void Domain::build( Params ¶ms, SmileiMPI *smpi, VectorPatch &vecPatches, OpenPMDparams &openPMD )
{
decomposition_ = DomainDecompositionFactory::createGlobal( params );
patch_ = PatchesFactory::create( params, smpi, decomposition_, vecPatches.refHindex_ / vecPatches.size() );
patch_->set( params, decomposition_, vecPatches );
vecPatch_.patches_.push_back( patch_ );
vecPatch_.refHindex_ = vecPatches.refHindex_ / vecPatches.size();
vecPatch_.update_field_list( smpi );
//vecPatch_.update_field_list(0, smpi);
vecPatch_.patches_[0]->finalizeMPIenvironment( params );
vecPatch_.nrequests = vecPatches( 0 )->requests_.size();
vecPatch_.nAntennas = vecPatch_( 0 )->EMfields->antennas.size();
vecPatch_.initExternals( params );
/* if ( params.nDim_field == 1 )
diag_ = new DiagnosticFields1D( params, smpi, vecPatch_, 0, openPMD );
else if ( params.nDim_field == 2 )
diag_ = new DiagnosticCartFields2D( params, smpi, vecPatch_, 0, openPMD );
else if ( params.nDim_field == 3 )
diag_ = new DiagnosticCartFields3D( params, smpi, vecPatch_, 0, openPMD );
for (unsigned int ifield=0 ; ifield<vecPatch_(0)->EMfields->Jx_s.size(); ifield++) {
if( vecPatch_(0)->EMfields->Jx_s[ifield]->data_ == NULL ){
delete vecPatch_(0)->EMfields->Jx_s[ifield];
vecPatch_(0)->EMfields->Jx_s[ifield]=NULL;
}
}
for (unsigned int ifield=0 ; ifield<vecPatch_(0)->EMfields->Jy_s.size(); ifield++) {
if( vecPatch_(0)->EMfields->Jy_s[ifield]->data_ == NULL ){
delete vecPatch_(0)->EMfields->Jy_s[ifield];
vecPatch_(0)->EMfields->Jy_s[ifield]=NULL;
}
}
for (unsigned int ifield=0 ; ifield<vecPatch_(0)->EMfields->Jz_s.size(); ifield++) {
if( vecPatch_(0)->EMfields->Jz_s[ifield]->data_ == NULL ){
delete vecPatch_(0)->EMfields->Jz_s[ifield];
vecPatch_(0)->EMfields->Jz_s[ifield]=NULL;
}
}
for (unsigned int ifield=0 ; ifield<vecPatch_(0)->EMfields->rho_s.size(); ifield++) {
if( vecPatch_(0)->EMfields->rho_s[ifield]->data_ == NULL ){
delete vecPatch_(0)->EMfields->rho_s[ifield];
vecPatch_(0)->EMfields->rho_s[ifield]=NULL;
}
}
diag_->init( params, smpi, vecPatch_ );
diag_->theTimeIsNow = diag_->prepare( 0 );
//if ( diag_->theTimeIsNow )
// diag_->run( smpi, vecPatch_, 0, simWindow );
*/
if( params.is_pxr ) {
vecPatch_( 0 )->EMfields->MaxwellAmpereSolver_->coupling( params, vecPatch_( 0 )->EMfields );
}
}
void Checkpoint::dumpAll( VectorPatch &vecPatches, unsigned int itime, SmileiMPI* smpi, SimWindow* simWin, Params ¶ms )
{
hid_t sid, aid, tid;
/*ostringstream nameDump("");
nameDump << "dump-" << setfill('0') << setw(4) << dump_times%dump_file_sequence << "-" << setfill('0') << setw(4) << smpi->getRank() << ".h5" ;
fid = H5Fcreate( nameDump.str().c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);*/
unsigned int num_dump=dump_times%dump_file_sequence;
hid_t fid = H5Fcreate( dumpName(num_dump,smpi).c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dump_times++;
MESSAGEALL("Step " << itime << " : DUMP fields and particles " << dumpName(num_dump,smpi));
H5::attr(fid, "Version", string(__VERSION));
//H5::attr(fid, "CommitDate", string(__COMMITDATE));
H5::attr(fid, "dump_step", itime);
H5::attr(fid, "Energy_time_zero", static_cast<DiagnosticScalar*>(vecPatches.globalDiags[0])->Energy_time_zero );
H5::attr(fid, "EnergyUsedForNorm", static_cast<DiagnosticScalar*>(vecPatches.globalDiags[0])->EnergyUsedForNorm);
for (unsigned int ipatch=0 ; ipatch<vecPatches.size(); ipatch++) {
// Open a group
ostringstream patch_name("");
patch_name << setfill('0') << setw(6) << vecPatches(ipatch)->Hindex();
string patchName="patch-"+patch_name.str();
hid_t patch_gid = H5Gcreate(fid, patchName.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
dumpPatch( vecPatches(ipatch)->EMfields, vecPatches(ipatch)->vecSpecies, patch_gid );
// Close a group
H5Gclose(patch_gid);
}
// Dump moving window status
if (simWin!=NULL)
dumpMovingWindow(fid, simWin);
H5Fclose( fid );
}
void Checkpoint::restartAll( VectorPatch &vecPatches, unsigned int &itime, SmileiMPI* smpi, SimWindow* simWin, Params ¶ms )
{
string nameDump("");
// This will open both dumps and pick the last one
for (unsigned int num_dump=0;num_dump<dump_file_sequence; num_dump++) {
//ostringstream nameDumpTmp("");
//nameDumpTmp << "dump-" << setfill('0') << setw(4) << i << "-" << setfill('0') << setw(4) << smpi->getRank() << ".h5" ;
//ifstream f(nameDumpTmp.str().c_str());
string dump_name=restart_dir+dumpName(num_dump,smpi);
ifstream f(dump_name.c_str());
if (f.good()) {
hid_t fid = H5Fopen( dump_name.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
hid_t aid = H5Aopen(fid, "dump_step", H5T_NATIVE_UINT);
unsigned int itimeTmp=0;
H5Aread(aid, H5T_NATIVE_UINT, &itimeTmp);
H5Aclose(aid);
H5Fclose(fid);
if (itimeTmp>itime) {
this_run_start_step=itimeTmp;
itime=itimeTmp;
nameDump=dump_name.c_str();
dump_times=num_dump;
}
}
f.close();
}
if (nameDump.empty()) ERROR("Cannot find a valid restart file");
MESSAGEALL(2, " : Restarting fields and particles " << nameDump << " step=" << this_run_start_step);
hid_t fid = H5Fopen( nameDump.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
if (fid < 0) ERROR(nameDump << " is not a valid HDF5 file");
string dump_version;
H5::getAttr(fid, "Version", dump_version);
string dump_date;
H5::getAttr(fid, "CommitDate", dump_date);
if ((dump_version != string(__VERSION)) || (dump_date != string(__COMMITDATE))) {
WARNING ("The code version that dumped the file is " << dump_version << " of " << dump_date);
WARNING (" while running version is " << string(__VERSION) << " of " << string(__COMMITDATE));
}
H5::getAttr(fid, "Energy_time_zero", static_cast<DiagnosticScalar*>(vecPatches.globalDiags[0])->Energy_time_zero );
H5::getAttr(fid, "EnergyUsedForNorm", static_cast<DiagnosticScalar*>(vecPatches.globalDiags[0])->EnergyUsedForNorm);
hid_t aid, gid, did, sid;
aid = H5Aopen(fid, "dump_step", H5T_NATIVE_UINT);
H5Aread(aid, H5T_NATIVE_UINT, &itime);
H5Aclose(aid);
for (unsigned int ipatch=0 ; ipatch<vecPatches.size(); ipatch++) {
ostringstream patch_name("");
patch_name << setfill('0') << setw(6) << vecPatches(ipatch)->Hindex();
string patchName="patch-"+patch_name.str();
hid_t patch_gid = H5Gopen(fid, patchName.c_str(),H5P_DEFAULT);
restartPatch( vecPatches(ipatch)->EMfields, vecPatches(ipatch)->vecSpecies, params, patch_gid );
H5Gclose(patch_gid);
}
// load window status
if (simWin!=NULL)
restartMovingWindow(fid, simWin);
H5Fclose( fid );
};