inline void Molecule::make_geometric_matrix()
{
geometric.resize(number_of_bonds, number_of_bonds);
for (int i = 0; i < number_of_bonds; i++)
{
std::pair<int, int> bond = get_bond_by_index(i);
sGTO first_sGTO= basis_[atoms_[bond.first].symbol];
sGTO second_sGTO= basis_[atoms_[bond.second].symbol];
double r = distance1(atoms_[bond.first].X, atoms_[bond.second].X);
geometric(i,i) = basis_.overlap_integral(first_sGTO, second_sGTO, r);
}
}
inline void Molecule::make_coulomb_integrals()
{
unsigned n = atoms_.size();
if (coulomb_.size() != n * n) coulomb_.resize(n, n);
for (unsigned i=0; i<n; i++)
{
const sGTO &sgto= basis_[atoms_[i].symbol];
for (unsigned j=0; j<i; j++)
{
const sGTO &sgto__= basis_[atoms_[j].symbol];
double r = distance1(atoms_[i].X, atoms_[j].X);
double s = basis_.coulomb_integral(sgto, sgto__, r);
coulomb_(i,j) = s;
coulomb_(j,i) = s;
}
coulomb_(i,i) = atoms_[i].hardness;
}
}
inline void Molecule::make_coulomb_integrals(std::vector<double> &coulomb_matrix)
{
unsigned n = atoms_.size();
if (coulomb_matrix.size() != n * n) coulomb_matrix.resize(n * n);
for (unsigned i=0; i<n; i++)
{
const sGTO &sgto= basis_[atoms_[i].symbol];
for (unsigned j=0; j<i; j++)
{
const sGTO &sgto__= basis_[atoms_[j].symbol];
double r = distance1(atoms_[i].X, atoms_[j].X);
double s = basis_.coulomb_integral(sgto, sgto__, r);
_E(n, &coulomb_matrix[0], i, j) = s;
_E(n, &coulomb_matrix[0], j, i) = s;
}
_E(n, &coulomb_matrix[0], i, i) = atoms_[i].hardness;
// for the diagonal elements, use hardness
}
}
void insert(std::string symbol, const v3dense &X)
{
// look up AtomSymbol to assign parameters
for (unsigned i=0; i<RAPPLE_GODDARD_PARAM_COUNT; i++)
{
if (symbol == RAPPLE_GODDARD_PARAMS[i].symbol)
{
Atom atom;
atom.symbol = symbol;
atom.electronegativity = RAPPLE_GODDARD_PARAMS[i].electronegativity;
atom.hardness = RAPPLE_GODDARD_PARAMS[i].hardness;
atom.X[0] = X[0] * ANGSTROM_2_BORH;
atom.X[1] = X[1] * ANGSTROM_2_BORH;
atom.X[2] = X[2] * ANGSTROM_2_BORH;
atoms_.push_back(atom);
basis_.insert(_Orbital(symbol, RAPPLE_GODDARD_PARAMS[i].gaussian_exponent));
return;
}
}
std::string msg = _S("[ERROR] Unknown element type : ") + symbol;
PRINT_ERR(msg);
}
