void OBOrbitalData::LoadBetaOrbitals(std::vector<double> energies, std::vector<std::string> symmetries, int betaHOMO)
{
if (energies.size() < symmetries.size())
return; // something is very weird -- it's OK to pass no symmetries (we'll assume "A")
if (energies.size() == 0)
return;
if (betaHOMO > energies.size())
return;
_betaHOMO = betaHOMO;
_betaOrbitals.clear();
_openShell = true;
if (symmetries.size() < energies.size()) // pad with "A" symmetry
for (unsigned int i = symmetries.size(); i < energies.size(); ++i)
symmetries.push_back("A");
OBOrbital currentOrbital;
for (unsigned int i = 0; i < energies.size(); ++i)
{
if (i < betaHOMO)
currentOrbital.SetData(energies[i], 2.0, symmetries[i]);
else
currentOrbital.SetData(energies[i], 0.0, symmetries[i]);
_betaOrbitals.push_back(currentOrbital);
}
}
/**
Method reads orbital information from input stream (ifs)
and writes them to supplied OBMol object (molecule).
Input stream must be set to begining of orbital data
section in nwo file. (Line after "... Molecular Orbital Analysis")
Stream will be set at next line after end of orbital section.
*/
void NWChemOutputFormat::ReadOrbitals(istream* ifs, OBMol* molecule)
{
if ((ifs == NULL) || (molecule == NULL))
return;
vector<string> vs;
char buffer[BUFF_SIZE];
vector<OBOrbital> orbitals;
OBOrbitalData* orbital_data = new OBOrbitalData;
ifs->getline(buffer, BUFF_SIZE); // ---------
ifs->getline(buffer, BUFF_SIZE); // blank line
while (ifs->getline(buffer,BUFF_SIZE))
{
if (strstr(buffer, ORBITAL_START_PATTERN))
{
tokenize(vs, buffer);
// Vector N Occ=X E= Y Symmetry=a'
// 0 1 2 3 4 5(optional)
if (vs.size() < 5)
break; // Orbital data is broken
double energy = atof(vs[4].c_str()) * HARTREE_TO_KCAL;
double occupation = atof(vs[2].c_str()+4); // Start from symbol after '='
string symbol;
if (vs.size() > 5)
symbol = vs[5].substr(9, string::npos);
else
symbol = " "; // Symmetry is unknown
OBOrbital orbital;
orbital.SetData(energy, occupation, symbol);
orbitals.push_back(orbital);
ifs->getline(buffer, BUFF_SIZE); // MO Center ...
ifs->getline(buffer, BUFF_SIZE); // Table header
ifs->getline(buffer,BUFF_SIZE); // ----------
while (ifs->getline(buffer,BUFF_SIZE))
if (strlen(buffer) < 2) // If blank line detected
break;
}// if Vector ...
else if ((strstr(buffer, ORBITAL_SECTION_PATTERN_2) != NULL)&&(strstr(buffer, ORBITAL_SECTION_PATTERN_1) != NULL))
{
orbital_data->SetAlphaOrbitals(orbitals);
orbital_data->SetOpenShell(true);
orbitals.clear();
ifs->getline(buffer, BUFF_SIZE); // ---------
ifs->getline(buffer, BUFF_SIZE); // blank line
}// if beta orbital section found
else
{
if (orbital_data->IsOpenShell())
orbital_data->SetBetaOrbitals(orbitals);
else
orbital_data->SetAlphaOrbitals(orbitals);
molecule->SetData(orbital_data);
return;
}
}
delete orbital_data;
}
