/*! Function to write the particles using the H5hut library. */
void WritePartclH5hut(int nspec, Grid3DCU *grid, Particles3Dcomm *part, Collective *col, VCtopology3D *vct, int cycle){
#ifdef USEH5HUT
H5output file;
string filename = col->getSaveDirName() + "/" + col->getSimName();
file.SetNameCycle(filename, cycle);
/* ------------------- */
/* Write the particles */
/* ------------------- */
file.OpenPartclFile(nspec, vct->getComm());
for (int i=0; i<nspec; i++){
file.WriteParticles(i, part[i].getNOP(),
part[i].getQall(),
part[i].getXall(),
part[i].getYall(),
part[i].getZall(),
part[i].getUall(),
part[i].getVall(),
part[i].getWall(),
vct->getComm());
}
file.ClosePartclFile();
#else
cout << " ERROR: The input file request the use of the H5hut library, but the code has been compiled using other method. " << endl;
cout << " Recompile the code using the H5hut options or change the input file. " << endl;
abort();
#endif
}
/*! Function to write the EM fields using the H5hut library. */
void WriteFieldsH5hut(int nspec, Grid3DCU *grid, EMfields3D *EMf, Collective *col, VCtopology3D *vct, int cycle){
#ifdef USEH5HUT
H5output file;
/* ---------------- */
/* Write the fields */
/* ---------------- */
string filename = col->getSaveDirName() + "/" + col->getSimName();
file.SetNameCycle(filename, cycle);
file.OpenFieldsFile("Node", nspec, col->getNxc()+1, col->getNyc()+1, col->getNzc()+1, vct->getCoordinates(), vct->getDivisions(), vct->getComm());
file.WriteFields(EMf->getEx(), "Ex", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getEy(), "Ey", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getEz(), "Ez", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getBx(), "Bx", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getBy(), "By", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getBz(), "Bz", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getBxTot(), "Btx", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getByTot(), "Bty", grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getBzTot(), "Btz", grid->getNXN(), grid->getNYN(), grid->getNZN());
//file.WriteFields(EMf->GetLambda(), "Lambda", grid->getNXN(), grid->getNYN(), grid->getNZN());
for (int is=0; is<nspec; is++) {
stringstream ss;
ss << is;
string s_is = ss.str();
file.WriteFields(EMf->getRHOns(is), "rho_"+ s_is, grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getJxs(is), "Jx_" + s_is, grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getJys(is), "Jy_" + s_is, grid->getNXN(), grid->getNYN(), grid->getNZN());
file.WriteFields(EMf->getJzs(is), "Jz_" + s_is, grid->getNXN(), grid->getNYN(), grid->getNZN());
}
file.CloseFieldsFile();
//--- SAVE FIELDS IN THE CELLS:
//
// file.OpenFieldsFile("Cell", nspec, col->getNxc(), col->getNyc(), col->getNzc(), vct->getCoordinates(), vct->getDivisions(), vct->getComm());
//
// file.WriteFields(EMf->getExc(), "Exc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// file.WriteFields(EMf->getEyc(), "Eyc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// file.WriteFields(EMf->getEzc(), "Ezc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// file.WriteFields(EMf->getBxc(), "Bxc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// file.WriteFields(EMf->getByc(), "Byc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// file.WriteFields(EMf->getBzc(), "Bzc", grid->getNXC(), grid->getNYC(), grid->getNZC());
//
// for (int is=0; is<nspec; is++) {
// stringstream ss;
// ss << is;
// string s_is = ss.str();
// file.WriteFields(EMf->getRHOcs(is), "rhoc_"+ s_is, grid->getNXC(), grid->getNYC(), grid->getNZC());
// }
//
// file.CloseFieldsFile();
//
//--- END SAVE FIELDS IN THE CELLS.
#else
cout << " ERROR: The input file request the use of the H5hut library, but the code has been compiled using other method. " << endl;
cout << " Recompile the code using the H5hut options or change the input file. " << endl;
abort();
#endif
}
int main (int argc, char *argv[])
{
int rank, size;
int *perio;
int *dimns;
int *coord;
int cycle0 = 0;
int tsave = 100;
int ncycle = 200;
int ndim = 3;
int reorder = 1;
int nspec = 2;
int ntcx = 64;
int ntcy = 64;
int ntcz = 64;
int ntxn;
int ntyn;
int ntzn;
double Lx = 10.0;
double Ly = 10.0;
double Lz = 10.0;
double L[3];
MPI_Comm CART_COMM;
Fields EMf;
H5input file;
H5output outfile;
H5hutpart *myPart;
/* -------------------------- */
/* Initialize MPI environment */
/* -------------------------- */
perio = new int[ndim];
dimns = new int[ndim];
coord = new int[ndim];
MPI_Init (&argc, &argv);
MPI_Comm_size (MPI_COMM_WORLD, &size);
if (ndim==3) MPI_Dims_create(size, 3, dimns);
else MPI_Dims_create(size, 2, dimns);
MPI_Cart_create(MPI_COMM_WORLD, ndim, dimns, perio, reorder, &CART_COMM);
MPI_Comm_rank (CART_COMM,&rank);
MPI_Cart_coords(CART_COMM, rank, ndim, coord);
/* ------------------------- */
/* Set simulation conditions */
/* ------------------------- */
ntxn = ntcx + 1;
ntyn = ntcy + 1;
ntzn = ntcz + 1;
int nxc = (ntcx / dimns[0]) + 2;
int nyc = (ntcy / dimns[1]) + 2;
int nzc = (ntcz / dimns[2]) + 2;
int nxn = nxc + 1;
int nyn = nyc + 1;
int nzn = nzc + 1;
L[0] = Lx;
L[1] = Ly;
L[2] = Lz;
/* ------------------ */
/* Read the particles */
/* ------------------ */
file.SetNameCycle("GEMtest", cycle0);
myPart = new H5hutpart[nspec];
file.OpenPartclFile(nspec);
file.ReadParticles(rank, size, dimns, L, CART_COMM);
for (int s = 0; s < nspec; s++){
myPart[s].memalloc(file.GetNp(s));
file.DumpPartclX(myPart[s].getXref(), s);
file.DumpPartclY(myPart[s].getYref(), s);
file.DumpPartclZ(myPart[s].getZref(), s);
file.DumpPartclU(myPart[s].getUref(), s);
file.DumpPartclV(myPart[s].getVref(), s);
file.DumpPartclW(myPart[s].getWref(), s);
file.DumpPartclQ(myPart[s].getQref(), s);
}
file.ClosePartclFile();
/* --------------- */
/* Read the fields */
/* --------------- */
EMf.Init(nspec, nxc, nyc, nzc);
file.OpenFieldsFile("Node", nspec, ntxn, ntyn, ntzn, coord, dimns, CART_COMM);
file.ReadFields(EMf.getEx(), "Ex", nxn, nyn, nzn);
file.ReadFields(EMf.getEy(), "Ey", nxn, nyn, nzn);
file.ReadFields(EMf.getEz(), "Ez", nxn, nyn, nzn);
file.ReadFields(EMf.getBx(), "Bx", nxn, nyn, nzn);
file.ReadFields(EMf.getBy(), "By", nxn, nyn, nzn);
file.ReadFields(EMf.getBz(), "Bz", nxn, nyn, nzn);
file.CloseFieldsFile();
/* -------------------------------------- */
/* Empty simulation with multiple outputs */
/* -------------------------------------- */
for (int t = cycle0; t <= cycle0+ncycle; t++) {
std::cout << " Cycle: " << t << std::endl;
/* here goes the computation */
if (t%tsave==0) {
outfile.SetNameCycle("Output", t);
/* ----------- */
/* Save fields */
/* ----------- */
outfile.OpenFieldsFile("Node", nspec, ntxn, ntyn, ntzn, coord, dimns, CART_COMM);
outfile.WriteFields(EMf.getEx(), "Ex", nxn, nyn, nzn);
outfile.WriteFields(EMf.getEy(), "Ey", nxn, nyn, nzn);
outfile.WriteFields(EMf.getEz(), "Ez", nxn, nyn, nzn);
outfile.WriteFields(EMf.getBx(), "Bx", nxn, nyn, nzn);
outfile.WriteFields(EMf.getBy(), "By", nxn, nyn, nzn);
outfile.WriteFields(EMf.getBz(), "Bz", nxn, nyn, nzn);
outfile.CloseFieldsFile();
/* -------------- */
/* Save particles */
/* -------------- */
outfile.OpenPartclFile(nspec, CART_COMM);
for (int i=0; i<nspec; i++) {
outfile.WriteParticles(i, myPart[i].getNP(),
myPart[i].getQ(),
myPart[i].getX(),
myPart[i].getY(),
myPart[i].getZ(),
myPart[i].getU(),
myPart[i].getV(),
myPart[i].getW(),
CART_COMM);
}
outfile.ClosePartclFile();
}
}
std::cout << rank << " : Freeing memory..." << std::endl;
delete [] myPart;
delete [] perio;
delete [] dimns;
delete [] coord;
std::cout << rank << " : Finalizing MPI" << std::endl;
MPI_Finalize();
return 0;
}