunction("DiffusionCoefficient", varName))
{
LibUtilities::EquationSharedPtr ffunc
= m_session->GetFunction("DiffusionCoefficient", varName);
m_diffCoeff[n] = ffunc->Evaluate();
}
if (m_session->DefinesFunction("SVVCutoffRatio", varName))
{
m_useSpecVanVisc[n] = true;
LibUtilities::EquationSharedPtr ffunc
= m_session->GetFunction("SVVcutoffRatio", varName);
m_sVVCutoffRatio[n] = ffunc->Evaluate();
}
if (m_session->DefinesFunction("SVVDiffCoeff", varName))
{
ASSERTL0(m_useSpecVanVisc[n], "SVV cut off ratio is not set for the variable:" + varName);
LibUtilities::EquationSharedPtr ffunc
= m_session->GetFunction("SVVDiffCoeff", varName);
m_sVVDiffCoeff[n] = ffunc->Evaluate();
}
}
// creation of the extrapolation object
if(m_equationType == eUnsteadyNavierStokes)
{
std::string vExtrapolation = "Standard";
if (m_session->DefinesSolverInfo("Extrapolation"))
{
vExtrapolation = m_session->GetSolverInfo("Extrapolation");
}
m_extrapolation = GetExtrapolateFactory().CreateInstance(
vExtrapolation,
m_session,
m_fields,
m_pressure,
m_velocity,
m_advObject);
}
// Integrate only the convective fields
for (n = 0; n < m_nConvectiveFields; ++n)
{
m_intVariables.push_back(n);
}
m_saved_aii_Dt = Array<OneD, NekDouble>(m_nConvectiveFields,
NekConstants::kNekUnsetDouble);
// Load parameters for Spectral Vanishing Viscosity
/*
m_session->MatchSolverInfo("SpectralVanishingViscosity","True",
m_useSpecVanVisc,false);
m_session->LoadParameter("SVVCutoffRatio",m_sVVCutoffRatio,0.75);
m_session->LoadParameter("SVVDiffCoeff", m_sVVDiffCoeff, 0.1);
// Needs to be set outside of next if so that it is turned off by default
m_session->MatchSolverInfo("SpectralVanishingViscosityHomo1D","True",
m_useHomo1DSpecVanVisc,false);
*/
m_session->MatchSolverInfo("SPECTRALHPDEALIASING","True",
m_specHP_dealiasing,false);
if(m_HomogeneousType == eHomogeneous1D)
{
ASSERTL0(m_nConvectiveFields > 2,"Expect to have three velocity fields with homogenous expansion");
/*
if(m_useHomo1DSpecVanVisc == false)
{
m_session->MatchSolverInfo("SpectralVanishingViscosity","True",m_useHomo1DSpecVanVisc,false);
}
*/
for (int i = 0; i < m_nConvectiveFields; ++i)
{
m_useHomo1DSpecVanVisc[i] = m_useSpecVanVisc[i];
if(m_useHomo1DSpecVanVisc[i])
{
Array<OneD, unsigned int> planes;
planes = m_fields[0]->GetZIDs();
int num_planes = planes.num_elements();
Array<OneD, NekDouble> SVV(num_planes,0.0);
NekDouble fac;
int kmodes = m_fields[0]->GetHomogeneousBasis()->GetNumModes();
int pstart;
pstart = m_sVVCutoffRatio[i]*kmodes;
for(n = 0; n < num_planes; ++n)
{
if(planes[n] > pstart)
{
fac = (NekDouble)((planes[n] - kmodes)*(planes[n] - kmodes))/
((NekDouble)((planes[n] - pstart)*(planes[n] - pstart)));
SVV[n] = m_sVVDiffCoeff[i]*exp(-fac)/m_diffCoeff[i];
}
}
/*
for(int j = 0; j < m_velocity.num_elements(); ++j)
{
m_fields[m_velocity[j]]->SetHomo1DSpecVanVisc(SVV);
}
*/
m_fields[i]->SetHomo1DSpecVanVisc(SVV);
}
}
}
m_session->MatchSolverInfo("SmoothAdvection", "True", m_SmoothAdvection, false);
// set explicit time-intregration class operators
m_ode.DefineOdeRhs(&VelocityCorrectionScheme::EvaluateAdvection_SetPressureBCs, this);
m_extrapolation->SubSteppingTimeIntegration(m_intScheme->GetIntegrationMethod(), m_intScheme);
m_extrapolation->GenerateHOPBCMap();
// set implicit time-intregration class operators
m_ode.DefineImplicitSolve(&VelocityCorrectionScheme::SolveUnsteadyStokesSystem,this);
}
int main(int argc, char *argv[])
{
SpatialDomains::PointGeomSharedPtr vPoint;
MultiRegions::ExpListSharedPtr vExp;
LibUtilities::SessionReaderSharedPtr vSession;
std::string vCellModel;
CellModelSharedPtr vCell;
std::vector<StimulusSharedPtr> vStimulus;
Array<OneD, Array<OneD, NekDouble> > vWsp(1);
Array<OneD, Array<OneD, NekDouble> > vSol(1);
NekDouble vDeltaT;
NekDouble vTime;
unsigned int nSteps;
// Create a session reader to read pacing parameters
vSession = LibUtilities::SessionReader::CreateInstance(argc, argv);
try
{
// Construct a field consisting of a single vertex
vPoint = MemoryManager<SpatialDomains::PointGeom>
::AllocateSharedPtr(3, 0, 0.0, 0.0, 0.0);
vExp = MemoryManager<MultiRegions::ExpList0D>
::AllocateSharedPtr(vPoint);
// Get cell model name and create it
vSession->LoadSolverInfo("CELLMODEL", vCellModel, "");
ASSERTL0(vCellModel != "", "Cell Model not specified.");
vCell = GetCellModelFactory().CreateInstance(
vCellModel, vSession, vExp);
vCell->Initialise();
// Load the stimuli
vStimulus = Stimulus::LoadStimuli(vSession, vExp);
// Set up solution arrays, workspace and read in parameters
vSol[0] = Array<OneD, NekDouble>(1, 0.0);
vWsp[0] = Array<OneD, NekDouble>(1, 0.0);
vDeltaT = vSession->GetParameter("TimeStep");
vTime = 0.0;
nSteps = vSession->GetParameter("NumSteps");
LibUtilities::EquationSharedPtr e =
vSession->GetFunction("InitialConditions", "u");
vSol[0][0] = e->Evaluate(0.0, 0.0, 0.0, 0.0);
// Time integrate cell model
for (unsigned int i = 0; i < nSteps; ++i)
{
// Compute J_ion
vCell->TimeIntegrate(vSol, vWsp, vTime);
// Add stimuli J_stim
for (unsigned int i = 0; i < vStimulus.size(); ++i)
{
vStimulus[i]->Update(vWsp, vTime);
}
// Time-step with forward Euler
Vmath::Svtvp(1, vDeltaT, vWsp[0], 1, vSol[0], 1, vSol[0], 1);
// Increment time
vTime += vDeltaT;
// Output current solution to stdout
cout << vTime << " " << vSol[0][0] << endl;
}
for (unsigned int i = 0; i < vCell->GetNumCellVariables(); ++i)
{
cout << "# " << vCell->GetCellVarName(i) << " "
<< vCell->GetCellSolution(i)[0] << endl;
}
}
catch (...)
{
cerr << "An error occured" << endl;
}
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
MultiRegions::ContField2DSharedPtr Exp,Fce;
int nq, coordim;
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
NekDouble lambda;
NekDouble ax,ay;
if((argc != 2)&&(argc != 3))
{
fprintf(stderr,"Usage: SteadyLinearAdvectionReaction2D meshfile [SysSolnType]\n");
exit(1);
}
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph2D = MemoryManager<SpatialDomains::MeshGraph2D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Get Advection Velocity
ax = vSession->GetParameter("Advection_x");
ay = vSession->GetParameter("Advection_y");
//----------------------------------------------
//----------------------------------------------
// Print summary of solution details
lambda = vSession->GetParameter("Lambda");
cout << " Lambda : " << lambda << endl;
const SpatialDomains::ExpansionMap &expansions = graph2D->GetExpansions();
LibUtilities::BasisKey bkey0
= expansions.begin()->second->m_basisKeyVector[0];
LibUtilities::BasisKey bkey1
= expansions.begin()->second->m_basisKeyVector[1];
cout << "Solving Steady 2D LinearAdvection :" << endl;
cout << " Advection_x : " << ax << endl;
cout << " Advection_y : " << ay << endl;
cout << " Expansion : (" << LibUtilities::BasisTypeMap[bkey0.GetBasisType()] <<","<< LibUtilities::BasisTypeMap[bkey1.GetBasisType()] << ")" << endl;
cout << " No. modes : " << bkey0.GetNumModes() << endl;
cout << endl;
//----------------------------------------------
//----------------------------------------------
// Define Expansion
Exp = MemoryManager<MultiRegions::ContField2D>::
AllocateSharedPtr(vSession,graph2D,vSession->GetVariable(0));
//----------------------------------------------
Timing("Read files and define exp ..");
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
coordim = Exp->GetCoordim(0);
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
switch(coordim)
{
case 1:
Exp->GetCoords(xc0);
break;
case 2:
Exp->GetCoords(xc0,xc1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
}
Array<OneD, Array< OneD, NekDouble> > Vel(2);
Vel[0] = Array<OneD, NekDouble> (nq,ax);
Vel[1] = Array<OneD, NekDouble> (nq,ay);
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc = vSession->GetFunction("Forcing",0);
ffunc->Evaluate(xc0,xc1,xc2,fce);
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::ContField2D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
Timing("Define forcing ..");
//----------------------------------------------
// Helmholtz solution taking physical forcing
Exp->LinearAdvectionReactionSolve(Vel, Fce->GetPhys(), Exp->UpdateCoeffs(), lambda, MultiRegions::eGlobal);
//----------------------------------------------
Timing("Linear Advection Solve ..");
//----------------------------------------------
// Backward Transform Solution to get solved values
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys(), MultiRegions::eGlobal);
//----------------------------------------------
//----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol = vSession->GetFunction("ExactSolution",0);
if(ex_sol)
{
//----------------------------------------------
// evaluate exact solution
ex_sol->Evaluate(xc0,xc1,xc2,fce);
//----------------------------------------------
//--------------------------------------------
// Calculate L_inf error
Fce->SetPhys(fce);
Fce->SetPhysState(true);
cout << "L infinity error: " << Exp->Linf(Fce->GetPhys()) << endl;
cout << "L 2 error: " << Exp->L2 (Fce->GetPhys()) << endl;
//--------------------------------------------
}
//----------------------------------------------
vSession->Finalise();
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
LibUtilities::CommSharedPtr vComm = vSession->GetComm();
string meshfile(argv[1]);
MultiRegions::DisContField3DHomogeneous1DSharedPtr Exp,Fce;
MultiRegions::ExpListSharedPtr DerExp1,DerExp2,DerExp3;
int i, nq;
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
StdRegions::ConstFactorMap factors;
NekDouble lz;
if(argc != 2)
{
fprintf(stderr,"Usage: Helmholtz2D meshfile\n");
exit(1);
}
LibUtilities::FieldIOSharedPtr fld = MemoryManager<LibUtilities::FieldIO>::AllocateSharedPtr(vComm);
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph2D = MemoryManager<SpatialDomains::MeshGraph2D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int nplanes = vSession->GetParameter("HomModesZ");
lz = vSession->GetParameter("LZ");
bool useFFT = false;
bool deal = false;
const LibUtilities::PointsKey Pkey(nplanes,LibUtilities::eFourierEvenlySpaced);
const LibUtilities::BasisKey Bkey(LibUtilities::eFourier,nplanes,Pkey);
Exp = MemoryManager<MultiRegions::DisContField3DHomogeneous1D>::
AllocateSharedPtr(vSession,Bkey,lz,useFFT,deal,graph2D,vSession->GetVariable(0));
//----------------------------------------------
Timing("Read files and define exp ..");
//----------------------------------------------
// Print summary of solution details
factors[StdRegions::eFactorLambda] = vSession->GetParameter("Lambda");
factors[StdRegions::eFactorTau] = 1.0;
const SpatialDomains::ExpansionMap &expansions = graph2D->GetExpansions();
LibUtilities::BasisKey bkey0
= expansions.begin()->second->m_basisKeyVector[0];
cout << "Solving 3D Helmholtz (Homogeneous in z-direction):" << endl;
cout << " Lambda : " << factors[StdRegions::eFactorLambda] << endl;
cout << " Lz : " << lz << endl;
cout << " No. modes : " << bkey0.GetNumModes() << endl;
cout << " No. hom. modes : " << Bkey.GetNumModes() << endl;
cout << endl;
//----------------------------------------------
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
Exp->GetCoords(xc0,xc1,xc2);
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc
= vSession->GetFunction("Forcing", 0);
ffunc->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::DisContField3DHomogeneous1D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
Timing("Define forcing ..");
//----------------------------------------------
// Helmholtz solution taking physical forcing
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
//----------------------------------------------
Timing("Helmholtz Solve ..");
#ifdef TIMING
for(i = 0; i < 100; ++i)
{
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
}
Timing("100 Helmholtz Solves:... ");
#endif
//-----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys());
//-----------------------------------------------
Timing("Backard Transform ..");
//-----------------------------------------------
// Write solution to file
string out = meshfile.substr(0, meshfile.find_last_of(".")) + ".fld";
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
for(i = 0; i < FieldDef.size(); ++i)
{
FieldDef[i]->m_fields.push_back("u");
Exp->AppendFieldData(FieldDef[i], FieldData[i]);
}
fld->Write(out, FieldDef, FieldData);
//-----------------------------------------------
//-----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol =
vSession->GetFunction("ExactSolution", 0);
if(ex_sol)
{
//----------------------------------------------
// evaluate exact solution
ex_sol->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//--------------------------------------------
// Calculate error
Fce->SetPhys(fce);
Fce->SetPhysState(true);
cout << "L infinity error: " << Exp->Linf(Exp->GetPhys(), Fce->GetPhys()) << endl;
cout << "L 2 error : " << Exp->L2 (Exp->GetPhys(), Fce->GetPhys()) << endl;
//--------------------------------------------
}
Timing("Output ..");
//----------------------------------------------
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
LibUtilities::CommSharedPtr vComm = vSession->GetComm();
MultiRegions::DisContField3DSharedPtr Exp,Fce;
int i, nq, coordim;
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
StdRegions::ConstFactorMap factors;
if(argc < 2)
{
fprintf(stderr,"Usage: PostProcHDG3D meshfile [solntype]\n");
exit(1);
}
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph3D = MemoryManager<SpatialDomains::MeshGraph3D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Print summary of solution details
factors[StdRegions::eFactorLambda] = vSession->GetParameter("Lambda");
factors[StdRegions::eFactorTau] = 1.0;
const SpatialDomains::ExpansionMap &expansions = graph3D->GetExpansions();
LibUtilities::BasisKey bkey0
= expansions.begin()->second->m_basisKeyVector[0];
//MAY NEED ADJUSTMENT FOR VARIOUS ELEMENT TYPES
int num_modes = bkey0.GetNumModes();
int num_points = bkey0.GetNumPoints();
if (vComm->GetRank() == 0)
{
cout << "Solving 3D Helmholtz:" << endl;
cout << " Lambda : " << factors[StdRegions::eFactorLambda] << endl;
cout << " No. modes : " << num_modes << endl;
cout << " No. points : " << num_points << endl;
cout << endl;
}
//----------------------------------------------
// Define Expansion
//----------------------------------------------
Exp = MemoryManager<MultiRegions::DisContField3D>::
AllocateSharedPtr(vSession,graph3D,vSession->GetVariable(0));
//----------------------------------------------
Timing("Read files and define exp ..");
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
coordim = Exp->GetCoordim(0);
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
switch(coordim)
{
case 1:
Exp->GetCoords(xc0);
break;
case 2:
Exp->GetCoords(xc0,xc1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
}
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc
= vSession->GetFunction("Forcing", 0);
ffunc->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::DisContField3D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
Timing("Define forcing ..");
//----------------------------------------------
// Helmholtz solution taking physical forcing
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
//----------------------------------------------
Timing("Helmholtz Solve ..");
//-----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys());
//-----------------------------------------------
Timing("Backward Transform ..");
//-----------------------------------------------
// Write solution to file
//string out = vSession->GetSessionName() + ".fld";
//std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
// = Exp->GetFieldDefinitions();
//std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
//for(i = 0; i < FieldDef.size(); ++i)
//{
// FieldDef[i]->m_fields.push_back("u");
// Exp->AppendFieldData(FieldDef[i], FieldData[i]);
//}
//LibUtilities::Write(out, FieldDef, FieldData);
//--------------------------------------------
//-----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol =
vSession->GetFunction("ExactSolution", 0);
//----------------------------------------------
// evaluate exact solution
ex_sol->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//Tetrahedron
const LibUtilities::PointsKey PkeyT1(num_points+1,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::PointsKey PkeyT2(num_points,LibUtilities::eGaussRadauMAlpha1Beta0);//need to doublecheck this one
const LibUtilities::PointsKey PkeyT3(num_points,LibUtilities::eGaussRadauMAlpha2Beta0);//need to doublecheck this one
LibUtilities::BasisKeyVector BkeyT;
BkeyT.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyT1));
BkeyT.push_back(LibUtilities::BasisKey(LibUtilities::eModified_B, num_modes+1, PkeyT2));
BkeyT.push_back(LibUtilities::BasisKey(LibUtilities::eModified_C, num_modes+1, PkeyT3));
//Prism
const LibUtilities::PointsKey PkeyP1(num_points+1,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::PointsKey PkeyP2(num_points+1,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::PointsKey PkeyP3(num_points,LibUtilities::eGaussRadauMAlpha1Beta0);//need to doublecheck this one
LibUtilities::BasisKeyVector BkeyP;
BkeyP.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyP1));
BkeyP.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyP2));
BkeyP.push_back(LibUtilities::BasisKey(LibUtilities::eModified_B, num_modes+1, PkeyP3));
//Hexahedron
const LibUtilities::PointsKey PkeyH(num_points+1,LibUtilities::eGaussLobattoLegendre);
LibUtilities::BasisKeyVector BkeyH;
BkeyH.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyH));
BkeyH.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyH));
BkeyH.push_back(LibUtilities::BasisKey(LibUtilities::eModified_A, num_modes+1, PkeyH));
graph3D->SetBasisKey(LibUtilities::eTetrahedron, BkeyT);
graph3D->SetBasisKey(LibUtilities::ePrism, BkeyP);
graph3D->SetBasisKey(LibUtilities::eHexahedron, BkeyH);
MultiRegions::DisContField3DSharedPtr PostProc =
MemoryManager<MultiRegions::DisContField3D>::AllocateSharedPtr(vSession,graph3D,vSession->GetVariable(0));
int ErrorCoordim = PostProc->GetCoordim(0);
int ErrorNq = PostProc->GetTotPoints();
Array<OneD,NekDouble> ErrorXc0(ErrorNq,0.0);
Array<OneD,NekDouble> ErrorXc1(ErrorNq,0.0);
Array<OneD,NekDouble> ErrorXc2(ErrorNq,0.0);
switch(ErrorCoordim)
{
case 1:
PostProc->GetCoords(ErrorXc0);
break;
case 2:
PostProc->GetCoords(ErrorXc0,ErrorXc1);
break;
case 3:
PostProc->GetCoords(ErrorXc0,ErrorXc1,ErrorXc2);
break;
}
// evaluate exact solution
Array<OneD,NekDouble> ppSol(ErrorNq);
ex_sol->Evaluate(ErrorXc0,ErrorXc1,ErrorXc2,ppSol);
// calcualte spectral/hp approximation on the quad points of this new
// expansion basis
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
std::string fieldstr = "u";
for(i = 0; i < FieldDef.size(); ++i)
{
FieldDef[i]->m_fields.push_back(fieldstr);
Exp->AppendFieldData(FieldDef[i], FieldData[i]);
PostProc->ExtractDataToCoeffs(FieldDef[i],FieldData[i],fieldstr,PostProc->UpdateCoeffs());
}
// Interpolation of trace
std::vector<LibUtilities::FieldDefinitionsSharedPtr> TraceDef
= Exp->GetTrace()->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > TraceData(TraceDef.size());
for(i = 0; i < TraceDef.size(); ++i)
{
TraceDef[i]->m_fields.push_back(fieldstr);
Exp->GetTrace()->AppendFieldData(TraceDef[i], TraceData[i]);
PostProc->GetTrace()->ExtractDataToCoeffs(TraceDef[i],TraceData[i],fieldstr,PostProc->GetTrace()->UpdateCoeffs());
}
PostProc->BwdTrans_IterPerExp(PostProc->GetCoeffs(),PostProc->UpdatePhys());
PostProc->EvaluateHDGPostProcessing(PostProc->UpdateCoeffs());
PostProc->BwdTrans_IterPerExp(PostProc->GetCoeffs(),PostProc->UpdatePhys());
NekDouble vLinfError = Exp->Linf(Exp->GetPhys(), fce);
NekDouble vL2Error = Exp->L2 (Exp->GetPhys(), fce);
NekDouble L2ErrorPostProc = PostProc->L2(PostProc->GetPhys(), ppSol);
NekDouble LinfErrorPostProc = PostProc->Linf(PostProc->GetPhys(), ppSol);
if (vSession->GetComm()->GetRank() == 0)
{
cout << "L infinity error : " << vLinfError << endl;
cout << "L 2 error : " << vL2Error << endl;
cout << "Postprocessed L infinity error : " << LinfErrorPostProc << endl;
cout << "Postprocessed L 2 error : " << L2ErrorPostProc << endl;
}
vSession->Finalise();
return 0;
}
int main(int argc, char *argv[])
{
MultiRegions::ContField3DSharedPtr Exp,Fce,Sol;
int i, nq, coordim;
Array<OneD,NekDouble> fce,sol;
Array<OneD,NekDouble> xc0,xc1,xc2;
NekDouble lambda;
vector<string> vFilenames;
if(argc != 6)
{
fprintf(stderr,"Usage: TimingCGHelmSolve3D Type MeshSize NumModes OptimisationLevel OperatorToTest\n");
fprintf(stderr," where: - Type is one of the following:\n");
fprintf(stderr," 1: Regular Hexahedrons \n");
fprintf(stderr," 2: Deformed Hexahedrons (may not be supported) \n");
fprintf(stderr," 3: Regular Tetrahedrons \n");
fprintf(stderr," where: - MeshSize is 1/h \n");
fprintf(stderr," where: - NumModes is the number of 1D modes of the expansion \n");
fprintf(stderr," where: - OptimisationLevel is one of the following:\n");
fprintf(stderr," 0: Use elemental sum-factorisation evaluation \n");
fprintf(stderr," 2: Use elemental matrix evaluation using blockmatrices \n");
fprintf(stderr," 3: Use global matrix evaluation \n");
fprintf(stderr," 4: Use optimal evaluation (this option requires optimisation-files being set-up) \n");
fprintf(stderr," where: - OperatorToTest is one of the following:\n");
fprintf(stderr," 0: BwdTrans \n");
fprintf(stderr," 1: Inner Product \n");
fprintf(stderr," 2: Mass Matrix \n");
exit(1);
}
boost::filesystem::path basePath(BASE_PATH);
int Type = atoi(argv[1]);
int MeshSize = atoi(argv[2]);
int NumModes = atoi(argv[3]);
int optLevel = atoi(argv[4]);
int opToTest = atoi(argv[5]);
//----------------------------------------------
// Retrieve the necessary input files
stringstream MeshFileName;
stringstream MeshFileDirectory;
stringstream BCfileName;
stringstream ExpansionsFileName;
stringstream GlobOptFileName;
switch(Type)
{
case 1:
{
MeshFileDirectory << "RegularHexMeshes";
MeshFileName << "UnitCube_RegularHexMesh_h_1_" << MeshSize << ".xml";
}
break;
case 2:
{
MeshFileDirectory << "DeformedHexMeshes";
MeshFileName << "UnitCube_DeformedHexMesh_h_1_" << MeshSize << ".xml";
}
break;
case 3:
{
MeshFileDirectory << "RegularTetMeshes";
MeshFileName << "UnitCube_RegularTetMesh_h_1_" << MeshSize << ".xml";
}
break;
default:
{
cerr << "Type should be equal to one of the following values: "<< endl;
cerr << " 1: Regular Hexahedrons" << endl;
cerr << " 2: Deformed Hexahedrons" << endl;
cerr << " 3: Regular Tetrahedrons" << endl;
exit(1);
}
}
BCfileName << "UnitCube_DirichletBoundaryConditions.xml";
ExpansionsFileName << "NektarExpansionsNummodes" << NumModes << ".xml";
switch(optLevel)
{
case 0:
{
GlobOptFileName << "NoGlobalMat.xml";
}
break;
case 2:
{
GlobOptFileName << "DoBlockMat.xml";
}
break;
case 3:
{
GlobOptFileName << "DoGlobalMat.xml";
}
break;
case 4:
{
ASSERTL0(false,"Optimisation level not set up");
}
break;
default:
{
ASSERTL0(false,"Unrecognised optimisation level");
}
}
boost::filesystem::path MeshFilePath = basePath /
boost::filesystem::path("InputFiles") /
boost::filesystem::path("Geometry") /
boost::filesystem::path(MeshFileDirectory.str()) /
boost::filesystem::path(MeshFileName.str());
vFilenames.push_back(PortablePath(MeshFilePath));
boost::filesystem::path BCfilePath = basePath /
boost::filesystem::path("InputFiles") /
boost::filesystem::path("Conditions") /
boost::filesystem::path(BCfileName.str());
vFilenames.push_back(PortablePath(BCfilePath));
boost::filesystem::path ExpansionsFilePath = basePath /
boost::filesystem::path("InputFiles") /
boost::filesystem::path("Expansions") /
boost::filesystem::path(ExpansionsFileName.str());
vFilenames.push_back(PortablePath(ExpansionsFilePath));
boost::filesystem::path GlobOptFilePath = basePath /
boost::filesystem::path("InputFiles") /
boost::filesystem::path("Optimisation") /
boost::filesystem::path(GlobOptFileName.str());
vFilenames.push_back(PortablePath(GlobOptFilePath));
//----------------------------------------------
StdRegions::MatrixType type;
switch (opToTest)
{
case 0:
type = StdRegions::eBwdTrans;
break;
case 1:
type = StdRegions::eIProductWRTBase;
break;
case 2:
type = StdRegions::eMass;
break;
case 3:
type = StdRegions::eHelmholtz;
break;
default:
cout << "Operator " << opToTest << " not defined." << endl;
}
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv, vFilenames);
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph3D = MemoryManager<SpatialDomains::MeshGraph3D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Print summary of solution details
lambda = vSession->GetParameter("Lambda");
//----------------------------------------------
//----------------------------------------------
// Define Expansion
Exp = MemoryManager<MultiRegions::ContField3D>
::AllocateSharedPtr(vSession, graph3D, vSession->GetVariable(0));
//----------------------------------------------
int NumElements = Exp->GetExpSize();
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
coordim = Exp->GetCoordim(0);
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
switch(coordim)
{
case 1:
Exp->GetCoords(xc0);
break;
case 2:
Exp->GetCoords(xc0,xc1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
}
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc = vSession->GetFunction("Forcing",0);
for(i = 0; i < nq; ++i)
{
fce[i] = ffunc->Evaluate(xc0[i],xc1[i],xc2[i]);
}
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::ContField3D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
//----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol = vSession->GetFunction("ExactSolution",0);
//----------------------------------------------
// evaluate exact solution
sol = Array<OneD,NekDouble>(nq);
for(i = 0; i < nq; ++i)
{
sol[i] = ex_sol->Evaluate(xc0[i],xc1[i],xc2[i]);
}
Sol = MemoryManager<MultiRegions::ContField3D>::AllocateSharedPtr(*Exp);
Sol->SetPhys(sol);
Sol->SetPhysState(true);
//----------------------------------------------
NekDouble L2Error;
NekDouble LinfError;
if (type == StdRegions::eHelmholtz)
{
FlagList flags;
flags.set(eUseGlobal, true);
StdRegions::ConstFactorMap factors;
factors[StdRegions::eFactorLambda] = lambda;
//----------------------------------------------
// Helmholtz solution taking physical forcing
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(),flags,factors);
// GeneralMatrixOp does not impose boundary conditions.
// MultiRegions::GlobalMatrixKey key(type, lambda, Exp->GetLocalToGlobalMap());
// Exp->GeneralMatrixOp (key, Fce->GetPhys(),Exp->UpdateContCoeffs(), true);
//----------------------------------------------
//----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys(),
MultiRegions::eGlobal);
//----------------------------------------------
L2Error = Exp->L2 (Sol->GetPhys());
LinfError = Exp->Linf(Sol->GetPhys());
}
else
{
Exp->FwdTrans(Sol->GetPhys(), Exp->UpdateCoeffs(),
MultiRegions::eGlobal);
//----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys(),
MultiRegions::eGlobal);
//----------------------------------------------
L2Error = Exp->L2 (Sol->GetPhys());
LinfError = Exp->Linf(Sol->GetPhys());
}
//--------------------------------------------
// alternative error calculation
/* const LibUtilities::PointsKey PkeyT1(30,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::PointsKey PkeyT2(30,LibUtilities::eGaussRadauMAlpha1Beta0);
const LibUtilities::PointsKey PkeyQ1(30,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::PointsKey PkeyQ2(30,LibUtilities::eGaussLobattoLegendre);
const LibUtilities::BasisKey BkeyT1(LibUtilities::eModified_A,NumModes,PkeyT1);
const LibUtilities::BasisKey BkeyT2(LibUtilities::eModified_B,NumModes,PkeyT2);
const LibUtilities::BasisKey BkeyQ1(LibUtilities::eModified_A,NumModes,PkeyQ1);
const LibUtilities::BasisKey BkeyQ2(LibUtilities::eModified_A,NumModes,PkeyQ2);
MultiRegions::ExpList3DSharedPtr ErrorExp =
MemoryManager<MultiRegions::ExpList3D>::AllocateSharedPtr(BkeyT1,BkeyT2,BkeyT3,BkeyQ1,BkeyQ2,BkeyQ3,graph3D);
int ErrorCoordim = ErrorExp->GetCoordim(0);
int ErrorNq = ErrorExp->GetTotPoints();
Array<OneD,NekDouble> ErrorXc0(ErrorNq,0.0);
Array<OneD,NekDouble> ErrorXc1(ErrorNq,0.0);
Array<OneD,NekDouble> ErrorXc2(ErrorNq,0.0);
switch(ErrorCoordim)
{
case 1:
ErrorExp->GetCoords(ErrorXc0);
break;
case 2:
ErrorExp->GetCoords(ErrorXc0,ErrorXc1);
break;
case 3:
ErrorExp->GetCoords(ErrorXc0,ErrorXc1,ErrorXc2);
break;
}
// evaluate exact solution
Array<OneD,NekDouble> ErrorSol(ErrorNq);
for(i = 0; i < ErrorNq; ++i)
{
ErrorSol[i] = ex_sol->Evaluate(ErrorXc0[i],ErrorXc1[i],ErrorXc2[i]);
}
// calcualte spectral/hp approximation on the quad points of this new
// expansion basis
Exp->GlobalToLocal(Exp->GetContCoeffs(),ErrorExp->UpdateCoeffs());
ErrorExp->BwdTrans_IterPerExp(ErrorExp->GetCoeffs(),ErrorExp->UpdatePhys());
NekDouble L2ErrorBis = ErrorExp->L2 (ErrorSol);
NekDouble LinfErrorBis = ErrorExp->Linf(ErrorSol);
*/
//--------------------------------------------
#if 0
cout << "L infinity error: " << LinfErrorBis << endl;
cout << "L 2 error: " << L2ErrorBis << endl;
#endif
//----------------------------------------------
NekDouble exeTime;
int NumCalls;
exeTime = TimeMatrixOp(type, Exp, Fce, NumCalls, lambda);
int nLocCoeffs = Exp->GetLocalToGlobalMap()->GetNumLocalCoeffs();
int nGlobCoeffs = Exp->GetLocalToGlobalMap()->GetNumGlobalCoeffs();
int nLocBndCoeffs = Exp->GetLocalToGlobalMap()->GetNumLocalBndCoeffs();
int nGlobBndCoeffs = Exp->GetLocalToGlobalMap()->GetNumGlobalBndCoeffs();
int nLocDirCoeffs = Exp->GetLocalToGlobalMap()->GetNumLocalDirBndCoeffs();
int nGlobDirCoeffs = Exp->GetLocalToGlobalMap()->GetNumGlobalDirBndCoeffs();
// MultiRegions::GlobalMatrixKey key(StdRegions::eHelmholtz,lambda,Exp->GetLocalToGlobalMap());
// int nnz = Exp->GetGlobalMatrixNnz(key);
ostream &outfile = cout;
outfile.precision(0);
outfile << setw(10) << Type << " ";
outfile << setw(10) << NumElements << " ";
outfile << setw(10) << NumModes << " ";
outfile << setw(10) << NumCalls << " ";
outfile << setw(10) << fixed << noshowpoint << exeTime << " ";
outfile << setw(10) << fixed << noshowpoint << ((NekDouble) (exeTime/((NekDouble)NumCalls))) << " ";
outfile.precision(7);
outfile << setw(15) << scientific << noshowpoint << L2Error << " ";
outfile << setw(15) << scientific << noshowpoint << "- "; // << L2ErrorBis << " ";
outfile << setw(15) << scientific << noshowpoint << LinfError << " ";
outfile << setw(15) << scientific << noshowpoint << "- ";// << LinfErrorBis << " ";
outfile << setw(10) << nLocCoeffs << " ";
outfile << setw(10) << nGlobCoeffs << " ";
outfile << setw(10) << nLocBndCoeffs << " ";
outfile << setw(10) << nGlobBndCoeffs << " ";
outfile << setw(10) << nLocDirCoeffs << " ";
outfile << setw(10) << nGlobDirCoeffs << " ";
outfile << setw(10) << "- "; // << nnz << " ";
outfile << setw(10) << optLevel << " ";
outfile << endl;
//----------------------------------------------
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
LibUtilities::CommSharedPtr vComm = vSession->GetComm();
MultiRegions::DisContField3DSharedPtr Exp, Fce;
int i, nq, coordim;
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
StdRegions::ConstFactorMap factors;
if(argc < 2)
{
fprintf(stderr,"Usage: HDGHelmholtz3D meshfile [solntype]\n");
exit(1);
}
LibUtilities::FieldIOSharedPtr fld = MemoryManager<LibUtilities::FieldIO>::AllocateSharedPtr(vComm);
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph3D =
MemoryManager<SpatialDomains::MeshGraph3D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Print summary of solution details
factors[StdRegions::eFactorLambda] = vSession->GetParameter("Lambda");
factors[StdRegions::eFactorTau] = 1.0;
const SpatialDomains::ExpansionMap &expansions = graph3D->GetExpansions();
LibUtilities::BasisKey bkey0
= expansions.begin()->second->m_basisKeyVector[0];
if (vComm->GetRank() == 0)
{
cout << "Solving 3D Helmholtz:" << endl;
cout << " - Communication: "
<< vSession->GetComm()->GetType() << " ("
<< vSession->GetComm()->GetSize()
<< " processes)" << endl;
cout << " - Solver type : "
<< vSession->GetSolverInfo("GlobalSysSoln") << endl;
cout << " - Lambda : "
<< factors[StdRegions::eFactorLambda] << endl;
cout << " - No. modes : "
<< bkey0.GetNumModes() << endl;
cout << endl;
}
//----------------------------------------------
//----------------------------------------------
// Define Expansion
Exp = MemoryManager<MultiRegions::DisContField3D>::
AllocateSharedPtr(vSession,graph3D,vSession->GetVariable(0));
//----------------------------------------------
Timing("Read files and define exp ..");
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
coordim = Exp->GetCoordim(0);
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
switch(coordim)
{
case 1:
Exp->GetCoords(xc0);
break;
case 2:
Exp->GetCoords(xc0,xc1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
}
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc = vSession->GetFunction("Forcing", 0);
ffunc->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::DisContField3D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
Timing("Define forcing ..");
//----------------------------------------------
// Helmholtz solution taking physical forcing
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
//----------------------------------------------
Timing("Helmholtz Solve ..");
#if 0
for(i = 0; i < 100; ++i)
{
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
}
Timing("100 Helmholtz Solves:... ");
#endif
//----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys());
//----------------------------------------------
Timing("Backward Transform ..");
//-----------------------------------------------
// Write solution to file
string out = vSession->GetSessionName() + ".fld";
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
for(i = 0; i < FieldDef.size(); ++i)
{
FieldDef[i]->m_fields.push_back("u");
Exp->AppendFieldData(FieldDef[i], FieldData[i]);
}
fld->Write(out, FieldDef, FieldData);
//-----------------------------------------------
//----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol =
vSession->GetFunction("ExactSolution", 0);
if(ex_sol)
{
//----------------------------------------------
// evaluate exact solution
ex_sol->Evaluate(xc0, xc1, xc2, fce);
//----------------------------------------------
//--------------------------------------------
// Calculate L_inf error
Fce->SetPhys(fce);
Fce->SetPhysState(true);
NekDouble vLinfError = Exp->Linf(Exp->GetPhys(), Fce->GetPhys());
NekDouble vL2Error = Exp->L2 (Exp->GetPhys(), Fce->GetPhys());
NekDouble vH1Error = Exp->H1 (Exp->GetPhys(), Fce->GetPhys());
if (vComm->GetRank() == 0)
{
cout << "L infinity error: " << vLinfError << endl;
cout << "L 2 error : " << vL2Error << endl;
cout << "H 1 error : " << vH1Error << endl;
}
//--------------------------------------------
}
Timing("Output ..");
//----------------------------------------------
vSession->Finalise();
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
LibUtilities::CommSharedPtr vComm = vSession->GetComm();
MultiRegions::ContField1DSharedPtr Exp,Fce;
int i, nq, coordim;
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
StdRegions::ConstFactorMap factors;
if( (argc != 2) && (argc != 3) && (argc != 4))
{
fprintf(stderr,"Usage: Helmholtz1D meshfile \n");
exit(1);
}
try
{
LibUtilities::FieldIOSharedPtr fld =
MemoryManager<LibUtilities::FieldIO>::AllocateSharedPtr(vComm);
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph1D =
SpatialDomains::MeshGraph::Read(vSession);
//----------------------------------------------
//----------------------------------------------
// Print summary of solution details
factors[StdRegions::eFactorLambda] = vSession->GetParameter("Lambda");
const SpatialDomains::ExpansionMap &expansions = graph1D->GetExpansions();
LibUtilities::BasisKey bkey0 = expansions.begin()->second->m_basisKeyVector[0];
if (vComm->GetRank() ==0)
{
cout << "Solving 1D Helmholtz: " << endl;
cout << " Communication: " << vComm->GetType() << endl;
cout << " Solver type : " << vSession->GetSolverInfo("GlobalSysSoln") << endl;
cout << " Lambda : " << factors[StdRegions::eFactorLambda] << endl;
cout << " No. modes : " << bkey0.GetNumModes() << endl;
}
//----------------------------------------------
//----------------------------------------------
// Define Expansion
Exp = MemoryManager<MultiRegions::ContField1D>::
AllocateSharedPtr(vSession,graph1D,vSession->GetVariable(0));
//----------------------------------------------
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
coordim = Exp->GetCoordim(0);
nq = Exp->GetTotPoints();
xc0 = Array<OneD,NekDouble>(nq);
xc1 = Array<OneD,NekDouble>(nq);
xc2 = Array<OneD,NekDouble>(nq);
switch(coordim)
{
case 1:
Exp->GetCoords(xc0);
Vmath::Zero(nq,&xc1[0],1);
Vmath::Zero(nq,&xc2[0],1);
break;
case 2:
Exp->GetCoords(xc0,xc1);
Vmath::Zero(nq,&xc2[0],1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
}
//----------------------------------------------
//----------------------------------------------
// Define forcing function for first variable defined in file
fce = Array<OneD,NekDouble>(nq);
LibUtilities::EquationSharedPtr ffunc
= vSession->GetFunction("Forcing", 0);
ffunc->Evaluate(xc0,xc1,xc2, fce);
//----------------------------------------------
//----------------------------------------------
// Setup expansion containing the forcing function
Fce = MemoryManager<MultiRegions::ContField1D>::AllocateSharedPtr(*Exp);
Fce->SetPhys(fce);
//----------------------------------------------
//----------------------------------------------
//Helmholtz solution taking physical forcing after setting
//initial condition to zero
Vmath::Zero(Exp->GetNcoeffs(),Exp->UpdateCoeffs(),1);
Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateCoeffs(), NullFlagList, factors);
//----------------------------------------------
//----------------------------------------------
// Backward Transform Solution to get solved values at
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys());
//----------------------------------------------
//----------------------------------------------
// Write solution
string out(strtok(argv[1],"."));
string endfile(".fld");
out += endfile;
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
for(i = 0; i < FieldDef.size(); ++i)
{
FieldDef[i]->m_fields.push_back("u");
Exp->AppendFieldData(FieldDef[i], FieldData[i]);
}
fld->Write(out, FieldDef, FieldData);
//----------------------------------------------
//----------------------------------------------
// See if there is an exact solution, if so
// evaluate and plot errors
LibUtilities::EquationSharedPtr ex_sol
= vSession->GetFunction("ExactSolution", 0);
if(ex_sol)
{
//----------------------------------------------
// evaluate exact solution
ex_sol->Evaluate(xc0,xc1,xc2, fce);
Fce->SetPhys(fce);
//----------------------------------------------
//--------------------------------------------
// Calculate errors
NekDouble vLinfError = Exp->Linf(Exp->GetPhys(), Fce->GetPhys());
NekDouble vL2Error = Exp->L2(Exp->GetPhys(), Fce->GetPhys());
NekDouble vH1Error = Exp->H1(Exp->GetPhys(), Fce->GetPhys());
if (vComm->GetRank() == 0)
{
cout << "L infinity error: " << vLinfError << endl;
cout << "L 2 error: " << vL2Error << endl;
cout << "H 1 error: " << vH1Error << endl;
}
//--------------------------------------------
}
//----------------------------------------------
}
catch (const std::runtime_error&)
{
cerr << "Caught exception." << endl;
return 1;
}
vComm->Finalise();
return 0;
}
