void Cio_data::write(vector<Cparticle> &ps, int timestep) {
H5PartFile *writer = H5PartOpenFile(filename.c_str(),H5PART_WRITE);
H5PartSetStep(writer,timestep);
int n = ps.size();
H5PartSetNumParticles(writer,n);
double r[NDIM][n],v[NDIM][n],mass[n],u[n];
long long tag[n];
double zero[n];
for (int i=0; i<n; i++) {
zero[i] = 0.0;
for (int j=0; j<NDIM; j++) {
r[j][i] = ps[i].r[j];
v[j][i] = ps[i].v[j];
}
mass[i] = ps[i].mass;
u[i] = ps[i].u;
tag[i] = ps[i].tag;
}
for (int i=0; i<NDIM; i++) {
H5PartWriteDataFloat64(writer,dimNames[i],r[i]);
H5PartWriteDataFloat64(writer,vdimNames[i],v[i]);
}
for (int i=NDIM; i<3; i++) {
H5PartWriteDataFloat64(writer,dimNames[i],zero);
H5PartWriteDataFloat64(writer,vdimNames[i],zero);
}
H5PartWriteDataFloat64(writer,"mass",mass);
H5PartWriteDataFloat64(writer,"u",u);
H5PartWriteDataInt64(writer,"id",tag);
}
static void
test_write_strided_data64(H5PartFile *file, int nparticles, int step)
{
int i,t;
h5part_int64_t status;
double *data;
data=(double*)malloc(6*nparticles*sizeof(double));
status = H5PartSetNumParticlesStrided(file, nparticles, 6);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticlesStrided");
TEST("Writing 64-bit strided data");
for (t=step; t<step+NTIMESTEPS; t++)
{
for (i=0; i<nparticles; i++)
{
data[6*i] = 0.0 + (double)(i+nparticles*t);
data[6*i+1] = 0.1 + (double)(i+nparticles*t);
data[6*i+2] = 0.2 + (double)(i+nparticles*t);
data[6*i+3] = 0.3 + (double)(i+nparticles*t);
data[6*i+4] = 0.4 + (double)(i+nparticles*t);
data[6*i+5] = 0.5 + (double)(i+nparticles*t);
}
status = H5PartSetStep(file, t);
RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
status = H5PartSetNumParticlesStrided(file, nparticles, 6);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticlesStrided");
status = H5PartWriteDataFloat64(file, "x", data+0);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "y", data+1);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "z", data+2);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "px", data+3);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "py", data+4);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "pz", data+5);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
test_write_step_attribs(file, t);
}
}
static void
test_write_data64(H5PartFile *file, int nparticles, int step)
{
int i,t;
h5part_int64_t status, val;
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));
/* invalid stride will produce a warning */
status = H5PartSetNumParticlesStrided(file, nparticles, -1);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticlesStrided");
/* invalid nparticles will produce an error */
status = H5PartSetNumParticlesStrided(file, -1, 2);
RETURN(status, H5PART_ERR_INVAL, "H5PartSetNumParticlesStrided");
#if PARALLEL_IO
TEST("Setting throttle");
status = H5PartSetThrottle(file, 2);
RETURN(status, H5PART_SUCCESS, "H5PartSetThrottle");
#endif
TEST("Writing 64-bit data");
for (t=step; t<step+NTIMESTEPS; t++)
{
for (i=0; i<nparticles; i++)
{
x[i] = 0.0 + (double)(i+nparticles*t);
y[i] = 0.1 + (double)(i+nparticles*t);
z[i] = 0.2 + (double)(i+nparticles*t);
px[i] = 0.3 + (double)(i+nparticles*t);
py[i] = 0.4 + (double)(i+nparticles*t);
pz[i] = 0.5 + (double)(i+nparticles*t);
id[i] = i + nparticles*t;
}
val = H5PartHasStep(file, t);
status = H5PartSetStep(file, t);
RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
if (val == 0) test_write_step_attribs(file, t);
status = H5PartSetNumParticles(file, nparticles);
RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticles");
status = H5PartWriteDataFloat64(file, "x", x);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "y", y);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "z", z);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "px", px);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "py", py);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataFloat64(file, "pz", pz);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataFloat64");
status = H5PartWriteDataInt64(file, "id", id);
RETURN(status, H5PART_SUCCESS, "H5PartWriteDataInt64");
}
}
void H5output::WriteParticles(int ispec, long long np, const double *q, const double *x, const double *y, const double *z, const double *u, const double *v, const double *w, MPI_Comm CART_COMM){
/* --------------------------------------------------------------------- */
/* Find out the total number of particles of species i in all the domain */
/* --------------------------------------------------------------------- */
long long ntpart;
MPI_Allreduce(&np, &ntpart, 1, MPI_LONG_LONG, MPI_SUM, CART_COMM);
const h5_int64_t ntp = ntpart;
/* --------------------------------------------- */
/* Write the number of particles as an attribute */
/* --------------------------------------------- */
std::stringstream sstm;
sstm << "npart_" << ispec;
std::string nparti = sstm.str();
H5WriteStepAttribInt64(partfile, nparti.c_str(), &ntp, 1);
sstm.str("");
H5PartSetNumParticles(partfile,np);
/* ------------------ */
/* Write the datasets */
/* ------------------ */
sstm << "q_" << ispec;
std::string dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),q);
sstm.str("");
sstm << "x_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),x);
sstm.str("");
sstm << "y_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),y);
sstm.str("");
sstm << "z_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),z);
sstm.str("");
sstm << "u_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),u);
sstm.str("");
sstm << "v_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),v);
sstm.str("");
sstm << "w_" << ispec;
dtset = sstm.str();
H5PartWriteDataFloat64(partfile,dtset.c_str(),w);
sstm.str("");
}