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newIoDataVtk.cpp
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#include "io_data_vtk.h"
#include <vtkPoints.h>
#include <vtkPointData.h>
#include <vtkCellArray.h>
#include <vtkDoubleArray.h>
#include <vtkLongArray.h>
#include <vtkFloatArray.h>
#include <vtkIntArray.h>
#include <vtkIdTypeArray.h>
#include <vtkUnstructuredGrid.h>
#include <vtkXMLPUnstructuredGridWriter.h>
#include <vtkXMLStructuredGridWriter.h>
#include <vtkXMLUnstructuredGridReader.h>
#include <vtkUnstructuredGridReader.h>
#include <vtkXMLPUnstructuredGridReader.h>
#include <vtkStructuredGrid.h>
#include <cstdlib>
#include <boost/tuple/tuple.hpp>
template <class double>
class typeMap {
typedef vtkDoubleArray vtkArrayType
typedef double vtkTupleType
static int components = 1;
}
template <class vect>
class typeMap {
typedef vtkDoubleArray vtkArrayType
typedef double[NDIM] vtkTupleType
static int components = NDIM;
}
template <class int>
class typeMap {
typedef vtkIntArray vtkArrayType
typedef int vtkTupleType
static int components = 1;
}
template <class particleT>
inline void readProcessTuple(int i, vtkUnstructuredGrid *vtkData, vector<particleT>::iterator p, const null_type&) {};
template <class particleT, class H, class T>
inline void readProcessTuple(int i, vtkUnstructuredGrid *vtkData, vector<particleT>::iterator p, cons<H,T> vars) {
typedef typeMap<vars.get_head()::type>::vtkArrayType vtkType
vtkType *vtkArray = static_cast<vtkType *> (dataset->GetPointData()->GetArray(vars.get_head().name));
vars.get_head()(*p) = vtkArray->getTuple(i);
readRestartProcessTuple(i,vtkData,data,vars.get_tail());
}
template <class particleT>
inline void writeProcessTuple(int i, vtkUnstructuredGrid *vtkData, vector<particleT>::iterator p, const null_type&) {};
template <class particleT, class H, class T>
inline void writeProcessTuple(int i, vtkUnstructuredGrid *vtkData, vector<particleT>::iterator p, cons<H,T> vars) {
typedef typeMap<H::type>::vtkArrayType vtkType
typedef typeMap<H::type>::vtkTupleType tupleType
vtkType *vtkArray = static_cast<vtkType *> (vtkData->GetPointData()->GetArray(vars.get_head().name));
typleType tuple = vars.get_head()(*p);
vtkArray->SetTuple(i, &tuple);
writeProcessTuple(i,vtkData,data,vars.get_tail());
}
template <class particleT>
inline void writeInitProcessTuple(int n, vtkUnstructuredGrid *vtkData, const null_type&) {};
template <class particleT, class H, class T>
inline void writeInitProcessTuple(int n, vtkUnstructuredGrid *vtkData, cons<H,T> vars) {
typedef typeMap<H::type>::vtkArrayType vtkType
typedef typeMap<H::type>::vtkTupleType tupleType
const int components = typeMap<H::type>::components;
vtkType *vtkArray = vtkType::New();
vtkArray->SetNumberOfComponents(components);
vtkArray->SetNumberOfTuples(n);
vtkArray->SetName(H::name);
vtkData->GetPointData()->AddArray(vtkArray);
writeInitProcessTuple(i,vtkData,vars.get_tail());
}
vtkXMLUnstructuredGridReader *openReader(int timestep,string filename,CglobalVars *globals) {
vtkXMLUnstructuredGridReader *reader = vtkXMLUnstructuredGridReader::New();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
char strRank[20];
sprintf(strRank,"%d",globals->mpiRank);
string theFilename = filename+strTimestep+"_"+strRank+".vtu";
cout << "Reading file " << theFilename << endl;
reader->SetFileName(theFilename.c_str());
reader->Update();
return reader;
}
vtkXMLUnstructuredGridWriter *openWriter(int timestep,string filename,CglobalVars *globals) {
vtkXMLPUnstructuredGridWriter *writer = vtkXMLPUnstructuredGridWriter::New();
writer->SetNumberOfPieces(globals->mpiSize);
writer->SetStartPiece(globals->mpiRank);
writer->SetEndPiece(globals->mpiRank);
writer->SetDataModeToBinary();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
string outFilename = filename+strTimestep+".pvtu";
writer->SetFileName(outFilename.c_str());
//writer->SetTimeStep(timestep);
return writer;
}
template <class particleT,class varsT>
void readParticles(string filename, int timestep,vector<particleT> *outPs,CglobalVars *globals,varsT vars) {
vtkXMLUnstructuredGridReader *reader = openFile(timestep,filename);
vtkUnstructuredGrid *vtkData = reader->GetOutput();
int n = dataset->GetNumberOfPoints();
if (globals->mpiRank==0) cout << "Found "<<n<<" points in the file..." << endl;
outPs->resize(n);
vector<particleT>::iterator psIter = outPs->begin();
for (int i=0;i<n;i++) {
readProcessTuple(i, *vtkData, psIter, vars);
psIter++;
}
reader->Delete();
}
void deleteArrays(vtkPoints *pts) {
const n = pts->GetNumberOfArrays();
for (int i=0;i<n;i++) {
pts->GetArray(i)->Delete();
}
}
template <class particleT,class varsT>
void writeParticles(string filename, int timestep,vector<particleT> *outPs,CglobalVars *globals,varsT vars) {
vtkUnstructuredGrid *vtkData);
const int n = outPs->size();
vtkPoints *newPts = vtkPoints::New();
vtkCellArray *newCells = vtkCellArray::New();
newPts->SetNumberOfPoints(n);
vtkUnstructuredGrid *vtkData = vtkUnstructuredGrid::New();
vtkData->SetPoints(newPts);
vtkData->SetCells(1,newCells);
writeInitProcessTuple(n, vtkUnstructuredGrid *vtkData, cons<H,T> vars) {
vector<particleT>::iterator psIter = outPs->begin();
for (int i=0;i<n;i++) {
newCells->InsertNextCell(1);
newCells->InsertCellPoint(i);
double r = psIter->r;
newPts->SetPoint(i,&r);
writeProcessTuple(i, vtkData, psIter, vars);
psIter++;
}
if (globals->mpiRank==0) cout << "\tWriting "<<n<<" particles to file: "<<outFilename<<endl;
vtkXMLUnstructuredGridWriter writer = openWriter(timestep,filename,globals);
writer->SetInput(vtkData);
writer->Write();
deleteArrays(newPts);
writer->Delete();
dataset->Delete();
newPts->Delete();
newCells->Delete();
}
template<class particleT>
void Cio_data_vtk::readRestartDem(int timestep,vector<particleT> *outPs,CglobalVars *globals) {
outPs->reserve(MAX_NUM_PARTICLES_PER_CPU);
readParticles(filename+"Restart",timestep,outPs,globals,particleT::restartVars());
}
template<class particleT>
void Cio_data_vtk::writeRestart(int timestep,vector<particleT> *outPs,CglobalVars *globals) {
writeParticles(filename+"Restart",timestep,outPs,globals,particleT::restartVars());
}
void Cio_data_vtk::readRestartSph(int timestep,vector<sphParticle> *outPs,CglobalVars *globals) {
vtkXMLUnstructuredGridReader *reader = vtkXMLUnstructuredGridReader::New();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
char strRank[20];
sprintf(strRank,"%d",globals->mpiRank);
string theFilename = filename+"Restart"+strTimestep+"_"+strRank+".vtu";
cout << "Reading file " << theFilename << endl;
reader->SetFileName(theFilename.c_str());
reader->Update();
vtkUnstructuredGrid *vtkData = reader->GetOutput();
//reader->SetOutput(dataset);
int n = dataset->GetNumberOfPoints();
cout << "Found "<<n<<" points in the file..." << endl;
vtkDoubleArray *dens = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("dens"));
vtkDoubleArray *h = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("h"));
vtkDoubleArray *u = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("u"));
vtkDoubleArray *mass = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("mass"));
vtkDoubleArray *colour = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("colour"));
vtkIntArray *iam = static_cast<vtkIntArray *> (dataset->GetPointData()->GetArray("iam"));
vtkIntArray *tag= static_cast<vtkIntArray *> (dataset->GetPointData()->GetArray("tag"));
vtkDoubleArray *v = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("v"));
vtkDoubleArray *vort = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("vort"));
#ifndef BACKCOMPAT_READ
vtkDoubleArray *vhat = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("vhat"));
vtkDoubleArray *norm1 = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("norm1"));
vtkDoubleArray *norm2 = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("norm2"));
#ifdef _3D_
vtkDoubleArray *norm3 = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("norm3"));
#endif
vtkDoubleArray *eFF = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("eFF"));
#endif
vtkDoubleArray *alpha = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("alpha"));
vtkDoubleArray *eBForce= static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("eBForce"));
vtkDoubleArray *eViscF = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("eViscF"));
vtkDoubleArray *eViscB = static_cast<vtkDoubleArray *> (dataset->GetPointData()->GetArray("eViscB"));
outPs->reserve(MAX_NUM_PARTICLES_PER_CPU);
outPs->resize(n);
vector<particleT>::iterator p = outPs->begin();
for (int i=0;i<n;i++) {
readRestartProcessTuple(i,vtkData,data,vars);
double r[3],vv[3],nn1[3],nn2[3],vvhat[3],vvort[3];
#ifdef _3D_
double nn3[3];
norm3->GetTuple(i,nn3);
#endif
dataset->GetPoint(i,r);
v->GetTuple(i,vv);
#ifndef BACKCOMPAT_READ
vort->GetTuple(i,vvort);
vhat->GetTuple(i,vvhat);
norm1->GetTuple(i,nn1);
norm2->GetTuple(i,nn2);
#endif
for (int j=0;j<NDIM;j++) {
p->r[j]=r[j];
p->v[j]=vv[j];
#ifndef BACKCOMPAT_READ
p->vort[j]=vvort[j];
p->vhat[j]=vvhat[j];
p->norm1[j]=nn1[j];
p->norm2[j]=nn2[j];
#ifdef _3D_
p->norm3[j]=nn3[j];
#endif
#else
p->vhat[j]=vv[j];
#endif
}
//cout << "Processor "<<globals->mpiRank<<": got particle at "<<p->r<<endl;
p->dens = dens->GetValue(i);
p->h = h->GetValue(i);
p->eBForce = eBForce->GetValue(i);
p->eViscF = eViscF->GetValue(i);
p->eViscB = eViscB->GetValue(i);
#ifndef BACKCOMPAT_READ
p->eFF = eFF->GetValue(i);
#endif
p->u = u->GetValue(i);
p->mass = mass->GetValue(i);
p->colour = colour->GetValue(i);
p->iam = (iamTypes)iam->GetValue(i);
p->tag= tag->GetValue(i);
p->alpha= alpha->GetValue(i);
#ifdef SLK
p->currR = p->r;
#endif
p++;
}
reader->Delete();
}
void Cio_data_vtk::readOutputDem(int timestep,vector<demParticle *outPs,CglobalVars *globals) {}
void Cio_data_vtk::readOutputSph(int timestep,vector<sphParticle *outPs,CglobalVars *globals) {
vtkXMLPUnstructuredGridReader *reader = vtkXMLPUnstructuredGridReader::New();
char strRank[20];
sprintf(strRank,"%d",globals->mpiRank);
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
string theFilename = filename+strTimestep+".pvtu";
reader->SetFileName(theFilename.c_str());
reader->Update();
vtkUnstructuredGrid *dataset = reader->GetOutput();
int n = dataset->GetNumberOfPoints();
//vtkFloatArray *colour = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("colour"));
vtkIntArray *tag= static_cast<vtkIntArray *> (dataset->GetPointData()->GetArray("tag"));
vtkIntArray *iam = static_cast<vtkIntArray *> (dataset->GetPointData()->GetArray("iam"));
vtkFloatArray *v = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("v"));
#ifdef SAVE_VHALF
vtkFloatArray *vHalf = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("vHalf"));
vtkFloatArray *rHalf = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("rHalf"));
#endif
vtkFloatArray *vhat = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("vhat"));
#ifdef AVE_VELOCITY
vtkFloatArray *aveV = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("aveV"));
#endif
vtkFloatArray *fv = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("fv"));
vtkFloatArray *vort= static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("vort"));
vtkFloatArray *h= static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("h"));
vtkFloatArray *dens = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("dens"));
vtkFloatArray *press = static_cast<vtkFloatArray *> (dataset->GetPointData()->GetArray("press"));
outPs->clear();
outPs->resize(n);
particleContainer::iterator p = outPs->begin();
for (int i=0;i<n;i++) {
double r[3],vv[3],fvv[3],vvhat[3],vvort[3];
#ifdef AVE_VELOCITY
double aaveV[3];
#endif
dataset->GetPoint(i,r);
v->GetTuple(i,vv);
vhat->GetTuple(i,vvhat);
vort->GetTuple(i,vvort);
#ifdef AVE_VELOCITY
aveV->GetTuple(i,aaveV);
#endif
fv->GetTuple(i,fvv);
#ifdef SAVE_VHALF
double vvHalf[3];
double rrHalf[3];
vHalf->GetTuple(i,vvHalf);
rHalf->GetTuple(i,rrHalf);
#endif
for (int j=0;j<NDIM;j++) {
p->r[j]=r[j];
p->v[j]=vv[j];
#ifdef SAVE_VHALF
p->vHalf[j]=vvHalf[j];
p->rHalf[j]=rrHalf[j];
#endif
p->vhat[j]=vvhat[j];
#ifdef AVE_VELOCITY
p->aveV[j]=aaveV[j];
#endif
p->fv[j]=fvv[j];
p->vort[j]=vvort[j];
}
//p->colour = colour->GetValue(i);
p->tag= tag->GetValue(i);
p->iam = (iamTypes)iam->GetValue(i);
p->h= h->GetValue(i);
p->dens = dens->GetValue(i);
p->press = press->GetValue(i);
//cout <<"Reading point with r = "<<p->r<<" v = "<<p->v<<" colour = "<<p->colour<<" h = "<<p->h<<" tag = "<<p->tag<<endl;
p++;
}
reader->Delete();
}
void Cio_data_vtk::writeRestartDem(int timestep,vector<sphParticle> &ps,CglobalVars *globals) {}
void Cio_data_vtk::writeRestartSph(int timestep,vector<demParticle> &ps,CglobalVars *globals) {
//construct points
int n = ps.size();
vtkPoints *newPts = vtkPoints::New();;
vtkDoubleArray *dens = vtkDoubleArray::New();
vtkDoubleArray *h = vtkDoubleArray::New();
vtkDoubleArray *u = vtkDoubleArray::New();
vtkDoubleArray *mass = vtkDoubleArray::New();
vtkDoubleArray *colour = vtkDoubleArray::New();
vtkIntArray *iam = vtkIntArray::New();
vtkDoubleArray *v = vtkDoubleArray::New();
vtkDoubleArray *vhat = vtkDoubleArray::New();
vtkDoubleArray *norm1 = vtkDoubleArray::New();
vtkDoubleArray *norm2 = vtkDoubleArray::New();
#ifdef _3D_
vtkDoubleArray *norm3 = vtkDoubleArray::New();
#endif
vtkDoubleArray *alpha = vtkDoubleArray::New();
vtkDoubleArray *vort = vtkDoubleArray::New();
vtkIntArray *tag = vtkIntArray::New();
vtkDoubleArray *eBForce = vtkDoubleArray::New();
vtkDoubleArray *eViscF = vtkDoubleArray::New();
vtkDoubleArray *eViscB = vtkDoubleArray::New();
vtkDoubleArray *eFF = vtkDoubleArray::New();
newPts->SetNumberOfPoints(n);
dens->SetNumberOfValues(n);
h->SetNumberOfValues(n);
eBForce->SetNumberOfValues(n);
eViscF->SetNumberOfValues(n);
eViscB->SetNumberOfValues(n);
eFF->SetNumberOfValues(n);
u->SetNumberOfValues(n);
mass->SetNumberOfValues(n);
colour->SetNumberOfValues(n);
iam->SetNumberOfValues(n);
tag->SetNumberOfValues(n);
v->SetNumberOfComponents(3);
v->SetNumberOfTuples(n);
vhat->SetNumberOfComponents(3);
vhat->SetNumberOfTuples(n);
vort->SetNumberOfComponents(3);
vort->SetNumberOfTuples(n);
norm1->SetNumberOfComponents(3);
norm1->SetNumberOfTuples(n);
norm2->SetNumberOfComponents(3);
norm2->SetNumberOfTuples(n);
#ifdef _3D_
norm3->SetNumberOfComponents(3);
norm3->SetNumberOfTuples(n);
#endif
alpha->SetNumberOfValues(n);
dens->SetName("dens");
h->SetName("h");
eBForce->SetName("eBForce");
eViscF->SetName("eViscF");
eViscB->SetName("eViscB");
eFF->SetName("eFF");
u->SetName("u");
mass->SetName("mass");
colour->SetName("colour");
iam->SetName("iam");
tag->SetName("tag");
v->SetName("v");
vhat->SetName("vhat");
vort->SetName("vort");
norm1->SetName("norm1");
norm2->SetName("norm2");
#ifdef _3D_
norm3->SetName("norm3");
#endif
alpha->SetName("alpha");
int i=0;
for (particleContainer::iterator p = ps.begin();p!=ps.end();p++) {
#if NDIM==1
newPts->SetPoint(i,p->r[0],0,0);
v->SetTuple3(i,p->v[0],0,0);
vhat->SetTuple3(i,p->vhat[0],0,0);
vort->SetTuple3(i,p->vort[0],0,0);
norm1->SetTuple3(i,p->norm1[0],0,0);
norm2->SetTuple3(i,p->norm2[0],0,0);
#elif NDIM==2
newPts->SetPoint(i,p->r[0],p->r[1],0);
v->SetTuple3(i,p->v[0],p->v[1],0);
vhat->SetTuple3(i,p->vhat[0],p->vhat[1],0);
vort->SetTuple3(i,p->vort[0],p->vort[1],0);
norm1->SetTuple3(i,p->norm1[0],p->norm1[1],0);
norm2->SetTuple3(i,p->norm2[0],p->norm2[1],0);
#elif NDIM==3
newPts->SetPoint(i,p->r[0],p->r[1],p->r[2]);
v->SetTuple3(i,p->v[0],p->v[1],p->v[2]);
vhat->SetTuple3(i,p->vhat[0],p->vhat[1],p->vhat[2]);
vort->SetTuple3(i,p->vort[0],p->vort[1],p->vort[2]);
norm1->SetTuple3(i,p->norm1[0],p->norm1[1],p->norm1[2]);
norm2->SetTuple3(i,p->norm2[0],p->norm2[1],p->norm2[2]);
norm3->SetTuple3(i,p->norm3[0],p->norm3[1],p->norm3[2]);
#endif
dens->SetValue(i,p->dens);
h->SetValue(i,p->h);
eBForce->SetValue(i,p->eBForce);
eViscF->SetValue(i,p->eViscF);
eViscB->SetValue(i,p->eViscB);
eFF->SetValue(i,p->eFF);
u->SetValue(i,p->u);
mass->SetValue(i,p->mass);
colour->SetValue(i,p->colour);
iam->SetValue(i,p->iam);
tag->SetValue(i,p->tag);
alpha->SetValue(i,p->alpha);
i++;
}
vtkUnstructuredGrid *dataset = vtkUnstructuredGrid::New();
dataset->SetPoints(newPts);
dataset->GetPointData()->AddArray(dens);
dataset->GetPointData()->AddArray(h);
dataset->GetPointData()->AddArray(eBForce);
dataset->GetPointData()->AddArray(eViscF);
dataset->GetPointData()->AddArray(eViscB);
dataset->GetPointData()->AddArray(eFF);
dataset->GetPointData()->AddArray(u);
dataset->GetPointData()->AddArray(mass);
dataset->GetPointData()->AddArray(colour);
dataset->GetPointData()->AddArray(iam);
dataset->GetPointData()->AddArray(tag);
dataset->GetPointData()->AddArray(v);
dataset->GetPointData()->AddArray(vhat);
dataset->GetPointData()->AddArray(vort);
dataset->GetPointData()->AddArray(norm1);
dataset->GetPointData()->AddArray(norm2);
#ifdef _3D_
dataset->GetPointData()->AddArray(norm3);
#endif
dataset->GetPointData()->AddArray(alpha);
dataset->GetPointData()->SetActiveScalars("iam");
dataset->GetPointData()->SetActiveVectors("v");
dataset->GetPointData()->SetActiveNormals("norm1");
dataset->GetPointData()->SetActiveGlobalIds("tag");
//write data
vtkXMLPUnstructuredGridWriter *writer = vtkXMLPUnstructuredGridWriter::New();
writer->SetNumberOfPieces(globals->mpiSize);
writer->SetStartPiece(globals->mpiRank);
writer->SetEndPiece(globals->mpiRank);
writer->SetInput(dataset);
writer->SetDataModeToBinary();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
string outFilename = filename+"Restart"+strTimestep+".pvtu";
writer->SetFileName(outFilename.c_str());
cout << "\tWriting "<<n<<" particles to file: "<<outFilename<<endl;
//writer->SetTimeStep(timestep);
writer->Write();
writer->Delete();
dataset->Delete();
newPts->Delete();
dens->Delete();
u->Delete();
v->Delete();
vhat->Delete();
h->Delete();
eBForce->Delete();
eViscF->Delete();
eViscB->Delete();
eFF->Delete();
mass->Delete();
colour->Delete();
iam->Delete();
tag->Delete();
vort->Delete();
norm1->Delete();
norm2->Delete();
#ifdef _3D_
norm3->Delete();
#endif
alpha->Delete();
}
void Cio_data_vtk::writeOutput(int timestep,particleContainer &ps,CcustomSimBase &customSim,CglobalVars *globals) {
//construct points
int n = ps.size();
vtkPoints *newPts = vtkPoints::New();
vtkCellArray *newCells = vtkCellArray::New();
vtkFloatArray *dens = vtkFloatArray::New();
vtkFloatArray *press= vtkFloatArray::New();
//vtkFloatArray *dddt= vtkFloatArray::New();
//vtkFloatArray *colour = vtkFloatArray::New();
vtkFloatArray *v = vtkFloatArray::New();
vtkFloatArray *vhat = vtkFloatArray::New();
#ifdef LIQ_DEM
vtkFloatArray *porosity= vtkFloatArray::New();
vtkFloatArray *fdrag = vtkFloatArray::New();
#endif
#ifdef MY_VAR_RES
vtkFloatArray *gradVx= vtkFloatArray::New();
vtkFloatArray *gradVy= vtkFloatArray::New();
#endif
#ifdef SLK
vtkFloatArray *dr= vtkFloatArray::New();
vtkFloatArray *mass= vtkFloatArray::New();
#endif
#ifdef AVE_VELOCITY
vtkFloatArray *aveV = vtkFloatArray::New();
#endif
#ifdef SAVE_VHALF
vtkDoubleArray *vHalf = vtkDoubleArray::New();
vtkDoubleArray *rHalf = vtkDoubleArray::New();
#endif
//vtkFloatArray *viscv = vtkFloatArray::New();
//vtkFloatArray *norm1 = vtkFloatArray::New();
//vtkFloatArray *norm2 = vtkFloatArray::New();
vtkFloatArray *ff = vtkFloatArray::New();
vtkFloatArray *fb = vtkFloatArray::New();
vtkFloatArray *fp = vtkFloatArray::New();
vtkFloatArray *fv = vtkFloatArray::New();
vtkFloatArray *vort = vtkFloatArray::New();
vtkFloatArray *h= vtkFloatArray::New();
vtkIdTypeArray *tag= vtkIdTypeArray::New();
vtkIntArray *iam = vtkIntArray::New();
//vtkFloatArray *dudt= vtkFloatArray::New();
//vtkFloatArray *u = vtkFloatArray::New();
//vtkFloatArray *tmp = vtkFloatArray::New();
//vtkFloatArray *deViscFdt = vtkFloatArray::New();
//vtkFloatArray *deViscBdt = vtkFloatArray::New();
//vtkFloatArray *deBForcedt = vtkFloatArray::New();
newPts->SetNumberOfPoints(n);
dens->SetNumberOfValues(n);
press->SetNumberOfValues(n);
//dddt->SetNumberOfValues(n);
//colour->SetNumberOfValues(n);
tag->SetNumberOfValues(n);
iam->SetNumberOfValues(n);
#ifdef LIQ_DEM
porosity->SetNumberOfValues(n);
fdrag->SetNumberOfComponents(3);
fdrag->SetNumberOfTuples(n);
#endif
#ifdef SAVE_VHALF
vHalf->SetNumberOfComponents(3);
vHalf->SetNumberOfTuples(n);
rHalf->SetNumberOfComponents(3);
rHalf->SetNumberOfTuples(n);
#endif
#ifdef SLK
dr->SetNumberOfComponents(3);
dr->SetNumberOfTuples(n);
mass->SetNumberOfValues(n);
#endif
v->SetNumberOfComponents(3);
v->SetNumberOfTuples(n);
vhat->SetNumberOfComponents(3);
vhat->SetNumberOfTuples(n);
#ifdef MY_VAR_RES
gradVx->SetNumberOfComponents(3);
gradVx->SetNumberOfTuples(n);
gradVy->SetNumberOfComponents(3);
gradVy->SetNumberOfTuples(n);
#endif
#ifdef AVE_VELOCITY
aveV->SetNumberOfComponents(3);
aveV->SetNumberOfTuples(n);
#endif
//viscv->SetNumberOfComponents(3);
//viscv->SetNumberOfTuples(n);
//norm1->SetNumberOfComponents(3);
//norm1->SetNumberOfTuples(n);
//norm2->SetNumberOfComponents(3);
//norm2->SetNumberOfTuples(n);
vort->SetNumberOfComponents(3);
vort->SetNumberOfTuples(n);
h->SetNumberOfValues(n);
//dudt->SetNumberOfValues(n);
//u->SetNumberOfValues(n);
//tmp->SetNumberOfValues(n);
//deViscFdt->SetNumberOfValues(n);
//deViscBdt->SetNumberOfValues(n);
//deBForcedt->SetNumberOfValues(n);
ff->SetNumberOfComponents(3);
ff->SetNumberOfTuples(n);
fb->SetNumberOfComponents(3);
fb->SetNumberOfTuples(n);
fv->SetNumberOfComponents(3);
fv->SetNumberOfTuples(n);
fp->SetNumberOfComponents(3);
fp->SetNumberOfTuples(n);
dens->SetName("dens");
press->SetName("press");
#ifdef LIQ_DEM
porosity->SetName("porosity");
fdrag->SetName("fdrag");
#endif
//dddt->SetName("dddt");
//colour->SetName("colour");
#ifdef SAVE_VHALF
vHalf->SetName("vHalf");
rHalf->SetName("rHalf");
#endif
#ifdef SLK
dr->SetName("dr");
mass->SetName("mass");
#endif
v->SetName("v");
vhat->SetName("vhat");
#ifdef MY_VAR_RES
gradVx->SetName("gradVx");
gradVy->SetName("gradVy");
#endif
#ifdef AVE_VELOCITY
aveV->SetName("aveV");
#endif
//viscv->SetName("viscv");
//norm1->SetName("norm1");
//norm2->SetName("norm2");
vort->SetName("vort");
h->SetName("h");
tag->SetName("tag");
iam->SetName("iam");
//dudt->SetName("dudt");
//u->SetName("u");
//tmp->SetName("tmp");
//deViscFdt->SetName("deViscFdt");
//deViscBdt->SetName("deViscBdt");
//deBForcedt->SetName("deBForcedt");
ff->SetName("ff");
fb->SetName("fb");
fv->SetName("fv");
fp->SetName("fp");
int i = 0;
for (particleContainer::iterator p = ps.begin();p!=ps.end();p++) {
newCells->InsertNextCell(1);
newCells->InsertCellPoint(i);
vect newr = customSim.rFilter(p->r);
vect newv = customSim.vFilter(p->v,p->r);
vect newvhat = customSim.vFilter(p->vhat,p->r);
#ifdef MY_VAR_RES
vect newgradVx = customSim.vFilter(p->gradV[0],p->r);
vect newgradVy = customSim.vFilter(p->gradV[1],p->r);
#endif
#ifdef AVE_VELOCITY
vect newaveV = customSim.vFilter(p->aveV,p->r);
#endif
#ifdef SAVE_VHALF
vect newrHalf = customSim.rFilter(p->rHalf);
vect newvHalf = customSim.vFilter(p->vHalf,p->rHalf);
#endif
//vect newviscv = customSim.vFilter(p->viscv,p->r);
#if NDIM==1
newPts->SetPoint(i,newr[0],0,0);
v->SetTuple3(i,newv[0],0,0);
vhat->SetTuple3(i,newvhat[0],0,0);
#ifdef AVE_VELOCITY
aveV->SetTuple3(i,newaveV[0],0,0);
#endif
//norm1->SetTuple3(i,p->norm1[0],0,0);
//norm2->SetTuple3(i,p->norm2[0],0,0);
vort->SetTuple3(i,p->vort[0],0,0);
ff->SetTuple3(i,p->ff[0],0,0);
fb->SetTuple3(i,p->fb[0],0,0);
fv->SetTuple3(i,p->fv[0],0,0);
fp->SetTuple3(i,p->fp[0],0,0);
#elif NDIM==2
newPts->SetPoint(i,newr[0],newr[1],0);
#ifdef SAVE_VHALF
vHalf->SetTuple3(i,newvHalf[0],newvHalf[1],0);
rHalf->SetTuple3(i,newrHalf[0],newrHalf[1],0);
#endif
v->SetTuple3(i,newv[0],newv[1],0);
vhat->SetTuple3(i,newvhat[0],newvhat[1],0);
#ifdef MY_VAR_RES
gradVx->SetTuple3(i,newgradVx[0],newgradVx[1],0);
gradVy->SetTuple3(i,newgradVy[0],newgradVy[1],0);
#endif
#ifdef SLK
vect tmp = p->currR-p->r;
dr->SetTuple3(i,tmp[0],tmp[1],0);
#endif
#ifdef AVE_VELOCITY
aveV->SetTuple3(i,newaveV[0],newaveV[1],0);
#endif
vort->SetTuple3(i,p->vort[0],p->vort[1],0);
ff->SetTuple3(i,p->ff[0],p->ff[1],0);
fb->SetTuple3(i,p->fb[0],p->fb[1],0);
fv->SetTuple3(i,p->fv[0],p->fv[1],0);
fp->SetTuple3(i,p->fp[0],p->fp[1],0);
#elif NDIM==3
newPts->SetPoint(i,newr[0],newr[1],newr[2]);
v->SetTuple3(i,newv[0],newv[1],newv[2]);
vhat->SetTuple3(i,newvhat[0],newvhat[1],newvhat[2]);
#ifdef AVE_VELOCITY
aveV->SetTuple3(i,newaveV[0],newaveV[1],newaveV[2]);
#endif
vort->SetTuple3(i,p->vort[0],p->vort[1],p->vort[2]);
ff->SetTuple3(i,p->ff[0],p->ff[1],p->ff[2]);
fb->SetTuple3(i,p->fb[0],p->fb[1],p->fb[2]);
fv->SetTuple3(i,p->fv[0],p->fv[1],p->fv[2]);
fp->SetTuple3(i,p->fp[0],p->fp[1],p->fp[2]);
#endif
#ifdef SLK
mass->SetValue(i,p->mass);
#endif
#ifdef LIQ_DEM
porosity->SetValue(i,p->porosity);
#if NDIM==2
fdrag->SetTuple3(i,p->fdrag[0],p->fdrag[1],0.0);
#else
fdrag->SetTuple3(i,p->fdrag[0],p->fdrag[1],p->fdrag[2]);
#endif
#endif
dens->SetValue(i,p->dens);
press->SetValue(i,p->press);
//dddt->SetValue(i,p->dddt);
//colour->SetValue(i,p->colour);
h->SetValue(i,p->h);
tag->SetValue(i,p->tag);
iam->SetValue(i,p->iam);
i++;
}
vtkUnstructuredGrid *dataset = vtkUnstructuredGrid::New();
dataset->SetPoints(newPts);
dataset->SetCells(1,newCells);
dataset->GetPointData()->AddArray(dens);
dataset->GetPointData()->AddArray(press);
//dataset->GetPointData()->AddArray(dddt);
//dataset->GetPointData()->AddArray(colour);
dataset->GetPointData()->AddArray(tag);
dataset->GetPointData()->AddArray(iam);
#ifdef SAVE_VHALF
dataset->GetPointData()->AddArray(vHalf);
dataset->GetPointData()->AddArray(rHalf);
#endif
dataset->GetPointData()->AddArray(v);
dataset->GetPointData()->AddArray(vhat);
#ifdef MY_VAR_RES
dataset->GetPointData()->AddArray(gradVx);
dataset->GetPointData()->AddArray(gradVy);
#endif
#ifdef LIQ_DEM
dataset->GetPointData()->AddArray(porosity);
dataset->GetPointData()->AddArray(fdrag);
#endif
#ifdef AVE_VELOCITY
dataset->GetPointData()->AddArray(aveV);
#endif
#ifdef SLK
dataset->GetPointData()->AddArray(dr);
dataset->GetPointData()->AddArray(mass);
#endif
//dataset->GetPointData()->AddArray(viscv);
//dataset->GetPointData()->AddArray(norm1);
//dataset->GetPointData()->AddArray(norm2);
dataset->GetPointData()->AddArray(vort);
dataset->GetPointData()->AddArray(h);
dataset->GetPointData()->AddArray(ff);
dataset->GetPointData()->AddArray(fb);
dataset->GetPointData()->AddArray(fv);
dataset->GetPointData()->AddArray(fp);
//dataset->GetPointData()->AddArray(dudt);
//dataset->GetPointData()->AddArray(u);
//dataset->GetPointData()->AddArray(tmp);
//dataset->GetPointData()->AddArray(deViscFdt);
//dataset->GetPointData()->AddArray(deViscBdt);
//dataset->GetPointData()->AddArray(deBForcedt);
dataset->GetPointData()->SetActiveScalars("dens");
dataset->GetPointData()->SetActiveVectors("v");
dataset->GetPointData()->SetActiveGlobalIds("tag");
//write data
vtkXMLPUnstructuredGridWriter *writer = vtkXMLPUnstructuredGridWriter::New();
writer->SetNumberOfPieces(globals->mpiSize);
writer->SetStartPiece(globals->mpiRank);
writer->SetEndPiece(globals->mpiRank);
writer->SetNumberOfTimeSteps(OUTSTEP);
writer->SetTimeStepRange(globals->outstep,globals->outstep);
writer->SetInput(dataset);
writer->SetDataModeToBinary();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
string outFilename = filename+strTimestep+".pvtu";
writer->SetFileName(outFilename.c_str());
if (globals->mpiRank==0) cout << "\tWriting "<<n<<" particles to file: "<<outFilename<<endl;
writer->SetTimeStep(timestep);
writer->WriteNextTime(globals->time);
//writer->Write();
writer->Delete();
dataset->Delete();
newPts->Delete();
newCells->Delete();
dens->Delete();
press->Delete();
//dddt->Delete();
//dudt->Delete();
//u->Delete();
//tmp->Delete();
//deViscFdt->Delete();
//deViscBdt->Delete();
//deBForcedt->Delete();
#ifdef LIQ_DEM
porosity->Delete();
fdrag->Delete();
#endif
#ifdef SAVE_VHALF
vHalf->Delete();
rHalf->Delete();
#endif
v->Delete();
vhat->Delete();
#ifdef MY_VAR_RES
gradVx->Delete();
gradVy->Delete();
#endif
#ifdef AVE_VELOCITY
aveV->Delete();
#endif
//viscv->Delete();
//norm1->Delete();
//norm2->Delete();
//colour->Delete();
vort->Delete();
h->Delete();
ff->Delete();
fb->Delete();
fv->Delete();
fp->Delete();
tag->Delete();
iam->Delete();
}
void Cio_data_vtk::writeAuxNoData(int timestep,particleContainer &ps,const char *name,CglobalVars *globals) {
int n = ps.size();
vtkPoints *newPts = vtkPoints::New();;
vtkIdTypeArray *tag= vtkIdTypeArray::New();
newPts->SetNumberOfPoints(n);
tag->SetNumberOfValues(n);
tag->SetName("tag");
int i = 0;
for (particleContainer::iterator p = ps.begin();p!=ps.end();p++) {
vect newr = p->r;
#if NDIM==1
newPts->SetPoint(i,newr[0],0,0);
#elif NDIM==2
newPts->SetPoint(i,newr[0],newr[1],0);
#elif NDIM==3
newPts->SetPoint(i,newr[0],newr[1],newr[2]);
#endif
tag->SetValue(i,p->tag);
i++;
}
vtkUnstructuredGrid *dataset = vtkUnstructuredGrid::New();
dataset->SetPoints(newPts);
dataset->GetPointData()->AddArray(tag);
dataset->GetPointData()->SetActiveScalars(name);
//dataset->GetPointData()->SetActiveGlobalIds("tag");
//write data
vtkXMLPUnstructuredGridWriter *writer = vtkXMLPUnstructuredGridWriter::New();
writer->SetNumberOfPieces(globals->mpiSize);
writer->SetStartPiece(globals->mpiRank);
writer->SetEndPiece(globals->mpiRank);
writer->SetInput(dataset);
writer->SetDataModeToBinary();
char strTimestep[20];
sprintf(strTimestep,"%7.7d",timestep);
string outFilename = filename+name+strTimestep+".pvtu";
writer->SetFileName(outFilename.c_str());
if (globals->mpiRank==0) cout << "\tWriting "<<n<<" particles to file: "<<outFilename<<endl;
//writer->SetTimeStep(timestep);
writer->Write();
writer->Delete();
dataset->Delete();
newPts->Delete();
tag->Delete();
}
void Cio_data_vtk::writeAux(int timestep,particleContainer &ps,vector<double> theData,const char *name,CglobalVars *globals) {
int n = ps.size();
vtkPoints *newPts = vtkPoints::New();;
vtkFloatArray *data = vtkFloatArray::New();
vtkIdTypeArray *tag= vtkIdTypeArray::New();
newPts->SetNumberOfPoints(n);
data->SetNumberOfValues(n);
tag->SetNumberOfValues(n);
data->SetName(name);
tag->SetName("tag");
int i = 0;
for (particleContainer::iterator p = ps.begin();p!=ps.end();p++) {
vect newr = p->r;
#if NDIM==1
newPts->SetPoint(i,newr[0],0,0);
#elif NDIM==2
newPts->SetPoint(i,newr[0],newr[1],0);
#elif NDIM==3
newPts->SetPoint(i,newr[0],newr[1],newr[2]);
#endif
data->SetValue(i,theData[i]);
tag->SetValue(i,p->tag);
i++;
}