void flip(index_t b)
{
_data[windex(b)] ^= 1 << woffset(b);
}
void clear(index_t b)
{
_data[windex(b)] &= ~(1 << woffset(b));
}
bool get(index_t b) const
{
return _data[windex(b)] & (1 << woffset(b));
}
void set(index_t b)
{
_data[windex(b)] |= 1 << woffset(b);
}
void HDFWalkerIOEngine::readAll(hid_t grp, const char* name, Communicate* comm)
{
int mynode=comm->rank();
int nprocs=comm->size();
vector<int> woffset(nprocs+1,0);
const int RANK = 3;
hsize_t offset[]={1,1,1};
hsize_t gcount[RANK],count[RANK];
hsize_t stride[]={1,1,1};
hid_t dataset = H5Dopen(grp,name);
hid_t dataspace = H5Dget_space(dataset);
int rank_n = H5Sget_simple_extent_ndims(dataspace);
int status_n = H5Sget_simple_extent_dims(dataspace, gcount, NULL);
//assign offsets and size
FairDivideLow(gcount[0],nprocs,woffset);
offset[0]=woffset[mynode]; offset[1] = 0; offset[2] = 0;
count[0]=woffset[mynode+1]-woffset[mynode];
count[1]=gcount[1];
count[2]=gcount[2];
app_log() << " Initial walker distribution: ";
std::copy(woffset.begin(),woffset.end(),ostream_iterator<int>(app_log()," "));
app_log() << endl;
vector<MCWalkerConfiguration::PosType> posIn(count[0]*count[1]);
hid_t memspace = H5Screate_simple(RANK, count, NULL);
herr_t status = H5Sselect_hyperslab(dataspace,H5S_SELECT_SET, offset,NULL,count,NULL);
#if defined(H5_HAVE_PARALLEL)
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(xfer_plist,H5FD_MPIO_COLLECTIVE);
#else
xfer_plist = H5P_DEFAULT;
#endif
hid_t type_id=get_h5_datatype(posIn[0][0]);
status = H5Dread(dataset, type_id, memspace, dataspace, xfer_plist, &(posIn[0][0]));
H5Sclose(dataspace);
H5Sclose(memspace);
H5Dclose(dataset);
#if defined(H5_HAVE_PARALLEL)
H5Pclose(xfer_plist);
#endif
int curWalker = W.getActiveWalkers();
if(curWalker) {
W.createWalkers(count[0]);
} else {
W.resize(count[0],count[1]);
}
MCWalkerConfiguration::iterator it = W.begin()+curWalker;
int ii=0;
for(int iw=0; iw<count[0]; iw++) {
//std::copy(Post_temp[iw],Post_temp[iw+1], (*it)->R.begin());
for(int iat=0; iat < count[1]; iat++,ii++){
(*it)->R(iat) = posIn[ii];
}
++it;
}
}
