void BasisSet::processDensity(BasisShell &shell)
{
BasisSet *set = shell.set;
unsigned int atomsSize = set->m_numAtoms;
unsigned int basisSize = set->m_symmetry.size();
unsigned int matrixSize = set->m_density.rows();
std::vector<int> &basis = set->m_symmetry;
vector<Vector3d> deltas;
vector<double> dr2;
deltas.reserve(atomsSize);
dr2.reserve(atomsSize);
// Calculate our position
Vector3d pos = shell.tCube->position(shell.pos) * ANGSTROM_TO_BOHR;
// Calculate the deltas for the position
for (unsigned int i = 0; i < atomsSize; ++i) {
deltas.push_back(pos - set->m_atomPos[i]);
dr2.push_back(deltas[i].squaredNorm());
}
// Calculate the basis set values at this point
MatrixXd values(matrixSize, 1);
for (unsigned int i = 0; i < basisSize; ++i) {
unsigned int cAtom = set->m_atomIndices[i];
switch(basis[i]) {
case S:
pointS(shell.set, dr2[cAtom], i, values);
break;
case P:
pointP(shell.set, deltas[cAtom], dr2[cAtom], i, values);
break;
case D:
pointD(shell.set, deltas[cAtom], dr2[cAtom], i, values);
break;
case D5:
pointD5(shell.set, deltas[cAtom], dr2[cAtom], i, values);
break;
default:
// Not handled - return a zero contribution
;
}
}
// Now calculate the value of the density at this point in space
double rho = 0.0;
for (unsigned int i = 0; i < matrixSize; ++i) {
// Calculate the off-diagonal parts of the matrix
for (unsigned int j = 0; j < i; ++j) {
rho += 2.0 * set->m_density.coeffRef(i, j)
* (values.coeffRef(i, 0) * values.coeffRef(j, 0));
}
// Now calculate the matrix diagonal
rho += set->m_density.coeffRef(i, i)
* (values.coeffRef(i, 0) * values.coeffRef(i, 0));
}
// Set the value
shell.tCube->setValue(shell.pos, rho);
}
/// This is the stuff we actually use right now - porting to new data structure
void BasisSet::processPoint(BasisShell &shell)
{
BasisSet *set = shell.set;
unsigned int atomsSize = set->m_numAtoms;
unsigned int basisSize = set->m_symmetry.size();
std::vector<int> &basis = set->m_symmetry;
vector<Vector3d> deltas;
vector<double> dr2;
deltas.reserve(atomsSize);
dr2.reserve(atomsSize);
unsigned int indexMO = shell.state-1;
// Calculate our position
Vector3d pos = shell.tCube->position(shell.pos) * ANGSTROM_TO_BOHR;
// Calculate the deltas for the position
for (unsigned int i = 0; i < atomsSize; ++i) {
deltas.push_back(pos - set->m_atomPos[i]);
dr2.push_back(deltas[i].squaredNorm());
}
// Now calculate the value at this point in space
double tmp = 0.0;
for (unsigned int i = 0; i < basisSize; ++i) {
switch(basis[i]) {
case S:
tmp += pointS(shell.set, i,
dr2[set->m_atomIndices[i]], indexMO);
break;
case P:
tmp += pointP(shell.set, i, deltas[set->m_atomIndices[i]],
dr2[set->m_atomIndices[i]], indexMO);
break;
case D:
tmp += pointD(shell.set, i, deltas[set->m_atomIndices[i]],
dr2[set->m_atomIndices[i]], indexMO);
break;
case D5:
tmp += pointD5(shell.set, i, deltas[set->m_atomIndices[i]],
dr2[set->m_atomIndices[i]], indexMO);
break;
default:
// Not handled - return a zero contribution
;
}
}
// Set the value
shell.tCube->setValue(shell.pos, tmp);
}
inline vector<double> GaussianSetTools::calculateValues(const Vector3 &position) const
{
m_basis->initCalculation();
unsigned int atomsSize = static_cast<unsigned int>(m_molecule->atomCount());
size_t basisSize = m_basis->symmetry().size();
const std::vector<int> &basis = m_basis->symmetry();
const std::vector<unsigned int> &atomIndices = m_basis->atomIndices();
vector<Vector3> deltas;
vector<double> dr2;
deltas.reserve(atomsSize);
dr2.reserve(atomsSize);
// Calculate our position
Vector3 pos(position * ANGSTROM_TO_BOHR);
// Calculate the deltas for the position
for (size_t i = 0; i < atomsSize; ++i) {
deltas.push_back(pos - (m_molecule->atom(i).position3d() * ANGSTROM_TO_BOHR));
dr2.push_back(deltas[i].squaredNorm());
}
// Allocate space for the values to be calculated.
size_t matrixSize = m_basis->moMatrix().rows();
vector<double> values;
values.resize(matrixSize, 0.0);
// Now calculate the values at this point in space
for (unsigned int i = 0; i < basisSize; ++i) {
switch (basis[i]) {
case GaussianSet::S:
pointS(i, dr2[atomIndices[i]], values);
break;
case GaussianSet::P:
pointP(i, deltas[atomIndices[i]], dr2[atomIndices[i]], values);
break;
case GaussianSet::D:
pointD(i, deltas[atomIndices[i]], dr2[atomIndices[i]], values);
break;
case GaussianSet::D5:
pointD5(i, deltas[atomIndices[i]], dr2[atomIndices[i]], values);
break;
default:
// Not handled - return a zero contribution
;
}
}
return values;
}