//! \return whether partial charges were successfully assigned to this molecule
bool EQEqCharges::ComputeCharges(OBMol &mol)
{
int i, j, a, c, N = mol.NumAtoms();
double cellVolume;
VectorXf chi(N), J(N), b(N), x(N);
MatrixXf J_ij(N, N), A(N, N);
OBUnitCell *obuc;
matrix3x3 unitcell, fourier;
vector3 dx;
int numNeighbors[3];
OBAtom *atom;
// If parameters have not yet been loaded, do that
if (!_paramFileLoaded)
{
if (ParseParamFile())
{
_paramFileLoaded = true;
} else
{
return false;
}
}
// Calculate atomic properties based around their ionic charge
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
a = atom->GetAtomicNum();
c = _chargeCenter[a];
// Fail if ionization data is missing for any atom in the molecule
if (_ionizations[a][c + 1] == -1 || _ionizations[a][c] == -1 || a > TABLE_OF_ELEMENTS_SIZE)
{
obErrorLog.ThrowError(__FUNCTION__, "Insufficient ionization data for atoms in the given molecule. Update `data/eqeqIonizations.txt` with missing information and re-run this function.", obError);
return false;
}
J(i) = _ionizations[a][c + 1] - _ionizations[a][c];
chi(i) = 0.5 * (_ionizations[a][c + 1] + _ionizations[a][c]) - (a == 1? 0 : c * J(i));
}
// If a unit cell is defined, use the periodic Ewald calculation
if (mol.HasData(OBGenericDataType::UnitCell))
{
// Get unit cell and calculate its Fourier transform + volume
obuc = (OBUnitCell *) mol.GetData(OBGenericDataType::UnitCell);
unitcell = obuc->GetCellMatrix();
fourier = (2 * PI * unitcell.inverse()).transpose();
cellVolume = obuc->GetCellVolume();
// Get the number of radial unit cells to use in x, y, and z
numNeighbors[0] = int(ceil(minCellLength / (2.0 * (obuc->GetA())))) - 1;
numNeighbors[1] = int(ceil(minCellLength / (2.0 * (obuc->GetB())))) - 1;
numNeighbors[2] = int(ceil(minCellLength / (2.0 * (obuc->GetC())))) - 1;
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
dx = atom->GetVector() - (mol.GetAtom(j + 1))->GetVector();
J_ij(i, j) = GetPeriodicEwaldJij(J(i), J(j), dx, (i == j), unitcell, fourier, cellVolume, numNeighbors);
}
}
// If no unit cell, use the simplified nonperiodic calculation
} else
{
for (i = 0; i < N; i++)
{
atom = mol.GetAtom(i + 1);
for (j = 0; j < N; j++)
{
J_ij(i, j) = GetNonperiodicJij(J(i), J(j), atom->GetDistance(j + 1), (i == j));
}
return false;
}
}
// Formulate problem as A x = b, where x is the calculated partial charges
// First equation is a simple overall balance: sum(Q) = 0
A.row(0) = VectorXf::Ones(N);
b(0) = 0;
// Remaining equations are based off of the fact that, at equilibrium, the
// energy of the system changes equally for a change in any charge:
// dE/dQ_1 = dE/dQ_2 = ... = dE/dQ_N
A.block(1, 0, N - 1, N) = J_ij.block(0, 0, N - 1, N) - J_ij.block(1, 0, N - 1, N);
b.tail(N - 1) = chi.tail(N - 1) - chi.head(N - 1);
// The solution is a list of charges in the system
x = A.colPivHouseholderQr().solve(b);
// Now we are done calculating, pass all this back to OpenBabel molecule
mol.SetPartialChargesPerceived();
OBPairData *dp = new OBPairData;
dp->SetAttribute("PartialCharges");
dp->SetValue("EQEq");
dp->SetOrigin(perceived);
mol.SetData(dp);
m_partialCharges.clear();
m_partialCharges.reserve(N);
m_formalCharges.clear();
m_formalCharges.reserve(N);
for (i = 0; i < N; i ++)
{
atom = mol.GetAtom(i + 1);
atom->SetPartialCharge(x(i));
m_partialCharges.push_back(x(i));
m_formalCharges.push_back(atom->GetFormalCharge());
}
obErrorLog.ThrowError(__FUNCTION__, "EQEq charges successfully assigned.", obInfo);
return true;
}
