vector<Cparticle> *Cio_data::read(int timestep) {
H5PartFile *reader = H5PartOpenFile(filename.c_str(),H5PART_READ);
if (H5PartGetNumSteps(reader) < timestep) {
cerr << "There is not "<<timestep<<"timesteps in the file"<<endl;
H5PartCloseFile(reader);
exit(-1);
}
H5PartSetStep(reader,timestep);
int n = H5PartGetNumParticles(reader);
vector<Cparticle> *output = new vector<Cparticle>(n);
double r[NDIM][n],v[NDIM][n],mass[n],u[n];
for (int i=0; i<NDIM; i++) {
if (!H5PartReadDataFloat64(reader,dimNames[i],r[i])) {
cerr << "Error reading particle position data" << endl;
exit(-1);
}
}
for (int i=0; i<NDIM; i++) {
if (!H5PartReadDataFloat64(reader,vdimNames[i],v[i])) {
cerr << "Error reading particle velocity data" << endl;
exit(-1);
}
}
if (!(H5PartReadDataFloat64(reader,"mass",mass))&&
(H5PartReadDataFloat64(reader,"u",u))) {
cerr << "Error reading particle data in file" << endl;
exit(-1);
}
for (int i=0; i<n; i++) {
for (int j=0; j<NDIM; i++) {
(*output)[i].r[j] = r[j][i];
(*output)[i].v[j] = r[j][i];
}
(*output)[i].mass = mass[i];
(*output)[i].u = u[i];
}
H5PartCloseFile(reader);
return output;
}
static void
test_read_strided_data64(H5PartFile *file, int nparticles, int step)
{
int i,t;
h5part_int64_t status;
double *data;
data=(double*)malloc(6*nparticles*sizeof(double));
TEST("Reading 64-bit strided data");
for (t=step; t<step+NTIMESTEPS; t++)
{
status = H5PartSetStep(file, t);
RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
status = H5PartSetNumParticlesStrided(file, nparticles, 6);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticlesStrided");
status = H5PartReadDataFloat64(file, "x", data+0);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "y", data+1);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "z", data+2);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "px", data+3);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
test_read_step_attribs(file, t);
status = H5PartReadDataFloat64(file, "py", data+4);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "pz", data+5);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
for (i=0; i<nparticles; i++)
{
FVALUE(data[6*i] , 0.0 + (double)(i+nparticles*t), "x data");
FVALUE(data[6*i+1], 0.1 + (double)(i+nparticles*t), "y data");
FVALUE(data[6*i+2], 0.2 + (double)(i+nparticles*t), "z data");
FVALUE(data[6*i+3], 0.3 + (double)(i+nparticles*t), "px data");
FVALUE(data[6*i+4], 0.4 + (double)(i+nparticles*t), "py data");
FVALUE(data[6*i+5], 0.5 + (double)(i+nparticles*t), "pz data");
}
}
}
static void
test_read_data64(H5PartFile *file, int nparticles, int step)
{
int i,t;
int rank, nprocs;
h5part_int64_t status, val, start, end, type, size;
char name1[4];
char name2[8];
h5part_int64_t indices[8];
double *x,*y,*z;
double *px,*py,*pz;
h5part_int64_t *id;
x=(double*)malloc(nparticles*sizeof(double));
y=(double*)malloc(nparticles*sizeof(double));
z=(double*)malloc(nparticles*sizeof(double));
px=(double*)malloc(nparticles*sizeof(double));
py=(double*)malloc(nparticles*sizeof(double));
pz=(double*)malloc(nparticles*sizeof(double));
id=(h5part_int64_t*)malloc(nparticles*sizeof(h5part_int64_t));
TEST("Verifying dataset info");
#if PARALLEL_IO
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
#else
nprocs = 1;
rank = 2;
#endif
val = H5PartGetNumParticles(file);
IVALUE(val, nprocs*nparticles, "particle count");
val = H5PartGetNumDatasets(file);
IVALUE(val, 7, "dataset count");
for (i=0; i<7; i++) {
status = H5PartGetDatasetName(file, i, name1, 2);
RETURN(status, H5PART_SUCCESS, "H5PartGetDatasetName");
status = H5PartGetDatasetInfo(
file, i, name2, 4, &type, &size);
RETURN(status, H5PART_SUCCESS, "H5PartGetDatasetInfo");
CVALUE(name1[0], name2[0], "dataset name");
status = H5PartGetDatasetName(file, i, name1, 4);
RETURN(status, H5PART_SUCCESS, "H5PartGetDatasetName");
CVALUE(name1[1], name2[1], "dataset name");
IVALUE(size, nprocs*nparticles, "dataset size");
if (name1[0] == 'i') IVALUE(type, H5PART_INT64, "dataset type");
else IVALUE(type, H5PART_FLOAT64, "dataset type");
}
#if PARALLEL_IO
TEST("Setting throttle");
status = H5PartSetThrottle(file, 3);
RETURN(status, H5PART_SUCCESS, "H5PartSetThrottle");
#endif
TEST("Reading 64-bit data");
for (t=step; t<step+NTIMESTEPS; t++)
{
val = H5PartHasStep(file, t);
IVALUE(val, 1, "has step");
status = H5PartSetStep(file, t);
RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
test_read_step_attribs(file, t);
status = H5PartSetNumParticles(file, nparticles);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticles");
status = H5PartResetView(file);
RETURN(status, H5PART_SUCCESS, "H5PartResetView");
start = rank;
end = -1;
status = H5PartSetView(file, start, end);
RETURN(status, H5PART_SUCCESS, "H5PartSetView");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
FVALUE(x[rank], (double)(start+rank+nparticles*t), "x data");
val = H5PartGetView(file, &start, &end);
IVALUE(val, nprocs*nparticles-start, "particle count");
IVALUE(start, rank, "view start");
IVALUE(end, nprocs*nparticles-1, "view end");
status = H5PartSetView(file, -1, -1);
RETURN(status, H5PART_SUCCESS, "H5PartSetView");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
IVALUE(x[rank], (double)(rank+nparticles*t), "x data");
indices[0] = rank*2 + 0;
indices[1] = rank*2 + 3;
indices[2] = rank*2 + 9;
indices[3] = rank*2 + 7;
status = H5PartSetViewIndices(file, indices, -1);
RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
FVALUE(x[2*rank], (double)(2*rank+nparticles*t), "x data");
status = H5PartResetView(file);
RETURN(status, H5PART_SUCCESS, "H5PartResetView");
status = H5PartSetViewIndices(file, indices, 4);
RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
val = H5PartGetNumParticles(file);
IVALUE(val, 4, "particle count");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
FVALUE(x[2], (double)(rank*2+9+nparticles*t), "x data");
val = H5PartGetNumParticles(file);
IVALUE(val, 4, "particle count");
status = H5PartSetViewIndices(file, NULL, 4);
RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
status = H5PartSetCanonicalView(file);
RETURN(status, H5PART_SUCCESS, "H5PartSetCanonicalView");
status = H5PartReadParticleStep (
file, t, x, y, z, px, py, pz, id);
RETURN(status, H5PART_SUCCESS, "H5PartReadParticleStep");
for (i=0; i<nparticles; i++)
{
FVALUE(x[i] , 0.0 + (double)(i+nparticles*t), " x data");
FVALUE(y[i] , 0.1 + (double)(i+nparticles*t), " y data");
FVALUE(z[i] , 0.2 + (double)(i+nparticles*t), " z data");
FVALUE(px[i], 0.3 + (double)(i+nparticles*t), " px data");
FVALUE(py[i], 0.4 + (double)(i+nparticles*t), " py data");
FVALUE(pz[i], 0.5 + (double)(i+nparticles*t), " pz data");
IVALUE(id[i], (i+nparticles*t), " id data");
}
}
}
void H5input::LoadParticles(int ndim, int rank, int nproc, const int *dimns, double *L, MPI_Comm CART_COMM){
int h5nspec;
int ranks_rdr[1] = {0};
int *ranks_rst;
long long offset;
long long nop;
h5_int64_t *h5npart;
double *q;
double *x;
double *y;
double *z;
double *u;
double *v;
double *w;
std::stringstream sstm;
MPI_Comm READER_COMM;
MPI_Group org_grp;
MPI_Group reader_grp;
part = new H5hutpart[nspec];
/* -------------------------------------------------- */
/* Create a new communicator for the reader processor */
/* This way only processor 0 reads the whole file. */
/* It would be better if each processor read one part */
/* of the file...currently not possible with H5hut. */
/* -------------------------------------------------- */
MPI_Comm_group (CART_COMM, &org_grp);
ranks_rst = new int[nproc-1];
for (int i=0; i<nproc-1; i++) ranks_rst[i] = i;
if (rank==0) MPI_Group_incl (org_grp, 1, ranks_rdr, &reader_grp);
else MPI_Group_incl (org_grp, nproc-1, ranks_rst, &reader_grp);
delete [] ranks_rst;
MPI_Comm_create(CART_COMM, reader_grp, &READER_COMM);
if (rank==0) {
/* -------------- */
/* Open HDF5 file */
/* -------------- */
std::stringstream filenmbr;
std::string filename;
filenmbr << std::setfill('0') << std::setw(6) << recycle;
filename = basename + "-Partcl" + "_" + filenmbr.str() + ".h5";
partfile = H5OpenFile(filename.c_str(), H5_O_RDONLY, READER_COMM);
H5SetStep(partfile, 0);
H5ReadStepAttribInt32(partfile, "nspec", &h5nspec);
if (nspec!=h5nspec) {
std::cout << "[H5hut-io]" << "ERROR in ReadParallelParticles: the number of species in the initial file" << std::endl;
std::cout << "[H5hut-io]" << " does not match the number of species requested." << std::endl;
abort();
}
h5npart = new h5_int64_t[nspec];
nop = 0;
for (int i=0; i<nspec; i++) {
sstm << "npart_" << i;
std::string nparti = sstm.str();
H5ReadStepAttribInt64(partfile, nparti.c_str(), &h5npart[i]);
sstm.str("");
nop += h5npart[i];
}
q = new double[nop];
x = new double[nop];
y = new double[nop];
z = new double[nop];
u = new double[nop];
v = new double[nop];
w = new double[nop];
offset = 0;
for (int i=0; i<nspec; i++) {
std::cout << "[H5hut-io]" << " Reading a total of " << h5npart[i] << " particles of species " << i << std::endl;
sstm << "q_" << i;
std::string dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),q+offset);
sstm.str("");
sstm << "x_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),x+offset);
sstm.str("");
sstm << "y_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),y+offset);
sstm.str("");
sstm << "z_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),z+offset);
sstm.str("");
sstm << "u_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),u+offset);
sstm.str("");
sstm << "v_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),v+offset);
sstm.str("");
sstm << "w_" << i;
dtset = sstm.str();
H5PartReadDataFloat64(partfile,dtset.c_str(),w+offset);
sstm.str("");
offset += h5npart[i];
}
H5CloseFile(partfile);
FindLocalParticles(nproc, ndim, h5npart, nop, dimns, L, CART_COMM, q, x, y, z, u, v, w);
delete [] q;
delete [] x;
delete [] y;
delete [] z;
delete [] u;
delete [] v;
delete [] w;
delete [] h5npart;
}
}
