int main(int argc, char *argv[])
{
LibUtilities::SessionReaderSharedPtr session;
string vDriverModule;
DriverSharedPtr drv;
try
{
// Create session reader.
session = LibUtilities::SessionReader::CreateInstance(argc, argv);
// Create driver
session->LoadSolverInfo("Driver", vDriverModule, "Standard");
drv = GetDriverFactory().CreateInstance(vDriverModule, session);
// Execute driver
drv->Execute();
// Finalise session
session->Finalise();
}
catch (const std::runtime_error& e)
{
return 1;
}
catch (const std::string& eStr)
{
cout << "Error: " << eStr << endl;
}
return 0;
}
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[])
{
if(argc != 2)
{
fprintf(stderr,"Usage: ./Aliasing file.xml \n");
fprintf(stderr,"\t Method will read intiial conditions section of .xml file for input \n");
exit(1);
}
LibUtilities::SessionReaderSharedPtr session;
string vDriverModule;
DriverSharedPtr drv;
try
{
// Create session reader.
session = LibUtilities::SessionReader::CreateInstance(argc, argv);
// Create driver
session->LoadSolverInfo("Driver", vDriverModule, "Standard");
drv = GetDriverFactory().CreateInstance(vDriverModule, session);
EquationSystemSharedPtr EqSys = drv->GetEqu()[0];
IncNavierStokesSharedPtr IncNav = EqSys->as<IncNavierStokes>();
IncNav->SetInitialConditions(0.0,false);
Array<OneD, MultiRegions::ExpListSharedPtr> fields = IncNav->UpdateFields();
int i;
int nConvectiveFields = IncNav->GetNConvectiveFields();
int nphys = fields[0]->GetTotPoints();
Array<OneD, Array<OneD, NekDouble> > VelFields(nConvectiveFields);
Array<OneD, Array<OneD, NekDouble> > NonLinear(nConvectiveFields);
Array<OneD, Array<OneD, NekDouble> > NonLinearDealiased(nConvectiveFields);
for(i = 0; i < nConvectiveFields; ++i)
{
VelFields[i] = fields[i]->UpdatePhys();
NonLinear[i] = Array<OneD, NekDouble> (nphys);
NonLinearDealiased[i] = Array<OneD, NekDouble> (nphys);
}
boost::shared_ptr<NavierStokesAdvection> A
= boost::dynamic_pointer_cast<NavierStokesAdvection>(IncNav->GetAdvObject());
if (!A)
{
cout << "Must use non-linear Navier-Stokes advection" << endl;
exit(-1);
}
// calculate non-linear terms without dealiasing
A->SetSpecHPDealiasing(false);
A->Advect(nConvectiveFields, fields,
VelFields, VelFields,
NonLinear, 0.0);
// calculate non-linear terms with dealiasing
A->SetSpecHPDealiasing(true);
A->Advect(nConvectiveFields, fields,
VelFields, VelFields,
NonLinearDealiased, 0.0);
// Evaulate Difference and put into fields;
for(i = 0; i < nConvectiveFields; ++i)
{
Vmath::Vsub(nphys,NonLinearDealiased[i],1,NonLinear[i],1,NonLinear[i],1);
fields[i]->FwdTrans_IterPerExp(NonLinear[i],fields[i]->UpdateCoeffs());
// Need to reset varibale name for output
string name = "NL_Aliasing_"+session->GetVariable(i);
session->SetVariable(i,name.c_str());
}
// Reset session name for output file
std::string outname = IncNav->GetSessionName();
outname += "_NonLinear_Aliasing";
IncNav->ResetSessionName(outname);
IncNav->Output();
}
catch (const std::runtime_error&)
{
return 1;
}
catch (const std::string& eStr)
{
cout << "Error: " << eStr << endl;
}
return 0;
}
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;
}
