void ReadPartclH5hut(int nspec, Particles3Dcomm *part, Collective *col, VCtopology3D *vct, Grid3DCU *grid){
#ifdef USEH5HUT
H5input infile;
double L[3] = {col->getLx(), col->getLy(), col->getLz()};
infile.SetNameCycle(col->getinitfile(), col->getLast_cycle());
infile.OpenPartclFile(nspec, vct->getCartesian_rank(), vct->getNproc(), vct->getComm());
for (int s = 0; s < nspec; s++){
infile.ReadParticles(vct->getCartesian_rank(),
vct->getNproc(), s,
vct->getDivisions(), L,
vct->getComm());
part[s].allocate(s, infile.get_nops(), col, vct, grid);
infile.LoadParticles(infile.get_nops(), vct->getCartesian_rank(),
vct->getNproc(), s,
vct->getDivisions(), L,
vct->getComm(),
part[s].getQall(),
part[s].getXall(),
part[s].getYall(),
part[s].getZall(),
part[s].getUall(),
part[s].getVall(),
part[s].getWall());
}
infile.ClosePartclFile();
//--- TEST PARTICLE LECTURE:
// for (int s = 0; s < nspec; s++){
// for (int n = 0; n < part[s].getNOP(); n++){
// double ix = part[s].getX(n);
// double iy = part[s].getY(n);
// double iz = part[s].getZ(n);
// if (ix<=0 || iy<=0 || iz <=0) {
// cout << " ERROR: This particle has negative position. " << endl;
// cout << " n = " << n << "/" << part[s].getNOP();
// cout << " ix = " << ix;
// cout << " iy = " << iy;
// cout << " iz = " << iz;
// }
// }
// }
//--- END TEST
#endif
}
void ReadFieldsH5hut(int nspec, bool readext, EMfields3D *EMf, Collective *col, VCtopology3D *vct, Grid3DCU *grid){
#ifdef USEH5HUT
H5input infile;
infile.SetNameCycle(col->getinitfile(), col->getLast_cycle());
infile.OpenFieldsFile("Node", nspec, col->getNxc()+1,
col->getNyc()+1,
col->getNzc()+1,
vct->getCoordinates(),
vct->getDivisions(),
vct->getComm());
infile.ReadFields(EMf->getEx(), "Ex", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getEy(), "Ey", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getEz(), "Ez", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getBx(), "Bx", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getBy(), "By", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getBz(), "Bz", grid->getNXN(), grid->getNYN(), grid->getNZN());
if (readext) {
infile.ReadFields(EMf->getBx_ext(), "Btx", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getBy_ext(), "Bty", grid->getNXN(), grid->getNYN(), grid->getNZN());
infile.ReadFields(EMf->getBz_ext(), "Btz", grid->getNXN(), grid->getNYN(), grid->getNZN());
}
for (int is = 0; is < nspec; is++){
std::stringstream ss;
ss << is;
std::string s_is = ss.str();
infile.ReadFields(EMf->getRHOns(is), "rho_"+s_is, grid->getNXN(), grid->getNYN(), grid->getNZN());
}
infile.CloseFieldsFile();
// initialize B on centers
// MPI_Barrier(MPI_COMM_WORLD); // This is time-consuming and should be debug code, only!
// Comm ghost nodes for B-field
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getBx(), col->bcBx[0],col->bcBx[1],col->bcBx[2],col->bcBx[3],col->bcBx[4],col->bcBx[5], vct);
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getBy(), col->bcBy[0],col->bcBy[1],col->bcBy[2],col->bcBy[3],col->bcBy[4],col->bcBy[5], vct);
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getBz(), col->bcBz[0],col->bcBz[1],col->bcBz[2],col->bcBz[3],col->bcBz[4],col->bcBz[5], vct);
grid->interpN2C(EMf->getBxc(), EMf->getBx());
grid->interpN2C(EMf->getByc(), EMf->getBy());
grid->interpN2C(EMf->getBzc(), EMf->getBz());
// communicate E
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getEx(), col->bcEx[0],col->bcEx[1],col->bcEx[2],col->bcEx[3],col->bcEx[4],col->bcEx[5], vct);
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getEy(), col->bcEy[0],col->bcEy[1],col->bcEy[2],col->bcEy[3],col->bcEy[4],col->bcEy[5], vct);
communicateNodeBC(grid->getNXN(), grid->getNYN(), grid->getNZN(), EMf->getEz(), col->bcEz[0],col->bcEz[1],col->bcEz[2],col->bcEz[3],col->bcEz[4],col->bcEz[5], vct);
for (int is = 0; is < nspec; is++)
grid->interpN2C(EMf->getRHOcs(), is, EMf->getRHOns());
//---READ FROM THE CELLS:
//
// infile.OpenFieldsFile("Cell", nspec, col->getNxc(),
// col->getNyc(),
// col->getNzc(),
// vct->getCoordinates(),
// vct->getDivisions(),
// vct->getComm());
//
// infile.ReadFields(EMf->getExc(), "Exc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// infile.ReadFields(EMf->getEyc(), "Eyc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// infile.ReadFields(EMf->getEzc(), "Ezc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// infile.ReadFields(EMf->getBxc(), "Bxc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// infile.ReadFields(EMf->getByc(), "Byc", grid->getNXC(), grid->getNYC(), grid->getNZC());
// infile.ReadFields(EMf->getBzc(), "Bzc", grid->getNXC(), grid->getNYC(), grid->getNZC());
//
// for (int is = 0; is < nspec; is++){
// std::stringstream ss;
// ss << is;
// std::string s_is = ss.str();
// infile.ReadFields(EMf->getRHOcs(is, 0), "rhoc_"+s_is, grid->getNXC(), grid->getNYC(), grid->getNZC());
// }
//
// infile.CloseFieldsFile();
//
// // initialize B on nodes
// grid->interpC2N(EMf->getBx(), EMf->getBxc());
// grid->interpC2N(EMf->getBy(), EMf->getByc());
// grid->interpC2N(EMf->getBz(), EMf->getBzc());
//
// for (int is = 0; is < nspec; is++)
// grid->interpC2N(EMf->getRHOns(), is, EMf->getRHOcs());
//
//---END READ FROM THE CELLS
#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;
}
