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_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"); } } }