int main(int argc, char *argv[])
{
int i,j;
int surfID;
if(argc != 5)
{
fprintf(stderr,"Usage: FldAddScalGrad meshfile infld outfld BoundaryID\n");
exit(1);
}
surfID = boost::lexical_cast<int>(argv[argc - 1]);
argv[argc -1] = argv[argc - 2];
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
//----------------------------------------------
// Read in mesh from input file
string meshfile(argv[argc-4]);
SpatialDomains::MeshGraphSharedPtr graphShPt = SpatialDomains::MeshGraph::Read(vSession);
//----------------------------------------------
//----------------------------------------------
// Import field file.
string fieldfile(argv[argc-3]);
vector<LibUtilities::FieldDefinitionsSharedPtr> fielddef;
vector<vector<NekDouble> > fielddata;
LibUtilities::Import(fieldfile,fielddef,fielddata);
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int expdim = graphShPt->GetMeshDimension();
int nfields = 1;
int addfields = 7;
Array<OneD, MultiRegions::ExpListSharedPtr> exp(nfields + addfields);
MultiRegions::AssemblyMapCGSharedPtr m_locToGlobalMap;
switch(expdim)
{
case 1:
{
ASSERTL0(false,"Expansion dimension not recognised");
}
break;
case 2:
{
ASSERTL0(false,"Expansion dimension not recognised");
}
break;
case 3:
{
MultiRegions::ContField3DSharedPtr originalfield =
MemoryManager<MultiRegions::ContField3D>
::AllocateSharedPtr(vSession, graphShPt,
vSession->GetVariable(0));
m_locToGlobalMap = originalfield->GetLocalToGlobalMap();
exp[0] = originalfield;
for (i=0; i<addfields; i++)
{
exp[i+1] = MemoryManager<MultiRegions::ContField3D>
::AllocateSharedPtr(*originalfield, graphShPt,
vSession->GetVariable(0));
}
}
break;
default:
ASSERTL0(false,"Expansion dimension not recognised");
break;
}
//----------------------------------------------
//----------------------------------------------
// Copy data from field file
for(j = 0; j < nfields+addfields; ++j)
{
for(int i = 0; i < fielddata.size(); ++i)
{
exp[j]->ExtractDataToCoeffs(fielddef [i],
fielddata[i],
fielddef [i]->m_fields[0],
exp[j]->UpdateCoeffs());
}
exp[j]->BwdTrans(exp[j]->GetCoeffs(),exp[j]->UpdatePhys());
}
//----------------------------------------------
//----------------------------------------------
int n, cnt, elmtid, nq, offset, nt, boundary, nfq;
nt = exp[0]->GetNpoints();
Array<OneD, Array<OneD, NekDouble> > grad(expdim);
Array<OneD, Array<OneD, NekDouble> > fgrad(expdim);
Array<OneD, Array<OneD, NekDouble> > values(addfields);
// Set up mapping from Boundary condition to element details.
StdRegions::StdExpansionSharedPtr elmt;
StdRegions::StdExpansion2DSharedPtr bc;
Array<OneD, int> BoundarytoElmtID;
Array<OneD, int> BoundarytoTraceID;
Array<OneD, Array<OneD, MultiRegions::ExpListSharedPtr> > BndExp(addfields);
Array<OneD, const NekDouble> U(nt);
Array<OneD, NekDouble> outvalues;
exp[0]->GetBoundaryToElmtMap(BoundarytoElmtID,BoundarytoTraceID);
//get boundary expansions for each field
for (i = 0; i<addfields; i++)
{
BndExp[i] = exp[i]->GetBndCondExpansions();
}
// loop over the types of boundary conditions
for(cnt = n = 0; n < BndExp[0].num_elements(); ++n)
{
// identify boundary which the user wanted
if(n == surfID)
{
for(i = 0; i < BndExp[0][n]->GetExpSize(); ++i, cnt++)
{
// find element and face of this expansion.
elmtid = BoundarytoElmtID[cnt];
elmt = exp[0]->GetExp(elmtid);
nq = elmt->GetTotPoints();
offset = exp[0]->GetPhys_Offset(elmtid);
// Initialise local arrays for the velocity gradients
// size of total number of quadrature points for each element (hence local).
for(j = 0; j < expdim; ++j)
{
grad[j] = Array<OneD, NekDouble>(nq);
}
if(expdim == 2)
{
}
else
{
for (j = 0; j< addfields; j++)
{
values[j] = BndExp[j][n]->UpdateCoeffs() + BndExp[j][n]->GetCoeff_Offset(i);
}
// Get face 2D expansion from element expansion
bc = boost::dynamic_pointer_cast<StdRegions::StdExpansion2D> (BndExp[0][n]->GetExp(i));
// Number of face quadrature points
nfq = bc->GetTotPoints();
//identify boundary of element
boundary = BoundarytoTraceID[cnt];
//Extract scalar field
U = exp[0]->GetPhys() + offset;
//Compute gradients
elmt->PhysDeriv(U,grad[0],grad[1],grad[2]);
if(i ==0)
{
for (j = 0; j< nq; j++)
{
cout << "element grad: " << grad[0][j] << endl;
}
}
for(j = 0; j < expdim; ++j)
{
fgrad[j] = Array<OneD, NekDouble>(nfq);
}
// Get gradient at the quadrature points of the face
for(j = 0; j < expdim; ++j)
{
elmt->GetFacePhysVals(boundary,bc,grad[j],fgrad[j]);
bc->FwdTrans(fgrad[j],values[j]);
}
if(i ==0)
{
for (j = 0; j< nfq; j++)
{
cout << "face grad: " << fgrad[0][j] << endl;
}
}
const SpatialDomains::GeomFactorsSharedPtr m_metricinfo=bc->GetMetricInfo();
const Array<OneD, const Array<OneD, NekDouble> > normals
= elmt->GetFaceNormal(boundary);
Array<OneD, NekDouble> gradnorm(nfq);
if (m_metricinfo->GetGtype() == SpatialDomains::eDeformed)
{
Vmath::Vvtvvtp(nfq,normals[0],1,fgrad[0],1,
normals[1],1,fgrad[1],1,gradnorm,1);
Vmath::Vvtvp (nfq,normals[2],1,fgrad[2],1,gradnorm,1,gradnorm,1);
}
else
{
Vmath::Svtsvtp(nfq,normals[0][0],fgrad[0],1,
normals[1][0],fgrad[1],1,gradnorm,1);
Vmath::Svtvp(nfq,normals[2][0],fgrad[2],1,gradnorm,1,gradnorm,1);
}
for(j = 0; j<expdim; j++)
{
bc->FwdTrans(normals[j],values[j+expdim]);
}
//gradient (grad(u) n)
Vmath::Smul(nfq,-1.0,gradnorm,1,gradnorm,1);
bc->FwdTrans(gradnorm,values[expdim*2]);
}
}
}
else
{
cnt += BndExp[0][n]->GetExpSize();
}
}
for(int j = 0; j < addfields; ++j)
{
int ncoeffs = exp[0]->GetNcoeffs();
Array<OneD, NekDouble> output(ncoeffs);
output=exp[j+1]->UpdateCoeffs();
int nGlobal=m_locToGlobalMap->GetNumGlobalCoeffs();
Array<OneD, NekDouble> outarray(nGlobal,0.0);
int bndcnt=0;
const Array<OneD,const int>& map = m_locToGlobalMap->GetBndCondCoeffsToGlobalCoeffsMap();
NekDouble sign;
for(int i = 0; i < BndExp[j].num_elements(); ++i)
{
if(i==surfID)
{
const Array<OneD,const NekDouble>& coeffs = BndExp[j][i]->GetCoeffs();
for(int k = 0; k < (BndExp[j][i])->GetNcoeffs(); ++k)
{
sign = m_locToGlobalMap->GetBndCondCoeffsToGlobalCoeffsSign(bndcnt);
outarray[map[bndcnt++]] = sign * coeffs[k];
}
}
else
{
bndcnt += BndExp[j][i]->GetNcoeffs();
}
}
m_locToGlobalMap->GlobalToLocal(outarray,output);
}
//-----------------------------------------------
// Write solution to file with additional computed fields
string out(argv[argc-2]);
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= exp[0]->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
vector<string > outname;
outname.push_back("du/dx");
outname.push_back("du/dy");
outname.push_back("du/dz");
outname.push_back("nx");
outname.push_back("ny");
outname.push_back("nz");
outname.push_back("gradient");
for(j = 0; j < nfields+addfields; ++j)
{
for(i = 0; i < FieldDef.size(); ++i)
{
if (j >= nfields)
{
FieldDef[i]->m_fields.push_back(outname[j-nfields]);
}
else
{
FieldDef[i]->m_fields.push_back(fielddef[i]->m_fields[j]);
}
exp[j]->AppendFieldData(FieldDef[i], FieldData[i]);
}
}
LibUtilities::Write(out, FieldDef, FieldData);
//-----------------------------------------------
return 0;
}
NekDouble TimeMatrixOp(StdRegions::MatrixType &type,
MultiRegions::ContField3DSharedPtr &Exp,
MultiRegions::ContField3DSharedPtr &Fce,
int &NumCalls,
NekDouble lambda)
{
//----------------------------------------------
// Do the timings
int i;
timeval timer1, timer2;
NekDouble time1, time2;
NekDouble exeTime;
// We first do a single run in order to estimate the number of calls
// we are going to make
gettimeofday(&timer1, NULL);
//Exp->HelmSolve(Fce->GetPhys(), Exp->UpdateContCoeffs(),lambda,true);
//Exp->BwdTrans (Exp->GetCoeffs(),Exp->UpdatePhys(),true);
if (type == StdRegions::eBwdTrans)
{
Exp->BwdTrans(Exp->GetCoeffs(), Exp->UpdatePhys(),
MultiRegions::eGlobal);
}
else if (type == StdRegions::eIProductWRTBase)
{
Exp->IProductWRTBase(Fce->GetPhys(), Exp->UpdateCoeffs(),
MultiRegions::eGlobal);
}
else
{
StdRegions::ConstFactorMap factors;
factors[StdRegions::eFactorLambda] = lambda;
MultiRegions::GlobalMatrixKey key(type, Exp->GetLocalToGlobalMap(), factors);
Exp->GeneralMatrixOp (key, Exp->GetCoeffs(),Exp->UpdatePhys(),
MultiRegions::eGlobal);
}
gettimeofday(&timer2, NULL);
time1 = timer1.tv_sec*1000000.0+(timer1.tv_usec);
time2 = timer2.tv_sec*1000000.0+(timer2.tv_usec);
exeTime = (time2-time1);
NumCalls = (int) ceil(1.0e6/exeTime);
if(NumCalls < 1)
{
NumCalls = 1;
}
#ifdef SHARK
NumCalls *= 20;
chudInitialize();
chudSetErrorLogFile(stderr);
chudUmarkPID(getpid(), TRUE);
chudAcquireRemoteAccess();
chudStartRemotePerfMonitor("TimingCGHelmSolve2D");
#endif
gettimeofday(&timer1, NULL);
if (type == StdRegions::eBwdTrans)
{
for(i = 0; i < NumCalls; ++i)
{
Exp->BwdTrans (Exp->GetCoeffs(),Exp->UpdatePhys(),
MultiRegions::eGlobal);
}
}
else if (type == StdRegions::eIProductWRTBase)
{
for(i = 0; i < NumCalls; ++i)
{
Exp->IProductWRTBase (Exp->GetPhys(),Exp->UpdateCoeffs(),
MultiRegions::eGlobal);
}
}
else
{
StdRegions::ConstFactorMap factors;
factors[StdRegions::eFactorLambda] = lambda;
MultiRegions::GlobalMatrixKey key(type, Exp->GetLocalToGlobalMap(), factors);
for(i = 0; i < NumCalls; ++i)
{
Exp->GeneralMatrixOp (key, Exp->GetCoeffs(),Exp->UpdatePhys(),
MultiRegions::eGlobal);
}
}
gettimeofday(&timer2, NULL);
#ifdef SHARK
chudStopRemotePerfMonitor();
chudReleaseRemoteAccess();
chudCleanup();
#endif
time1 = timer1.tv_sec*1000000.0+(timer1.tv_usec);
time2 = timer2.tv_sec*1000000.0+(timer2.tv_usec);
exeTime = (time2-time1);
return exeTime;
}