void step()
{
boost::scoped_ptr<
typename multi_particle_container_type::transaction_type>
tx(pc_.create_transaction());
typedef typename multi_particle_container_type::transaction_type::particle_id_pair_generator particle_id_pair_generator;
typedef typename multi_particle_container_type::transaction_type::particle_id_pair_and_distance_list particle_id_pair_and_distance_list;
last_reaction_setter rs(*this);
volume_clearer vc(*this);
BDPropagator<traits_type> ppg(
*tx, *main_.network_rules(), main_.rng(),
base_type::dt_,
1 /* FIXME: dissociation_retry_moves */, &rs, &vc,
make_select_first_range(pc_.get_particles_range()));
last_event_ = NONE;
while (ppg())
{
if (last_reaction_)
{
last_event_ = REACTION;
break;
}
}
}
/** Creating StructureFactor
*
* Currently testing only 1 component for PBCs.
*/
void ParticleSet::createSK()
{
if(!sorted_ids && !reordered_ids)
{
//save ID and GroupID
orgID=ID;
orgGroupID=GroupID;
if(groups()<1)
{
int nspecies=mySpecies.getTotalNum();
vector<int> ppg(nspecies,0);
for(int iat=0; iat<GroupID.size(); ++iat) ppg[GroupID[iat]]+=1;
SubPtcl.resize(nspecies+1);
SubPtcl[0]=0;
for(int i=0; i<nspecies; ++i) SubPtcl[i+1]=SubPtcl[i]+ppg[i];
int new_id=0;
for(int i=0; i<nspecies; ++i)
for(int iat=0; iat<GroupID.size(); ++iat) if(GroupID[iat]==i) orgID[new_id++]=ID[iat];
bool grouped=true;
for(int iat=0; iat<ID.size(); ++iat) grouped &= (orgID[iat]==ID[iat]);
if(grouped)
{
app_log() << " ParticleSet is grouped. No need to reorder." << endl;
}
else
{
app_log() << " Need to reorder. Only R is swapped." << endl;
ParticlePos_t oldR(R);
for(int iat=0; iat<R.size(); ++iat) R[iat]=oldR[orgID[iat]];
for(int i=0; i<groups(); ++i)
for(int iat=first(i); iat<last(i); ++iat) GroupID[iat]=i;
reordered_ids=true;
}
}//once group is set, nothing to be done
sorted_ids=true;
}
int membersize= mySpecies.addAttribute("membersize");
for(int ig=0; ig<mySpecies.size(); ++ig)
SubPtcl[ig+1]=SubPtcl[ig]+mySpecies(membersize,ig);
convert2Cart(R); //make sure that R is in Cartesian coordinates
//if(Lattice.BoxBConds[0] && SK == 0)
if(Lattice.SuperCellEnum != SUPERCELL_OPEN)
{
Lattice.SetLRCutoffs();
if(SK)
{
app_log() << "\n Structure Factor is reset by " << Lattice.LR_kc << endl;
SK->UpdateNewCell(Lattice.LR_kc);
}
else
{
app_log() << "\n Creating Structure Factor for periodic systems." <<endl;
SK = new StructFact(*this,Lattice.LR_kc);
}
//Lattice.print(app_log());
//This uses the copy constructor to avoid recomputing the data.
//SKOld = new StructFact(*SK);
}
}
