FilterEnergyBase::FilterEnergyBase(
const LibUtilities::SessionReaderSharedPtr &pSession,
const std::map<std::string, std::string> &pParams,
const bool pConstDensity)
: Filter (pSession),
m_index (-1),
m_homogeneous (false),
m_planes (),
m_constDensity(pConstDensity)
{
std::string outName;
if (pParams.find("OutputFile") == pParams.end())
{
outName = m_session->GetSessionName();
}
else
{
ASSERTL0(!(pParams.find("OutputFile")->second.empty()),
"Missing parameter 'OutputFile'.");
outName = pParams.find("OutputFile")->second;
}
m_comm = pSession->GetComm();
outName += ".eny";
if (m_comm->GetRank() == 0)
{
m_outFile.open(outName.c_str());
ASSERTL0(m_outFile.good(), "Unable to open: '" + outName + "'");
m_outFile.setf(ios::scientific, ios::floatfield);
m_outFile << "# Time Kinetic energy "
<< "Enstrophy"
<< endl
<< "# ---------------------------------------------"
<< "--------------"
<< endl;
}
pSession->LoadParameter("LZ", m_homogeneousLength, 0.0);
ASSERTL0(pParams.find("OutputFrequency") != pParams.end(),
"Missing parameter 'OutputFrequency'.");
m_outputFrequency = atoi(
pParams.find("OutputFrequency")->second.c_str());
}
/**
* Allocates a new DNekSparseMat object from the given specification.
* @param rows Number of rows in matrix.
* @param columns Number of columns in matrix.
* @param cooMat ?
*/
GlobalMatrix::GlobalMatrix(
const LibUtilities::SessionReaderSharedPtr& pSession,
unsigned int rows,
unsigned int columns,
const COOMatType &cooMat,
const MatrixStorage& matStorage):
m_smvbsrmatrix(),
m_rows(rows),
m_mulCallsCounter(0)
{
MatrixStorageType storageType = pSession->
GetSolverInfoAsEnum<MatrixStorageType>("GlobalMatrixStorageType");
unsigned int brows, bcols;
// Size of dense matrix sub-blocks
int block_size = 1;
BCOMatType bcoMat;
// assuming current sparse format allows
// block-sparse data representation
if(pSession->DefinesParameter("SparseBlockSize"))
{
pSession->LoadParameter("SparseBlockSize", block_size);
ASSERTL1(block_size > 0,"SparseBlockSize parameter must to be positive");
}
brows = rows / block_size + (rows % block_size > 0);
bcols = columns / block_size + (columns % block_size > 0);
if (rows % block_size > 0) m_copyOp = true;
if (m_copyOp)
{
m_tmpin = Array<OneD, NekDouble> (brows*block_size, 0.0);
m_tmpout = Array<OneD, NekDouble> (brows*block_size, 0.0);
}
convertCooToBco(brows, bcols, block_size, cooMat, bcoMat);
size_t matBytes;
switch(storageType)
{
case eSmvBSR:
{
// Create zero-based Smv-multiply BSR sparse storage holder
DNekSmvBsrMat::SparseStorageSharedPtr sparseStorage =
MemoryManager<DNekSmvBsrMat::StorageType>::
AllocateSharedPtr(
brows, bcols, block_size, bcoMat, matStorage );
// Create sparse matrix
m_smvbsrmatrix = MemoryManager<DNekSmvBsrMat>::
AllocateSharedPtr( sparseStorage );
matBytes = m_smvbsrmatrix->GetMemoryFootprint();
}
break;
default:
NEKERROR(ErrorUtil::efatal,"Unsupported sparse storage type chosen");
}
cout << "Global matrix storage type: "
<< MatrixStorageTypeMap[storageType] << endl;
std::cout << "Global matrix memory, bytes = " << matBytes;
if (matBytes/(1024*1024) > 0)
{
std::cout << " ("<< matBytes/(1024*1024) <<" MB)" << std::endl;
}
else
{
std::cout << " ("<< matBytes/1024 <<" KB)" << std::endl;
}
std::cout << "Sparse storage block size = " << block_size << std::endl;
}
int main(int argc, char *argv[])
{
string fname = std::string(argv[2]);
int fdot = fname.find_last_of('.');
if (fdot != std::string::npos)
{
string ending = fname.substr(fdot);
// If .chk or .fld we exchange the extension in the output file.
// For all other files (e.g. .bse) we append the extension to avoid
// conflicts.
if (ending == ".chk" || ending == ".fld")
{
fname = fname.substr(0,fdot);
}
}
fname = fname + ".txt";
int cnt;
int id1, id2;
int i, j, n, e, b;
Array<OneD, NekDouble> auxArray;
int nBndEdgePts, nBndEdges, nBndRegions;
if (argc < 3)
{
fprintf(stderr,
"Usage: ExtractSurface3DCFS meshfile fieldFile\n");
fprintf(stderr,
"Extracts a surface from a 3D fld file"
"(only for CompressibleFlowSolver and purely 3D .fld files)\n");
exit(1);
}
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(3, argv);
std::string m_ViscosityType;
NekDouble m_gamma;
NekDouble m_pInf;
NekDouble m_rhoInf;
NekDouble m_uInf;
NekDouble m_vInf;
NekDouble m_wInf;
NekDouble m_gasConstant;
NekDouble m_Twall;
NekDouble m_mu;
NekDouble m_thermalConductivity;
int m_spacedim = 3;
int nDimensions = m_spacedim;
int phys_offset;
// Get gamma parameter from session file.
ASSERTL0(vSession->DefinesParameter("Gamma"),
"Compressible flow sessions must define a Gamma parameter.");
vSession->LoadParameter("Gamma", m_gamma, 1.4);
// Get E0 parameter from session file.
ASSERTL0(vSession->DefinesParameter("pInf"),
"Compressible flow sessions must define a pInf parameter.");
vSession->LoadParameter("pInf", m_pInf, 101325);
// Get rhoInf parameter from session file.
ASSERTL0(vSession->DefinesParameter("rhoInf"),
"Compressible flow sessions must define a rhoInf parameter.");
vSession->LoadParameter("rhoInf", m_rhoInf, 1.225);
// Get uInf parameter from session file.
ASSERTL0(vSession->DefinesParameter("uInf"),
"Compressible flow sessions must define a uInf parameter.");
vSession->LoadParameter("uInf", m_uInf, 0.1);
// Get vInf parameter from session file.
if (m_spacedim == 2 || m_spacedim == 3)
{
ASSERTL0(vSession->DefinesParameter("vInf"),
"Compressible flow sessions must define a vInf parameter"
"for 2D/3D problems.");
vSession->LoadParameter("vInf", m_vInf, 0.0);
}
// Get wInf parameter from session file.
if (m_spacedim == 3)
{
ASSERTL0(vSession->DefinesParameter("wInf"),
"Compressible flow sessions must define a wInf parameter"
"for 3D problems.");
vSession->LoadParameter("wInf", m_wInf, 0.0);
}
vSession->LoadParameter ("GasConstant", m_gasConstant, 287.058);
vSession->LoadParameter ("Twall", m_Twall, 300.15);
vSession->LoadSolverInfo("ViscosityType", m_ViscosityType, "Constant");
vSession->LoadParameter ("mu", m_mu, 1.78e-05);
vSession->LoadParameter ("thermalConductivity",
m_thermalConductivity, 0.0257);
//--------------------------------------------------------------------------
// Read in mesh from input file
string meshfile(argv[1]);
SpatialDomains::MeshGraphSharedPtr graphShPt =
SpatialDomains::MeshGraph::Read(vSession);
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
// Import field file
string fieldFile(argv[2]);
vector<LibUtilities::FieldDefinitionsSharedPtr> fieldDef;
vector<vector<NekDouble> > fieldData;
LibUtilities::Import(fieldFile, fieldDef, fieldData);
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
// Set up Expansion information
vector< vector<LibUtilities::PointsType> > pointsType;
for (i = 0; i < fieldDef.size(); ++i)
{
vector<LibUtilities::PointsType> ptype;
for (j = 0; j < 3; ++j)
{
ptype.push_back(LibUtilities::ePolyEvenlySpaced);
}
pointsType.push_back(ptype);
}
graphShPt->SetExpansions(fieldDef, pointsType);
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
// Define Expansion
int nfields = fieldDef[0]->m_fields.size();
Array<OneD, MultiRegions::ExpListSharedPtr> Exp(nfields);
Array<OneD, MultiRegions::ExpListSharedPtr> pFields(nfields);
for(i = 0; i < pFields.num_elements(); i++)
{
pFields[i] = MemoryManager<MultiRegions
::DisContField3D>::AllocateSharedPtr(vSession, graphShPt,
vSession->GetVariable(i));
}
MultiRegions::ExpList3DSharedPtr Exp3D;
Exp3D = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(vSession, graphShPt);
Exp[0] = Exp3D;
for (i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(*Exp3D);
}
// Count of the point on the surface
int nSurfacePts = 0;
if (pFields[0]->GetBndCondExpansions().num_elements())
{
nSurfacePts = 0;
cnt = 0;
nBndRegions = pFields[0]->GetBndCondExpansions().num_elements();
for (b = 0; b < nBndRegions; ++b)
{
nBndEdges = pFields[0]->GetBndCondExpansions()[b]->GetExpSize();
for (e = 0; e < nBndEdges; ++e)
{
nBndEdgePts = pFields[0]->
GetBndCondExpansions()[b]->GetExp(e)->GetTotPoints();
if (pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallViscous" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallAdiabatic" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "Wall")
{
nSurfacePts += nBndEdgePts;
}
}
}
}
int nSolutionPts = pFields[0]->GetNpoints();
int nTracePts = pFields[0]->GetTrace()->GetTotPoints();
int nElements = pFields[0]->GetExpSize();
Array<OneD, NekDouble> tmp(nSolutionPts, 0.0);
Array<OneD, NekDouble> x(nSolutionPts);
Array<OneD, NekDouble> y(nSolutionPts);
Array<OneD, NekDouble> z(nSolutionPts);
Array<OneD, NekDouble> traceX(nTracePts);
Array<OneD, NekDouble> traceY(nTracePts);
Array<OneD, NekDouble> traceZ(nTracePts);
Array<OneD, NekDouble> surfaceX(nSurfacePts);
Array<OneD, NekDouble> surfaceY(nSurfacePts);
Array<OneD, NekDouble> surfaceZ(nSurfacePts);
pFields[0]->GetCoords(x, y, z);
pFields[0]->ExtractTracePhys(x, traceX);
pFields[0]->ExtractTracePhys(y, traceY);
pFields[0]->ExtractTracePhys(z, traceZ);
//--------------------------------------------------------------------------
//--------------------------------------------------------------------------
// Copy data from field file
Array<OneD, Array<OneD, NekDouble> > uFields(nfields);
Array<OneD, Array<OneD, NekDouble> > traceFields(nfields);
Array<OneD, Array<OneD, NekDouble> > surfaceFields(nfields);
// Extract the physical values of the solution at the boundaries
for (j = 0; j < nfields; ++j)
{
uFields[j] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
traceFields[j] = Array<OneD, NekDouble>(nTracePts, 0.0);
surfaceFields[j] = Array<OneD, NekDouble>(nSurfacePts, 0.0);
for (i = 0; i < fieldData.size(); ++i)
{
Exp[j]->ExtractDataToCoeffs(fieldDef[i], fieldData[i],
fieldDef[i]->m_fields[j],
Exp[j]->UpdateCoeffs());
}
Exp[j]->BwdTrans(Exp[j]->GetCoeffs(), Exp[j]->UpdatePhys());
Vmath::Vcopy(nSolutionPts, Exp[j]->GetPhys(), 1, uFields[j], 1);
pFields[0]->ExtractTracePhys(uFields[j], traceFields[j]);
}
//Fields to add in the output file
int nfieldsAdded = 34;
Array<OneD, Array<OneD, NekDouble> > traceFieldsAdded(nfieldsAdded);
Array<OneD, Array<OneD, NekDouble> > surfaceFieldsAdded(nfieldsAdded);
for (j = 0; j < nfieldsAdded; ++j)
{
traceFieldsAdded[j] = Array<OneD, NekDouble>(nTracePts, 0.0);
surfaceFieldsAdded[j] = Array<OneD, NekDouble>(nSurfacePts, 0.0);
}
/******** Evaluation of normals and tangents on the trace *****************
* nx -> traceFieldsAdded[0];
* ny -> traceFieldsAdded[1];
* nz -> traceFieldsAdded[2];
* bx -> traceFieldsAdded[3];
* by -> traceFieldsAdded[4];
* bz -> traceFieldsAdded[5];
* tx -> traceFieldsAdded[6];
* ty -> traceFieldsAdded[7];
* tz -> traceFieldsAdded[8];
***************************************************************************/
Array<OneD, Array<OneD, NekDouble> > m_traceNormals (nDimensions);
for(i = 0; i < nDimensions; ++i)
{
m_traceNormals[i] = Array<OneD, NekDouble> (nTracePts, 0.0);
}
pFields[0]->GetTrace()->GetNormals(m_traceNormals);
Array<OneD, Array<OneD, NekDouble> > m_traceTangents (nDimensions);
Array<OneD, Array<OneD, NekDouble> > m_traceBinormals (nDimensions);
Array<OneD, Array<OneD, NekDouble> > h (nDimensions);
Array<OneD, NekDouble > tmpNorm (nTracePts, 1.0);
Array<OneD, NekDouble > NormH (nTracePts, 0.0);
Array<OneD, NekDouble > tmpTrace (nTracePts, 0.0);
for(i = 0; i < nDimensions; ++i)
{
m_traceTangents[i] = Array<OneD, NekDouble> (nTracePts, 0.0);
m_traceBinormals[i] = Array<OneD, NekDouble> (nTracePts, 0.0);
h[i] = Array<OneD, NekDouble> (nTracePts, 0.0);
}
// Normals
// nx
Vmath::Vcopy(nTracePts,
&m_traceNormals[0][0], 1,
&traceFieldsAdded[0][0], 1);
// ny
Vmath::Vcopy(nTracePts,
&m_traceNormals[1][0], 1,
&traceFieldsAdded[1][0], 1);
// nz
Vmath::Vcopy(nTracePts,
&m_traceNormals[2][0], 1,
&traceFieldsAdded[2][0], 1);
// Tangents and Binormals
// h1
Vmath::Vadd(nTracePts,
&m_traceNormals[0][0], 1,
&tmpNorm[0], 1,
&h[0][0], 1);
// h2
Vmath::Vcopy(nTracePts,
&m_traceNormals[1][0], 1,
&h[1][0], 1);
// h3
Vmath::Vcopy(nTracePts,
&m_traceNormals[2][0], 1,
&h[2][0], 1);
// Norm of h
for (i = 0; i < m_spacedim; i++)
{
Vmath::Vvtvp (nTracePts, &h[i][0], 1, &h[i][0], 1,
&NormH[0],1, &NormH[0],1);
}
//b1
Vmath::Vmul(nTracePts,
&h[0][0], 1,
&h[1][0], 1,
&tmpTrace[0],1);
Vmath::Vdiv(nTracePts,
&tmpTrace[0],1,
&NormH[0], 1,
&tmpTrace[0],1);
Vmath::Smul(nTracePts, -2.0,
&tmpTrace[0], 1,
&m_traceBinormals[0][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceBinormals[0][0], 1,
&traceFieldsAdded[3][0], 1);
//b2
Vmath::Vmul(nTracePts,
&h[1][0], 1,
&h[1][0], 1,
&tmpTrace[0],1);
Vmath::Vdiv(nTracePts,
&tmpTrace[0],1,
&NormH[0], 1,
&tmpTrace[0],1);
Vmath::Smul(nTracePts, -2.0,
&tmpTrace[0], 1,
&tmpTrace[0], 1);
Vmath::Vadd(nTracePts,
&tmpTrace[0], 1,
&tmpNorm[0], 1,
&m_traceBinormals[1][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceBinormals[1][0], 1,
&traceFieldsAdded[4][0], 1);
//b3
Vmath::Vmul(nTracePts,
&h[1][0], 1,
&h[2][0], 1,
&tmpTrace[0],1);
Vmath::Vdiv(nTracePts,
&tmpTrace[0],1,
&NormH[0], 1,
&tmpTrace[0],1);
Vmath::Smul(nTracePts, -2.0,
&tmpTrace[0], 1,
&m_traceBinormals[2][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceBinormals[2][0], 1,
&traceFieldsAdded[5][0], 1);
//t1
Vmath::Vmul(nTracePts,
&h[0][0], 1,
&h[2][0], 1,
&tmpTrace[0],1);
Vmath::Vdiv(nTracePts,
&tmpTrace[0],1,
&NormH[0], 1,
&tmpTrace[0],1);
Vmath::Smul(nTracePts, -2.0,
&tmpTrace[0], 1,
&m_traceTangents[0][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceTangents[0][0], 1,
&traceFieldsAdded[6][0], 1);
//t2
Vmath::Vcopy(nTracePts,
&m_traceBinormals[2][0], 1,
&m_traceTangents[1][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceTangents[1][0], 1,
&traceFieldsAdded[7][0], 1);
//t3
Vmath::Vmul(nTracePts,
&h[2][0], 1,
&h[2][0], 1,
&tmpTrace[0],1);
Vmath::Vdiv(nTracePts,
&tmpTrace[0],1,
&NormH[0], 1,
&tmpTrace[0],1);
Vmath::Smul(nTracePts, -2.0,
&tmpTrace[0], 1,
&tmpTrace[0], 1);
Vmath::Vadd(nTracePts,
&tmpTrace[0], 1,
&tmpNorm[0], 1,
&m_traceTangents[2][0], 1);
Vmath::Vcopy(nTracePts,
&m_traceTangents[2][0], 1,
&traceFieldsAdded[8][0], 1);
/******** Evaluation of the pressure ***************************************
* P = (E-1/2.*rho.*((rhou./rho).^2+(rhov./rho).^2))*(gamma - 1);
* P -> traceFieldsAdded[9];
***************************************************************************/
Array<OneD, NekDouble> pressure(nSolutionPts, 0.0);
NekDouble gammaMinusOne = m_gamma - 1.0;
for (i = 0; i < m_spacedim; i++)
{
Vmath::Vmul(nSolutionPts,
&uFields[i + 1][0], 1,
&uFields[i + 1][0], 1,
&tmp[0],1);
Vmath::Smul(nSolutionPts, 0.5,
&tmp[0], 1,
&tmp[0], 1);
Vmath::Vadd(nSolutionPts,
&pressure[0], 1,
&tmp[0], 1,
&pressure[0], 1);
}
Vmath::Vdiv(nSolutionPts,
&pressure[0], 1,
&uFields[0][0], 1,
&pressure[0],1);
Vmath::Vsub(nSolutionPts,
&uFields[nfields - 1][0], 1,
&pressure[0], 1,
&pressure[0],1);
Vmath::Smul(nSolutionPts, gammaMinusOne,
&pressure[0], 1,
&pressure[0], 1);
// Extract trace
pFields[0]->ExtractTracePhys(pressure, traceFieldsAdded[9]);
/******** Evaluation of the temperature ************************************
* T = P/(R*rho);
* T -> traceFieldsAdded[10];
***************************************************************************/
Array<OneD, NekDouble> temperature(nSolutionPts, 0.0);
Vmath::Vdiv(nSolutionPts,
&pressure[0], 1,
&uFields[0][0], 1,
&temperature[0],1);
NekDouble GasConstantInv = 1.0/m_gasConstant;
Vmath::Smul(nSolutionPts, GasConstantInv,
&temperature[0], 1,
&temperature[0], 1);
// Extract trace
pFields[0]->ExtractTracePhys(temperature, traceFieldsAdded[10]);
/*** Evaluation of the temperature gradient in the normal direction ********
* DT_n -> traceFieldsAdded[11]
***************************************************************************/
Array<OneD, Array<OneD, NekDouble> > Dtemperature(nDimensions);
Array<OneD, Array<OneD, NekDouble> > traceDtemperature(nDimensions);
for (i = 0; i < nDimensions; ++ i)
{
Dtemperature[i] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
traceDtemperature[i] = Array<OneD, NekDouble>(nTracePts, 0.0);
}
for (i = 0; i < nDimensions; ++ i)
{
for (n = 0; n < nElements; n++)
{
phys_offset = pFields[0]->GetPhys_Offset(n);
pFields[i]->GetExp(n)->PhysDeriv(
i, temperature + phys_offset,
auxArray = Dtemperature[i] + phys_offset);
}
// Extract trace
pFields[0]->ExtractTracePhys(Dtemperature[i], traceDtemperature[i]);
}
for(i = 0; i < nDimensions; ++i)
{
Vmath::Vmul(nTracePts,
&m_traceNormals[i][0], 1,
&traceDtemperature[i][0], 1,
&tmp[0],1);
Vmath::Vadd(nTracePts,
&traceFieldsAdded[11][0], 1,
&tmp[0], 1,
&traceFieldsAdded[11][0], 1);
}
/*** Evaluation of the pressure gradient ***********************************
* DP_t -> traceFieldsAdded[12] tangent direction
* DP_b -> traceFieldsAdded[13] binormal direction
* DP_x -> traceFieldsAdded[14]
* DP_y -> traceFieldsAdded[15]
* DP_z -> traceFieldsAdded[16]
***************************************************************************/
Array<OneD, Array<OneD, NekDouble> > Dpressure(nDimensions);
Array<OneD, Array<OneD, NekDouble> > traceDpressure(nDimensions);
for (i = 0; i < nDimensions; ++ i)
{
Dpressure[i] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
traceDpressure[i] = Array<OneD, NekDouble>(nTracePts, 0.0);
}
for (i = 0; i < nDimensions; ++ i)
{
for (n = 0; n < nElements; n++)
{
phys_offset = pFields[0]->GetPhys_Offset(n);
pFields[i]->GetExp(n)->PhysDeriv(
i, pressure + phys_offset,
auxArray = Dpressure[i] + phys_offset);
}
// Extract trace
pFields[0]->ExtractTracePhys(Dpressure[i], traceDpressure[i]);
}
// Dp_t
for(i = 0; i < nDimensions; ++i)
{
Vmath::Vmul(nTracePts,
&m_traceTangents[i][0], 1,
&traceDpressure[i][0], 1,
&tmp[0],1);
Vmath::Vadd(nTracePts,
&traceFieldsAdded[12][0], 1,
&tmp[0], 1,
&traceFieldsAdded[12][0], 1);
}
// Dp_b
for(i = 0; i < nDimensions; ++i)
{
Vmath::Vmul(nTracePts,
&m_traceBinormals[i][0], 1,
&traceDpressure[i][0], 1,
&tmp[0],1);
Vmath::Vadd(nTracePts,
&traceFieldsAdded[13][0], 1,
&tmp[0], 1,
&traceFieldsAdded[13][0], 1);
}
// Dp_x
Vmath::Vcopy(nTracePts,
&traceDpressure[0][0], 1,
&traceFieldsAdded[14][0], 1);
// Dp_y
Vmath::Vcopy(nTracePts,
&traceDpressure[1][0], 1,
&traceFieldsAdded[15][0], 1);
// Dp_z
Vmath::Vcopy(nTracePts,
&traceDpressure[2][0], 1,
&traceFieldsAdded[16][0], 1);
/** Evaluation of the velocity gradient in the cartesian directions
* Du_x: traceFieldsAdded[17]
* Du_y: traceFieldsAdded[18]
* Du_z: traceFieldsAdded[19]
* Dv_x: traceFieldsAdded[20]
* Dv_y: traceFieldsAdded[21]
* Dv_z: traceFieldsAdded[22]
* Dw_x: traceFieldsAdded[23]
* Dw_y: traceFieldsAdded[24]
* Dw_z: traceFieldsAdded[25]
**/
Array<OneD, Array<OneD, Array<OneD, NekDouble> > > Dvelocity(nDimensions);
Array<OneD, Array<OneD, Array<OneD, NekDouble> > > traceDvelocity(nDimensions);
Array<OneD, Array<OneD, NekDouble> > velocity(nDimensions);
for (i = 0; i < nDimensions; ++ i)
{
Dvelocity[i] = Array<OneD, Array<OneD, NekDouble> >(nDimensions);
traceDvelocity[i] = Array<OneD, Array<OneD, NekDouble> >(nDimensions);
velocity[i] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
Vmath::Vdiv(nSolutionPts, uFields[i+1], 1, uFields[0], 1,
velocity[i], 1);
for (j = 0; j < nDimensions; ++j)
{
Dvelocity[i][j] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
traceDvelocity[i][j] = Array<OneD, NekDouble>(nTracePts, 0.0);
}
}
for (i = 0; i < nDimensions; ++i)
{
for (j = 0; j < nDimensions; ++j)
{
for (n = 0; n < nElements; n++)
{
phys_offset = pFields[0]->GetPhys_Offset(n);
pFields[i]->GetExp(n)->PhysDeriv(
j, velocity[i] + phys_offset,
auxArray = Dvelocity[i][j] + phys_offset);
}
// Extract trace
pFields[0]->ExtractTracePhys(Dvelocity[i][j], traceDvelocity[i][j]);
}
}
Vmath::Vcopy(nTracePts,
&traceDvelocity[0][0][0], 1,
&traceFieldsAdded[17][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[0][1][0], 1,
&traceFieldsAdded[18][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[0][2][0], 1,
&traceFieldsAdded[19][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[1][0][0], 1,
&traceFieldsAdded[20][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[1][1][0], 1,
&traceFieldsAdded[21][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[1][2][0], 1,
&traceFieldsAdded[22][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[2][0][0], 1,
&traceFieldsAdded[23][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[2][1][0], 1,
&traceFieldsAdded[24][0], 1);
Vmath::Vcopy(nTracePts,
&traceDvelocity[2][2][0], 1,
&traceFieldsAdded[25][0], 1);
/*** Evaluation of shear stresses ******************************************
* tau_xx -> traceFieldsAdded[26]
* tau_yy -> traceFieldsAdded[27]
* tau_zz -> traceFieldsAdded[28]
* tau_xy -> traceFieldsAdded[29]
* tau_xz -> traceFieldsAdded[30]
* tau_yz -> traceFieldsAdded[31]
***************************************************************************/
// Stokes hypotesis
const NekDouble lambda = -2.0/3.0;
// Auxiliary variables
Array<OneD, NekDouble > mu (nSolutionPts, 0.0);
Array<OneD, NekDouble > mu2 (nSolutionPts, 0.0);
Array<OneD, NekDouble > divVel(nSolutionPts, 0.0);
// Variable viscosity through the Sutherland's law
if (m_ViscosityType == "Variable")
{
NekDouble mu_star = m_mu;
NekDouble T_star = m_pInf / (m_rhoInf * m_gasConstant);
NekDouble ratio;
for (int i = 0; i < nSolutionPts; ++i)
{
ratio = temperature[i] / T_star;
mu[i] = mu_star * ratio * sqrt(ratio) *
(T_star + 110.0) / (temperature[i] + 110.0);
}
}
else
{
Vmath::Fill(nSolutionPts, m_mu, &mu[0], 1);
}
// Computing diagonal terms of viscous stress tensor
Array<OneD, Array<OneD, NekDouble> > temp(m_spacedim);
Array<OneD, Array<OneD, NekDouble> > Sgg(m_spacedim);
// mu2 = 2 * mu
Vmath::Smul(nSolutionPts, 2.0, &mu[0], 1, &mu2[0], 1);
// Velocity divergence
Vmath::Vadd(nSolutionPts, &divVel[0], 1,
&Dvelocity[0][0][0], 1, &divVel[0], 1);
Vmath::Vadd(nSolutionPts, &divVel[0], 1,
&Dvelocity[1][1][0], 1, &divVel[0], 1);
// Velocity divergence scaled by lambda * mu
Vmath::Smul(nSolutionPts, lambda, &divVel[0], 1, &divVel[0], 1);
Vmath::Vmul(nSolutionPts, &mu[0], 1, &divVel[0], 1, &divVel[0], 1);
// Diagonal terms of viscous stress tensor (Sxx, Syy)
// Sjj = 2 * mu * du_j/dx_j - (2 / 3) * mu * sum_j(du_j/dx_j)
for (j = 0; j < m_spacedim; ++j)
{
temp[j] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
Sgg[j] = Array<OneD, NekDouble>(nSolutionPts, 0.0);
Vmath::Vmul(nSolutionPts, &mu2[0], 1, &Dvelocity[j][j][0], 1,
&temp[j][0], 1);
Vmath::Vadd(nSolutionPts, &temp[j][0], 1, &divVel[0], 1, &Sgg[j][0], 1);
}
// Extra diagonal terms of viscous stress tensor
Array<OneD, NekDouble > Sxy(nSolutionPts, 0.0);
Array<OneD, NekDouble > Sxz(nSolutionPts, 0.0);
Array<OneD, NekDouble > Syz(nSolutionPts, 0.0);
// Sxy = (du/dy + dv/dx)
Vmath::Vadd(nSolutionPts, &Dvelocity[0][1][0], 1,
&Dvelocity[1][0][0], 1, &Sxy[0], 1);
// Sxz = (du/dz + dw/dx)
Vmath::Vadd(nSolutionPts, &Dvelocity[0][2][0], 1,
&Dvelocity[2][0][0], 1, &Sxz[0], 1);
// Syz = (dv/dz + dw/dy)
Vmath::Vadd(nSolutionPts, &Dvelocity[1][2][0], 1,
&Dvelocity[2][1][0], 1, &Syz[0], 1);
// Sxy = mu * (du/dy + dv/dx)
Vmath::Vmul(nSolutionPts, &mu[0], 1, &Sxy[0], 1, &Sxy[0], 1);
// Sxz = mu * (du/dy + dv/dx)
Vmath::Vmul(nSolutionPts, &mu[0], 1, &Sxz[0], 1, &Sxz[0], 1);
// Syz = mu * (du/dy + dv/dx)
Vmath::Vmul(nSolutionPts, &mu[0], 1, &Syz[0], 1, &Syz[0], 1);
pFields[0]->ExtractTracePhys(Sgg[0], traceFieldsAdded[26]);
pFields[0]->ExtractTracePhys(Sgg[1], traceFieldsAdded[27]);
pFields[0]->ExtractTracePhys(Sgg[2], traceFieldsAdded[28]);
pFields[0]->ExtractTracePhys(Sxy, traceFieldsAdded[29]);
pFields[0]->ExtractTracePhys(Sxz, traceFieldsAdded[30]);
pFields[0]->ExtractTracePhys(Syz, traceFieldsAdded[31]);
/*** Evaluation of dinamic viscosity ***************************************
* mu -> traceFieldsAdded[32]
***************************************************************************/
pFields[0]->ExtractTracePhys(mu, traceFieldsAdded[32]);
/*** Evaluation of Mach number *********************************************
* M -> traceFieldsAdded[33]
***************************************************************************/
NekDouble gamma = m_gamma;
// Speed of sound
Array<OneD, NekDouble> soundspeed(nSolutionPts, 0.0);
Vmath::Vdiv (nSolutionPts, pressure, 1, uFields[0], 1, soundspeed, 1);
Vmath::Smul (nSolutionPts, gamma, soundspeed, 1, soundspeed, 1);
Vmath::Vsqrt(nSolutionPts, soundspeed, 1, soundspeed, 1);
// Mach
Array<OneD, NekDouble> mach(nSolutionPts, 0.0);
for (int i = 0; i < m_spacedim; ++i)
{
Vmath::Vvtvp(nSolutionPts,
uFields[i + 1], 1,
uFields[i + 1], 1,
mach, 1, mach, 1);
}
Vmath::Vdiv(nSolutionPts, mach, 1, uFields[0], 1, mach, 1);
Vmath::Vdiv(nSolutionPts, mach, 1, uFields[0], 1, mach, 1);
Vmath::Vsqrt(nSolutionPts, mach, 1, mach, 1);
Vmath::Vdiv(nSolutionPts, mach, 1, soundspeed, 1, mach, 1);
pFields[0]->ExtractTracePhys(mach, traceFieldsAdded[33]);
/**************************************************************************/
// Extract coordinates
if (pFields[0]->GetBndCondExpansions().num_elements())
{
id1 = 0;
cnt = 0;
nBndRegions = pFields[0]->GetBndCondExpansions().num_elements();
for (b = 0; b < nBndRegions; ++b)
{
nBndEdges = pFields[0]->GetBndCondExpansions()[b]->GetExpSize();
for (e = 0; e < nBndEdges; ++e)
{
nBndEdgePts = pFields[0]->
GetBndCondExpansions()[b]->GetExp(e)->GetTotPoints();
id2 = pFields[0]->GetTrace()->
GetPhys_Offset(pFields[0]->GetTraceMap()->
GetBndCondTraceToGlobalTraceMap(cnt++));
if (pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallViscous" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallAdiabatic" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "Wall")
{
Vmath::Vcopy(nBndEdgePts, &traceX[id2], 1,
&surfaceX[id1], 1);
Vmath::Vcopy(nBndEdgePts, &traceY[id2], 1,
&surfaceY[id1], 1);
Vmath::Vcopy(nBndEdgePts, &traceZ[id2], 1,
&surfaceZ[id1], 1);
id1 += nBndEdgePts;
}
}
}
}
// Extract fields
if (pFields[0]->GetBndCondExpansions().num_elements())
{
for (j = 0; j < nfields; ++j)
{
cout << "field " << j << endl;
id1 = 0;
cnt = 0;
nBndRegions = pFields[j]->GetBndCondExpansions().num_elements();
for (b = 0; b < nBndRegions; ++b)
{
nBndEdges = pFields[j]->GetBndCondExpansions()[b]->GetExpSize();
for (e = 0; e < nBndEdges; ++e)
{
nBndEdgePts = pFields[j]->
GetBndCondExpansions()[b]->GetExp(e)->GetTotPoints();
id2 = pFields[j]->GetTrace()->
GetPhys_Offset(pFields[j]->GetTraceMap()->
GetBndCondTraceToGlobalTraceMap(cnt++));
if (pFields[j]->GetBndConditions()[b]->
GetUserDefined() == "WallViscous" ||
pFields[j]->GetBndConditions()[b]->
GetUserDefined() == "WallAdiabatic" ||
pFields[j]->GetBndConditions()[b]->
GetUserDefined() == "Wall")
{
Vmath::Vcopy(nBndEdgePts, &traceFields[j][id2], 1,
&surfaceFields[j][id1], 1);
id1 += nBndEdgePts;
}
}
}
}
}
// Extract fields added
if (pFields[0]->GetBndCondExpansions().num_elements())
{
for (j = 0; j < nfieldsAdded; ++j)
{
cout << "field added " << j << endl;
id1 = 0;
cnt = 0;
nBndRegions = pFields[0]->GetBndCondExpansions().num_elements();
for (b = 0; b < nBndRegions; ++b)
{
nBndEdges = pFields[0]->GetBndCondExpansions()[b]->GetExpSize();
for (e = 0; e < nBndEdges; ++e)
{
nBndEdgePts = pFields[0]->
GetBndCondExpansions()[b]->GetExp(e)->GetTotPoints();
id2 = pFields[0]->GetTrace()->
GetPhys_Offset(pFields[0]->GetTraceMap()->
GetBndCondTraceToGlobalTraceMap(cnt++));
if (pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallViscous" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "WallAdiabatic" ||
pFields[0]->GetBndConditions()[b]->
GetUserDefined() == "Wall")
{
Vmath::Vcopy(nBndEdgePts, &traceFieldsAdded[j][id2], 1,
&surfaceFieldsAdded[j][id1], 1);
id1 += nBndEdgePts;
}
}
}
}
}
//==========================================================================
//==========================================================================
//==========================================================================
// Print the surface coordinates and the surface solution in a .txt file
ofstream outfile;
outfile.open(fname.c_str());
outfile << "% x[m] " << " \t"
<< "y[m] " << " \t"
<< "z[m] " << " \t"
<< "nx[] " << " \t"
<< "ny[] " << " \t"
<< "nz[] " << " \t"
<< "bx[] " << " \t"
<< "by[] " << " \t"
<< "bz[] " << " \t"
<< "tx[] " << " \t"
<< "ty[] " << " \t"
<< "tz[] " << " \t"
<< "rho[kg/m^3] " << " \t"
<< "rhou[kg/(m^2 s)] " << " \t"
<< "rhov[kg/(m^2 s)] " << " \t"
<< "rhow[kg/(m^2 s)] " << " \t"
<< "E[Pa] " << " \t"
<< "p[Pa] " << " \t"
<< "T[k] " << " \t"
<< "dT/dn[k/m] " << " \t"
<< "dp/dT[Pa/m] " << " \t"
<< "dp/dB[Pa/m] " << " \t"
<< "dp/dx[Pa/m] " << " \t"
<< "dp/dy[Pa/m] " << " \t"
<< "dp/dz[Pa/m] " << " \t"
<< "du/dx[s^-1] " << " \t"
<< "du/dy[s^-1] " << " \t"
<< "du/dz[s^-1] " << " \t"
<< "dv/dx[s^-1] " << " \t"
<< "dv/dy[s^-1] " << " \t"
<< "dv/dz[s^-1] " << " \t"
<< "dw/dx[s^-1] " << " \t"
<< "dw/dy[s^-1] " << " \t"
<< "dw/dz[s^-1] " << " \t"
<< "tau_xx[Pa] " << " \t"
<< "tau_yy[Pa] " << " \t"
<< "tau_zz[Pa] " << " \t"
<< "tau_xy[Pa] " << " \t"
<< "tau_xz[Pa] " << " \t"
<< "tau_yz[Pa] " << " \t"
<< "mu[Pa s] " << " \t"
<< "M[] " << " \t"
<< endl;
for (i = 0; i < nSurfacePts; ++i)
{
outfile << scientific
<< setw (17)
<< setprecision(16)
<< surfaceX[i] << " \t "
<< surfaceY[i] << " \t "
<< surfaceZ[i] << " \t "
<< surfaceFieldsAdded[0][i] << " \t "
<< surfaceFieldsAdded[1][i] << " \t "
<< surfaceFieldsAdded[2][i] << " \t "
<< surfaceFieldsAdded[3][i] << " \t "
<< surfaceFieldsAdded[4][i] << " \t "
<< surfaceFieldsAdded[5][i] << " \t "
<< surfaceFieldsAdded[6][i] << " \t "
<< surfaceFieldsAdded[7][i] << " \t "
<< surfaceFieldsAdded[8][i] << " \t "
<< surfaceFields[0][i] << " \t "
<< surfaceFields[1][i] << " \t "
<< surfaceFields[2][i] << " \t "
<< surfaceFields[3][i] << " \t "
<< surfaceFields[4][i] << " \t "
<< surfaceFieldsAdded[9][i] << " \t "
<< surfaceFieldsAdded[10][i] << " \t "
<< surfaceFieldsAdded[11][i] << " \t "
<< surfaceFieldsAdded[12][i] << " \t "
<< surfaceFieldsAdded[13][i] << " \t "
<< surfaceFieldsAdded[14][i] << " \t "
<< surfaceFieldsAdded[15][i] << " \t "
<< surfaceFieldsAdded[16][i] << " \t "
<< surfaceFieldsAdded[17][i] << " \t "
<< surfaceFieldsAdded[18][i] << " \t "
<< surfaceFieldsAdded[19][i] << " \t "
<< surfaceFieldsAdded[20][i] << " \t "
<< surfaceFieldsAdded[21][i] << " \t "
<< surfaceFieldsAdded[22][i] << " \t "
<< surfaceFieldsAdded[23][i] << " \t "
<< surfaceFieldsAdded[24][i] << " \t "
<< surfaceFieldsAdded[25][i] << " \t "
<< surfaceFieldsAdded[26][i] << " \t "
<< surfaceFieldsAdded[27][i] << " \t "
<< surfaceFieldsAdded[28][i] << " \t "
<< surfaceFieldsAdded[29][i] << " \t "
<< surfaceFieldsAdded[30][i] << " \t "
<< surfaceFieldsAdded[31][i] << " \t "
<< surfaceFieldsAdded[32][i] << " \t "
<< surfaceFieldsAdded[33][i] << " \t "
<< endl;
}
outfile << endl << endl;
outfile.close();
return 0;
}
int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr vSession = LibUtilities::SessionReader::CreateInstance(argc, argv);
LibUtilities::CommSharedPtr vComm = vSession->GetComm();
MultiRegions::ContField3DHomogeneous1DSharedPtr Exp_u, Exp_v, Exp_w;
StdRegions::ConstFactorMap factors;
FlagList flags;
if( (argc != 2) && (argc != 3))
{
fprintf(stderr,"Usage: Deriv3DHomo2D meshfile [SysSolnType] \n");
exit(1);
}
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graph2D = MemoryManager<SpatialDomains::MeshGraph2D>::AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int nzpoints;
NekDouble lz;
int FFT;
vSession->LoadParameter("HomModesZ", nzpoints);
vSession->LoadParameter("LZ", lz);
vSession->LoadParameter("USEFFT", FFT);
bool useFFT = false;
bool deal = false;
if(FFT==1){useFFT = true;}
const LibUtilities::PointsKey PkeyZ(nzpoints,LibUtilities::eFourierSingleModeSpaced);
const LibUtilities::BasisKey BkeyZ(LibUtilities::eFourierHalfModeRe,nzpoints,PkeyZ);
Exp_u = MemoryManager<MultiRegions::ContField3DHomogeneous1D>::AllocateSharedPtr(vSession,BkeyZ,lz,useFFT,deal,graph2D,vSession->GetVariable(0));
Exp_v = MemoryManager<MultiRegions::ContField3DHomogeneous1D>::AllocateSharedPtr(vSession,BkeyZ,lz,useFFT,deal,graph2D,vSession->GetVariable(1));
Exp_w = MemoryManager<MultiRegions::ContField3DHomogeneous1D>::AllocateSharedPtr(vSession,BkeyZ,lz,useFFT,deal,graph2D,vSession->GetVariable(2));
//----------------------------------------------
// Print summary of solution details
flags.set(eUseGlobal, false);
const SpatialDomains::ExpansionMap &expansions = graph2D->GetExpansions();
LibUtilities::BasisKey bkey0 = expansions.begin()->second->m_basisKeyVector[0];
cout << "Calculating Derivatives (Homogeneous in z-plane):" << endl;
cout << " Lz : " << lz << endl;
cout << " N.modes : " << bkey0.GetNumModes() << endl;
cout << " N.Z h**o modes : " << BkeyZ.GetNumModes() << endl;
cout << endl;
//----------------------------------------------
//----------------------------------------------
// Set up coordinates of mesh for Forcing function evaluation
int nq = Exp_u->GetTotPoints();
Array<OneD,NekDouble> xc0,xc1,xc2;
xc0 = Array<OneD,NekDouble>(nq,0.0);
xc1 = Array<OneD,NekDouble>(nq,0.0);
xc2 = Array<OneD,NekDouble>(nq,0.0);
Exp_u->GetCoords(xc0,xc1,xc2);
//----------------------------------------------
Array<OneD,NekDouble> dudx,dvdy,dwdz;
Array<OneD,NekDouble> dump;
dump = Array<OneD,NekDouble>(nq,0.0);
dudx = Array<OneD,NekDouble>(nq,0.0);
dvdy = Array<OneD,NekDouble>(nq,0.0);
dwdz = Array<OneD,NekDouble>(nq,0.0);
//----------------------------------------------
// Define initial fields
LibUtilities::EquationSharedPtr ffunc_u = vSession->GetFunction("InitialCondition", 0);
LibUtilities::EquationSharedPtr ffunc_v = vSession->GetFunction("InitialCondition", 1);
LibUtilities::EquationSharedPtr ffunc_w = vSession->GetFunction("InitialCondition", 2);
LibUtilities::EquationSharedPtr exac_u = vSession->GetFunction("ExactSolution", 0);
LibUtilities::EquationSharedPtr exac_v = vSession->GetFunction("ExactSolution", 1);
LibUtilities::EquationSharedPtr exac_w = vSession->GetFunction("ExactSolution", 2);
ffunc_u->Evaluate(xc0,xc1,xc2,Exp_u->UpdatePhys());
ffunc_v->Evaluate(xc0,xc1,xc2,Exp_v->UpdatePhys());
ffunc_w->Evaluate(xc0,xc1,xc2,Exp_w->UpdatePhys());
exac_u->Evaluate(xc0,xc1,xc2,dudx);
exac_v->Evaluate(xc0,xc1,xc2,dvdy);
exac_w->Evaluate(xc0,xc1,xc2,dwdz);
//----------------------------------------------
//Taking derivative and printing the error
cout << "Deriv u" << endl;
Exp_u->PhysDeriv(Exp_u->GetPhys(),Exp_u->UpdatePhys(),dump,dump);
cout << "Deriv u done" << endl;
cout << "L infinity error: " << Exp_u->Linf(Exp_u->GetPhys(), dudx) << endl;
cout << "L 2 error : " << Exp_u->L2 (Exp_u->GetPhys(), dudx) << endl;
Exp_v->PhysDeriv(Exp_v->GetPhys(),dump,Exp_v->UpdatePhys(),dump);
cout << "L infinity error: " << Exp_v->Linf(Exp_v->GetPhys(), dvdy) << endl;
cout << "L 2 error : " << Exp_v->L2 (Exp_v->GetPhys(), dvdy) << endl;
Exp_w->PhysDeriv(Exp_w->GetPhys(),dump,dump,Exp_w->UpdatePhys());
cout << "L infinity error: " << Exp_w->Linf(Exp_w->GetPhys(), dwdz) << endl;
cout << "L 2 error : " << Exp_w->L2 (Exp_w->GetPhys(), dwdz) << endl;
return 0;
}
int main(int argc, char *argv[])
{
Array<OneD,NekDouble> fce;
Array<OneD,NekDouble> xc0,xc1,xc2;
if(argc < 2)
{
fprintf(stderr,"Usage: XmlToTecplot meshfile\n");
exit(1);
}
LibUtilities::SessionReader::RegisterCmdLineFlag(
"multi-zone", "m", "Output multi-zone format (one element per zone).");
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
//----------------------------------------------
// Read in mesh from input file
string meshfile(argv[argc-1]);
SpatialDomains::MeshGraphSharedPtr graphShPt
= SpatialDomains::MeshGraph::Read(vSession);
//----------------------------------------------
//----------------------------------------------
// Set up Expansion information
SpatialDomains::ExpansionMap emap = graphShPt->GetExpansions();
SpatialDomains::ExpansionMapIter it;
for (it = emap.begin(); it != emap.end(); ++it)
{
for (int i = 0; i < it->second->m_basisKeyVector.size(); ++i)
{
LibUtilities::BasisKey tmp1 = it->second->m_basisKeyVector[i];
LibUtilities::PointsKey tmp2 = tmp1.GetPointsKey();
it->second->m_basisKeyVector[i] = LibUtilities::BasisKey(
tmp1.GetBasisType(), tmp1.GetNumModes(),
LibUtilities::PointsKey(tmp1.GetNumModes(),
LibUtilities::ePolyEvenlySpaced));
}
}
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int expdim = graphShPt->GetMeshDimension();
Array<OneD, MultiRegions::ExpListSharedPtr> Exp(1);
switch(expdim)
{
case 1:
{
MultiRegions::ExpList1DSharedPtr Exp1D;
Exp1D = MemoryManager<MultiRegions::ExpList1D>::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp1D;
break;
}
case 2:
{
if(vSession->DefinesSolverInfo("HOMOGENEOUS"))
{
std::string HomoStr = vSession->GetSolverInfo("HOMOGENEOUS");
MultiRegions::ExpList3DHomogeneous1DSharedPtr Exp3DH1;
ASSERTL0(
HomoStr == "HOMOGENEOUS1D" || HomoStr == "Homogeneous1D" ||
HomoStr == "1D" || HomoStr == "Homo1D",
"Only 3DH1D supported for XML output currently.");
int nplanes;
vSession->LoadParameter("HomModesZ", nplanes);
// choose points to be at evenly spaced points at nplanes + 1
// points
const LibUtilities::PointsKey Pkey(
nplanes + 1, LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey Bkey(
LibUtilities::eFourier, nplanes, Pkey);
NekDouble lz = vSession->GetParameter("LZ");
Exp3DH1 = MemoryManager<MultiRegions::ExpList3DHomogeneous1D>
::AllocateSharedPtr(
vSession, Bkey, lz, false, false, graphShPt);
Exp[0] = Exp3DH1;
}
else
{
MultiRegions::ExpList2DSharedPtr Exp2D;
Exp2D = MemoryManager<MultiRegions::ExpList2D>::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp2D;
}
break;
}
case 3:
{
MultiRegions::ExpList3DSharedPtr Exp3D;
Exp3D = MemoryManager<MultiRegions::ExpList3D>::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp3D;
break;
}
default:
ASSERTL0(false,"Expansion dimension not recognised");
break;
}
//-----------------------------------------------
//----------------------------------------------
// Write solution depending on #define
string outfile(strtok(argv[argc-1],"."));
outfile += ".dat";
ofstream outstrm(outfile.c_str());
Exp[0]->WriteTecplotHeader(outstrm);
if (vSession->DefinesCmdLineArgument("multi-zone"))
{
int nExp = Exp[0]->GetExpSize();
for (int i = 0; i < nExp; ++i)
{
Exp[0]->WriteTecplotZone (outstrm, i);
Exp[0]->WriteTecplotConnectivity(outstrm, i);
}
}
else
{
Exp[0]->WriteTecplotZone (outstrm);
Exp[0]->WriteTecplotConnectivity(outstrm);
}
outstrm.close();
//----------------------------------------------
return 0;
}
int main(int argc, char *argv[])
{
unsigned int i,j;
if(argc < 3)
{
fprintf(stderr,"Usage: FldToPts meshfile fieldfile(s)\n");
exit(1);
}
int nExtraPoints;
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
vSession->LoadParameter("OutputExtraPoints",nExtraPoints,0);
//----------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graphShPt = SpatialDomains::MeshGraph::Read(vSession);//->GetFilename(), false);
//----------------------------------------------
for (int n = 2; n < argc; ++n)
{
string fname = std::string(argv[n]);
int fdot = fname.find_last_of('.');
if (fdot != std::string::npos)
{
string ending = fname.substr(fdot);
if (ending == ".chk" || ending == ".fld")
{
fname = fname.substr(0,fdot);
}
}
fname = fname + ".pts";
if (argc > 3)
{
if (fexist(fname.c_str()))
{
cout << "Skipping converted file: " << argv[n] << endl;
continue;
}
cout << "Processing " << argv[n] << endl;
}
//----------------------------------------------
// Import field file.
string fieldfile(argv[n]);
vector<SpatialDomains::FieldDefinitionsSharedPtr> fielddef;
vector<vector<NekDouble> > fielddata;
graphShPt->Import(fieldfile,fielddef,fielddata);
bool useFFT = false;
bool dealiasing = false;
//----------------------------------------------
//----------------------------------------------
// Set up Expansion information
for(i = 0; i < fielddef.size(); ++i)
{
vector<LibUtilities::PointsType> ptype;
for(j = 0; j < 3; ++j)
{
ptype.push_back(LibUtilities::ePolyEvenlySpaced);
}
fielddef[i]->m_pointsDef = true;
fielddef[i]->m_points = ptype;
vector<unsigned int> porder;
if(fielddef[i]->m_numPointsDef == false)
{
for(j = 0; j < fielddef[i]->m_numModes.size(); ++j)
{
porder.push_back(fielddef[i]->m_numModes[j]+nExtraPoints);
}
fielddef[i]->m_numPointsDef = true;
}
else
{
for(j = 0; j < fielddef[i]->m_numPoints.size(); ++j)
{
porder.push_back(fielddef[i]->m_numPoints[j]+nExtraPoints);
}
}
fielddef[i]->m_numPoints = porder;
}
graphShPt->SetExpansions(fielddef);
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int expdim = graphShPt->GetMeshDimension();
int nfields = fielddef[0]->m_fields.size();
Array<OneD, MultiRegions::ExpListSharedPtr> Exp(nfields);
switch(expdim)
{
case 1:
{
ASSERTL0(fielddef[0]->m_numHomogeneousDir <= 2,"NumHomogeneousDir is only set up for 1 or 2");
if(fielddef[0]->m_numHomogeneousDir == 1)
{
MultiRegions::ExpList2DHomogeneous1DSharedPtr Exp2DH1;
// Define Homogeneous expansion
//int nplanes = fielddef[0]->m_numModes[1];
int nplanes;
vSession->LoadParameter("HomModesZ",nplanes,fielddef[0]->m_numModes[1]);
// choose points to be at evenly spaced points at
const LibUtilities::PointsKey Pkey(nplanes+1,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey Bkey(fielddef[0]->m_basis[1],nplanes,Pkey);
NekDouble ly = fielddef[0]->m_homogeneousLengths[0];
Exp2DH1 = MemoryManager<MultiRegions::ExpList2DHomogeneous1D>::AllocateSharedPtr(vSession,Bkey,ly,useFFT,dealiasing,graphShPt);
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList2DHomogeneous1D>::AllocateSharedPtr(*Exp2DH1);
}
}
else if(fielddef[0]->m_numHomogeneousDir == 2)
{
MultiRegions::ExpList3DHomogeneous2DSharedPtr Exp3DH2;
// Define Homogeneous expansion
//int nylines = fielddef[0]->m_numModes[1];
//int nzlines = fielddef[0]->m_numModes[2];
int nylines;
int nzlines;
vSession->LoadParameter("HomModesY",nylines,fielddef[0]->m_numModes[1]);
vSession->LoadParameter("HomModesZ",nzlines,fielddef[0]->m_numModes[2]);
// choose points to be at evenly spaced points at
const LibUtilities::PointsKey PkeyY(nylines+1,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey BkeyY(fielddef[0]->m_basis[1],nylines,PkeyY);
const LibUtilities::PointsKey PkeyZ(nzlines+1,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey BkeyZ(fielddef[0]->m_basis[2],nzlines,PkeyZ);
NekDouble ly = fielddef[0]->m_homogeneousLengths[0];
NekDouble lz = fielddef[0]->m_homogeneousLengths[1];
Exp3DH2 = MemoryManager<MultiRegions::ExpList3DHomogeneous2D>::AllocateSharedPtr(vSession,BkeyY,BkeyZ,ly,lz,useFFT,dealiasing,graphShPt);
Exp[0] = Exp3DH2;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3DHomogeneous2D>::AllocateSharedPtr(*Exp3DH2);
}
}
else
{
MultiRegions::ExpList1DSharedPtr Exp1D;
Exp1D = MemoryManager<MultiRegions::ExpList1D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp1D;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList1D>
::AllocateSharedPtr(*Exp1D);
}
}
}
break;
case 2:
{
ASSERTL0(fielddef[0]->m_numHomogeneousDir <= 1,"NumHomogeneousDir is only set up for 1");
if(fielddef[0]->m_numHomogeneousDir == 1)
{
MultiRegions::ExpList3DHomogeneous1DSharedPtr Exp3DH1;
// Define Homogeneous expansion
//int nplanes = fielddef[0]->m_numModes[2];
int nplanes;
vSession->LoadParameter("HomModesZ",nplanes,fielddef[0]->m_numModes[2]);
// choose points to be at evenly spaced points at
// nplanes + 1 points
const LibUtilities::PointsKey Pkey(nplanes+1,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey Bkey(fielddef[0]->m_basis[2],nplanes,Pkey);
NekDouble lz = fielddef[0]->m_homogeneousLengths[0];
Exp3DH1 = MemoryManager<MultiRegions::ExpList3DHomogeneous1D>::AllocateSharedPtr(vSession,Bkey,lz,useFFT,dealiasing,graphShPt);
Exp[0] = Exp3DH1;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3DHomogeneous1D>::AllocateSharedPtr(*Exp3DH1);
}
}
else
{
MultiRegions::ExpList2DSharedPtr Exp2D;
Exp2D = MemoryManager<MultiRegions::ExpList2D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp2D;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList2D>
::AllocateSharedPtr(*Exp2D);
}
}
}
break;
case 3:
{
MultiRegions::ExpList3DSharedPtr Exp3D;
Exp3D = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp3D;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(*Exp3D);
}
}
break;
default:
ASSERTL0(false,"Expansion dimension not recognised");
break;
}
//----------------------------------------------
//----------------------------------------------
// Copy data from field file
for(j = 0; j < nfields; ++j)
{
for(int i = 0; i < fielddata.size(); ++i)
{
Exp[j]->ExtractDataToCoeffs(fielddef [i],
fielddata[i],
fielddef [i]->m_fields[j],
Exp[j]->UpdateCoeffs());
}
Exp[j]->BwdTrans(Exp[j]->GetCoeffs(),Exp[j]->UpdatePhys());
}
//----------------------------------------------
//----------------------------------------------
// Write solution
//string outname(strtok(argv[n],"."));
//outname += ".vtu";
ofstream outfile(fname.c_str());
// For each field write out field data for each expansion.
outfile << "Fields: x y ";
for(i = 0; i < Exp.num_elements(); ++i)
{
outfile << fielddef[0]->m_fields[i];
}
outfile << endl;
Array<OneD,NekDouble> x(Exp[0]->GetNpoints());
Array<OneD,NekDouble> y(Exp[0]->GetNpoints());
Exp[0]->GetCoords(x,y);
for(i = 0; i < Exp[0]->GetNpoints(); ++i)
{
outfile << x[i] << " " << y[i] << " ";
for(j = 0; j < Exp.num_elements(); ++j)
{
outfile << (Exp[j]->GetPhys())[i] << " ";
}
outfile << endl;
}
cout << "Written file: " << fname << endl;
//----------------------------------------------
}
return 0;
}
int main(int argc, char *argv[])
{
int i;
NekDouble cr = 0;
if(argc !=3)
{
fprintf(stderr,"Usage: ./ExtractCriticalLayer meshfile fieldfile \n");
exit(1);
}
//------------------------------------------------------------
// Create Session file.
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
//-----------------------------------------------------------
//-------------------------------------------------------------
// Read in mesh from input file
SpatialDomains::MeshGraphSharedPtr graphShPt = SpatialDomains::MeshGraph::Read(vSession);
//------------------------------------------------------------
//-------------------------------------------------------------
// Define Streak Expansion
MultiRegions::ExpListSharedPtr streak;
streak = MemoryManager<MultiRegions::ExpList2D>
::AllocateSharedPtr(vSession,graphShPt);
//---------------------------------------------------------------
//----------------------------------------------
// Import field file.
string fieldfile(argv[argc-1]);
vector<LibUtilities::FieldDefinitionsSharedPtr> fielddef;
vector<vector<NekDouble> > fielddata;
LibUtilities::Import(fieldfile,fielddef,fielddata);
//----------------------------------------------
//----------------------------------------------
// Copy data from field file
string streak_field("w");
for(unsigned int i = 0; i < fielddata.size(); ++i)
{
streak->ExtractDataToCoeffs(fielddef [i],
fielddata[i],
streak_field,
streak->UpdateCoeffs());
}
//----------------------------------------------
int npts;
vSession->LoadParameter("NumCriticalLayerPts",npts,30);
Array<OneD, NekDouble> x_c(npts);
Array<OneD, NekDouble> y_c(npts);
NekDouble trans;
vSession->LoadParameter("WidthOfLayers",trans,0.1);
Computestreakpositions(streak,x_c, y_c,cr,trans);
cout << "# x_c y_c" << endl;
for(i = 0; i < npts; ++i)
{
fprintf(stdout,"%12.10lf %12.10lf \n",x_c[i],y_c[i]);
//cout << x_c[i] << " " << y_c[i] << endl;
}
}
int main(int argc, char *argv[])
{
int i,j;
if(argc != 4)
{
fprintf(stderr,"Usage: FldAddVort meshfile infld outfld\n");
exit(1);
}
LibUtilities::SessionReaderSharedPtr vSession
= LibUtilities::SessionReader::CreateInstance(argc, argv);
//----------------------------------------------
// Read in mesh from input file
string meshfile(argv[argc-3]);
SpatialDomains::MeshGraphSharedPtr graphShPt = SpatialDomains::MeshGraph::Read(vSession);//meshfile);
//----------------------------------------------
//----------------------------------------------
// Import field file.
string fieldfile(argv[argc-2]);
vector<LibUtilities::FieldDefinitionsSharedPtr> fielddef;
vector<vector<NekDouble> > fielddata;
LibUtilities::Import(fieldfile,fielddef,fielddata);
bool useFFT = false;
bool dealiasing = false;
//----------------------------------------------
//----------------------------------------------
// Define Expansion
int expdim = graphShPt->GetMeshDimension();
int nfields = fielddef[0]->m_fields.size();
int addfields = (nfields == 4)? 3:1;
Array<OneD, MultiRegions::ExpListSharedPtr> Exp(nfields + addfields);
switch(expdim)
{
case 1:
{
ASSERTL0(fielddef[0]->m_numHomogeneousDir <= 2,"Quasi-3D approach is only set up for 1 or 2 homogeneous directions");
if(fielddef[0]->m_numHomogeneousDir == 1)
{
MultiRegions::ExpList2DHomogeneous1DSharedPtr Exp2DH1;
// Define Homogeneous expansion
//int nplanes = fielddef[0]->m_numModes[1];
int nplanes;
vSession->LoadParameter("HomModesZ",nplanes,fielddef[0]->m_numModes[1]);
// choose points to be at evenly spaced points at
// nplanes points
const LibUtilities::PointsKey Pkey(nplanes,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey Bkey(fielddef[0]->m_basis[1],nplanes,Pkey);
NekDouble ly = fielddef[0]->m_homogeneousLengths[0];
Exp2DH1 = MemoryManager<MultiRegions::ExpList2DHomogeneous1D>::AllocateSharedPtr(vSession,Bkey,ly,useFFT,dealiasing,graphShPt);
Exp[0] = Exp2DH1;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList2DHomogeneous1D>::AllocateSharedPtr(*Exp2DH1);
}
}
else if(fielddef[0]->m_numHomogeneousDir == 2)
{
MultiRegions::ExpList3DHomogeneous2DSharedPtr Exp3DH2;
// Define Homogeneous expansion
//int nylines = fielddef[0]->m_numModes[1];
//int nzlines = fielddef[0]->m_numModes[2];
int nylines;
int nzlines;
vSession->LoadParameter("HomModesY",nylines,fielddef[0]->m_numModes[1]);
vSession->LoadParameter("HomModesZ",nzlines,fielddef[0]->m_numModes[2]);
// choose points to be at evenly spaced points at
// nplanes points
const LibUtilities::PointsKey PkeyY(nylines,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey BkeyY(fielddef[0]->m_basis[1],nylines,PkeyY);
const LibUtilities::PointsKey PkeyZ(nzlines,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey BkeyZ(fielddef[0]->m_basis[2],nzlines,PkeyZ);
NekDouble ly = fielddef[0]->m_homogeneousLengths[0];
NekDouble lz = fielddef[0]->m_homogeneousLengths[1];
Exp3DH2 = MemoryManager<MultiRegions::ExpList3DHomogeneous2D>::AllocateSharedPtr(vSession,BkeyY,BkeyZ,ly,lz,useFFT,dealiasing,graphShPt);
Exp[0] = Exp3DH2;
for(i = 1; i < nfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3DHomogeneous2D>::AllocateSharedPtr(*Exp3DH2);
}
}
else
{
MultiRegions::ExpList1DSharedPtr Exp1D;
Exp1D = MemoryManager<MultiRegions::ExpList1D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp1D;
for(i = 1; i < nfields + addfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList1D>
::AllocateSharedPtr(*Exp1D);
}
}
}
break;
case 2:
{
ASSERTL0(fielddef[0]->m_numHomogeneousDir <= 1,"NumHomogeneousDir is only set up for 1");
if(fielddef[0]->m_numHomogeneousDir == 1)
{
MultiRegions::ExpList3DHomogeneous1DSharedPtr Exp3DH1;
// Define Homogeneous expansion
//int nplanes = fielddef[0]->m_numModes[2];
int nplanes;
vSession->LoadParameter("HomModesZ",nplanes,fielddef[0]->m_numModes[2]);
// choose points to be at evenly spaced points at
// nplanes points
const LibUtilities::PointsKey Pkey(nplanes,LibUtilities::ePolyEvenlySpaced);
const LibUtilities::BasisKey Bkey(fielddef[0]->m_basis[2],nplanes,Pkey);
NekDouble lz = fielddef[0]->m_homogeneousLengths[0];
Exp3DH1 = MemoryManager<MultiRegions::ExpList3DHomogeneous1D>::AllocateSharedPtr(vSession,Bkey,lz,useFFT,dealiasing,graphShPt);
Exp[0] = Exp3DH1;
for(i = 1; i < nfields + addfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3DHomogeneous1D>::AllocateSharedPtr(*Exp3DH1);
}
}
else
{
MultiRegions::ExpList2DSharedPtr Exp2D;
Exp2D = MemoryManager<MultiRegions::ExpList2D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp2D;
for(i = 1; i < nfields + addfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList2D>
::AllocateSharedPtr(*Exp2D);
}
}
}
break;
case 3:
{
MultiRegions::ExpList3DSharedPtr Exp3D;
Exp3D = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(vSession,graphShPt);
Exp[0] = Exp3D;
for(i = 1; i < nfields + addfields; ++i)
{
Exp[i] = MemoryManager<MultiRegions::ExpList3D>
::AllocateSharedPtr(*Exp3D);
}
}
break;
default:
ASSERTL0(false,"Expansion dimension not recognised");
break;
}
//----------------------------------------------
//----------------------------------------------
// Copy data from field file
for(j = 0; j < nfields; ++j)
{
for(int i = 0; i < fielddata.size(); ++i)
{
Exp[j]->ExtractDataToCoeffs(fielddef [i],
fielddata[i],
fielddef [i]->m_fields[j],
Exp[j]->UpdateCoeffs());
}
Exp[j]->BwdTrans(Exp[j]->GetCoeffs(),Exp[j]->UpdatePhys());
}
//----------------------------------------------
//----------------------------------------------
// Compute gradients of fields
ASSERTL0(nfields >= 3, "Need two fields (u,v) to add reentricity");
int nq = Exp[0]->GetNpoints();
Array<OneD, Array<OneD, NekDouble> > grad(nfields*nfields);
Array<OneD, Array<OneD, NekDouble> > outfield(addfields);
for(i = 0; i < nfields*nfields; ++i)
{
grad[i] = Array<OneD, NekDouble>(nq);
}
for(i = 0; i < addfields; ++i)
{
outfield[i] = Array<OneD, NekDouble>(nq);
}
// Calculate Gradient & Vorticity
if(nfields == 3)
{
for(i = 0; i < nfields; ++i)
{
Exp[i]->PhysDeriv(Exp[i]->GetPhys(), grad[i*nfields],grad[i*nfields+1]);
}
// W_z = Vx - Uy
Vmath::Vsub(nq,grad[1*nfields+0],1,grad[0*nfields+1],1,outfield[0],1);
}
else
{
for(i = 0; i < nfields; ++i)
{
Exp[i]->PhysDeriv(Exp[i]->GetPhys(), grad[i*nfields],grad[i*nfields+1],grad[i*nfields+2]);
}
// W_x = Wy - Vz
Vmath::Vsub(nq,grad[2*nfields+1],1,grad[1*nfields+2],1,outfield[0],1);
// W_y = Uz - Wx
Vmath::Vsub(nq,grad[0*nfields+2],1,grad[2*nfields+0],1,outfield[1],1);
// W_z = Vx - Uy
Vmath::Vsub(nq,grad[1*nfields+0],1,grad[0*nfields+1],1,outfield[2],1);
}
for (i = 0; i < addfields; ++i)
{
Exp[nfields + i]->FwdTrans(outfield[i], Exp[nfields+i]->UpdateCoeffs());
}
//-----------------------------------------------
// Write solution to file with additional computed fields
string out(argv[argc-1]);
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp[0]->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
vector<string > outname;
if(addfields == 1)
{
outname.push_back("W_z");
}
else
{
outname.push_back("W_x");
outname.push_back("W_y");
outname.push_back("W_z");
}
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;
}
