void OpenSMOKE_GasStream::AssignMoleFractions(const vector<string> _names, const vector<double> _values)
{
BzzVector mole(mix->NumberOfSpecies());
for(int k=0; k<int(_names.size()); k++)
mole[mix->recognize_species(_names[k])] = _values[k];
AssignMoleFractions(mole);
}
// Equivalence Ratio (most general)
BzzVector OpenSMOKE_GasStream::EquivalenceRatio(const double equivalence_ratio, const vector<string> fuel_names, BzzVector &moles_fuel,
const vector<string> oxidizer_names, BzzVector &moles_oxidizer)
{
int j;
int number_of_fuels = moles_fuel.Size();
int number_of_oxidizers = moles_oxidizer.Size();
BzzVector nC(number_of_fuels);
BzzVector nH(number_of_fuels);
BzzVector nO(number_of_fuels);
BzzVector nOxidizers(number_of_oxidizers);
int jC = mix->recognize_element_without_error("c");
int jH = mix->recognize_element_without_error("h");
int jO = mix->recognize_element_without_error("o");
if (jC>0)
for(j=1;j<=number_of_fuels;j++)
nC[j] = mix->elements[jC][mix->recognize_species(fuel_names[j])];
if (jH>0)
for(j=1;j<=number_of_fuels;j++)
nH[j] = mix->elements[jH][mix->recognize_species(fuel_names[j])];
if (jO>0)
for(j=1;j<=number_of_fuels;j++)
nO[j] = mix->elements[jO][mix->recognize_species(fuel_names[j])];
double nFuel = equivalence_ratio*moles_fuel.GetSumElements();
int jO2 = 0;
for(j=1;j<=number_of_oxidizers;j++)
if (oxidizer_names[j] == "O2") { jO2 = j; break;}
double nO2 = ( 2.*Dot(nC,moles_fuel) +
0.50*Dot(nH,moles_fuel) -
Dot(nO,moles_fuel))/2.;
for(j=1;j<=number_of_oxidizers;j++)
nOxidizers[j] = moles_oxidizer[j]/moles_oxidizer[jO2]*nO2;
double n = nFuel + nOxidizers.GetSumElements();
BzzVector mole(mix->NumberOfSpecies());
for(j=1;j<=number_of_fuels;j++)
mole[mix->recognize_species(fuel_names[j])] += equivalence_ratio*moles_fuel[j]/n;
for(j=1;j<=number_of_oxidizers;j++)
mole[mix->recognize_species(oxidizer_names[j])] += nOxidizers[j]/n;
//for(j=1;j<=number_of_fuels;j++)
// cout << fuel_names[j] << " " << mole[mix->recognize_species(fuel_names[j])] << endl;
//for(j=1;j<=number_of_oxidizers;j++)
// cout << oxidizer_names[j] << " " << mole[mix->recognize_species(oxidizer_names[j])] << endl;
return mole;
}
// Avogadro constant
inline quantity N_sub_A() { return mole() / mole() * // to help msvc
Rep( 6.02214199e+23L ) / mole(); }
ParticleSet* ParticleSetPool::createESParticleSet(xmlNodePtr cur, const string& target)
{
TinyVector<int,OHMMS_DIM> tilefactor;
Tensor<int,OHMMS_DIM> tilematrix(1,0,0,0,1,0,0,0,1);
double lr_cut=10;
string h5name;
string source("i");
string bc("p p p");
OhmmsAttributeSet attribs;
attribs.add(h5name, "href");
attribs.add(tilefactor, "tile");
attribs.add(tilematrix, "tilematrix");
attribs.add(source, "source");
attribs.add(bc, "bconds");
attribs.add(lr_cut, "LR_dim_cutoff");
attribs.put(cur);
ParticleSet* ions=getParticleSet(source);
if(ions==0)
{
ions=new MCWalkerConfiguration;
ions->setName(source);
}
//set the boundary condition
ions->Lattice.LR_dim_cutoff=lr_cut;
std::istringstream is(bc);
char c;
int idim=0;
while(!is.eof() && idim<OHMMS_DIM)
{
if(is>>c) ions->Lattice.BoxBConds[idim++]=(c=='p');
}
//initialize ions from hdf5
hid_t h5=-1;
if(myComm->rank()==0)
h5 = H5Fopen(h5name.c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
ESHDFIonsParser ap(*ions,h5,myComm);
ap.put(cur);
ap.expand(tilematrix);
if(h5>-1) H5Fclose(h5);
//failed to initialize the ions
if(ions->getTotalNum() == 0) return 0;
typedef ParticleSet::SingleParticleIndex_t SingleParticleIndex_t;
vector<SingleParticleIndex_t> grid(OHMMS_DIM,SingleParticleIndex_t(1));
ions->Lattice.reset();
ions->Lattice.makeGrid(grid);
if(SimulationCell==0)
{
SimulationCell = new ParticleSet::ParticleLayout_t(ions->Lattice);
}
//create the electrons
MCWalkerConfiguration* qp = new MCWalkerConfiguration;
qp->setName(target);
qp->Lattice.copy(ions->Lattice);
//qp->Lattice.reset();
//qp->Lattice.makeGrid(grid);
app_log() << " Simulation cell radius = " << qp->Lattice.SimulationCellRadius << endl;
app_log() << " Wigner-Seitz radius = " << qp->Lattice.WignerSeitzRadius << endl;
SimulationCell->print(app_log());
myPool[target]=qp;
myPool[source]=ions;
//addParticleSet(qp);
//addParticleSet(ions);
{//get the number of electrons per spin
vector<int> num_spin;
xmlNodePtr cur1=cur->children;
while(cur1!=NULL)
{
string cname1((const char*)cur1->name);
if(cname1 == OrbitalBuilderBase::sd_tag)
{
num_spin.clear();
xmlNodePtr cur2=cur1->children;
while(cur2!=NULL)
{
string cname2((const char*)cur2->name);
if(cname2 == OrbitalBuilderBase::det_tag)
{
int n=0;
OhmmsAttributeSet a;
a.add(n,"size");
a.put(cur2);
if(num_spin.size()<2) num_spin.push_back(n);
}
cur2=cur2->next;
}
}
cur1=cur1->next;
}
//create species
SpeciesSet& species=qp->getSpeciesSet();
//add up and down
species.addSpecies("u");
if(num_spin.size()>1) species.addSpecies("d");
int chid=species.addAttribute("charge");
for(int i=0; i<num_spin.size(); ++i) species(chid,i)=-1.0;
int mid=species.addAttribute("membersize");
for(int i=0; i<num_spin.size(); ++i) species(mid,i)=num_spin[i];
mid=species.addAttribute("mass");
for(int i=0; i<num_spin.size(); ++i) species(mid,i)=1.0;
qp->create(num_spin);
}
//name it with the target
qp->setName(target);
//assign non-trivial positions for the quanmtum particles
if(qp->Lattice.SuperCellEnum)
{
makeUniformRandom(qp->R);
qp->R.setUnit(PosUnit::LatticeUnit);
qp->convert2Cart(qp->R);
qp->createSK();
}
else
{
InitMolecularSystem mole(this);
if(ions->getTotalNum()>1)
mole.initMolecule(ions,qp);
else
mole.initAtom(ions,qp);
}
//for(int i=0; i<qp->getTotalNum(); ++i)
// cout << qp->GroupID[i] << " " << qp->R[i] << endl;
if(qp->getTotalNum() == 0 || ions->getTotalNum() == 0)
{
delete qp;
delete ions;
APP_ABORT("ParticleSetPool failed to create particlesets for the electron structure calculation");
return 0;
}
return qp;
}
