private static void CalculateIonicForces(Molecule molecule,
Dictionary <uint, Vector3D> forceLookup,
AtomNeighborhoodMap neighborhoodMap)
{
var vertexIds = molecule.MoleculeStructure.Vertices.Select(v => v.Id);
foreach (var vertexId in vertexIds)
{
var atom = molecule.GetAtom(vertexId);
var charge1 = atom.EffectiveCharge;
var atom1Position = atom.Position;
var neighborhood = neighborhoodMap.GetNeighborhood(vertexId);
foreach (var neighborVertexId in neighborhood)
{
if (neighborVertexId <= vertexId)
{
continue;
}
var neighborAtom = molecule.GetAtom(neighborVertexId);
var charge2 = neighborAtom.EffectiveCharge;
var r = atom1Position.VectorTo(neighborAtom.Position);
var distance = r.Magnitude().In(SIPrefix.Pico, Unit.Meter);
var chargeProduct = PhysicalConstants.CoulombsConstant.Value
* charge1.Value
* charge2.Value;
var ionicForce = -5 * 1e-1 * (chargeProduct / (distance * distance)) * r.Normalize().ToVector3D();
forceLookup[vertexId] += ionicForce;
forceLookup[neighborVertexId] += -ionicForce;
}
}
}
private static void CalculateAtomShellRepulsion(Molecule molecule,
Dictionary <uint, Vector3D> forceLookup,
AtomNeighborhoodMap neighborhoodMap)
{
var vertices = molecule.MoleculeStructure.Vertices.Select(v => v.Id);
foreach (var vertex in vertices)
{
var atom = molecule.GetAtom(vertex);
var atom1Position = atom.Position;
var atom1Radius = atom.Radius.Value;
//var bondedNeighbors = new HashSet<Atom>(atom.OuterOrbitals
// .Where(o => o.IsPartOfBond)
// .Select(o => GetBondedAtom(o, atom)));
var neighborhood = neighborhoodMap.GetNeighborhood(vertex);
foreach (var neighborVertex in neighborhood)
{
if (neighborVertex <= vertex)
{
continue;
}
var neighborAtom = molecule.GetAtom(neighborVertex);
//if (bondedNeighbors.Contains(neighborAtom))
// continue;
var atom2Radius = atom.Radius.Value;
var atomRadiusSum = atom1Radius + atom2Radius;
var r = atom1Position.VectorTo(neighborAtom.Position);
var distance = r.Magnitude().In(SIPrefix.Pico, Unit.Meter);
var shellRepulsionForce = -(1e-5 * (1e-12 / distance)
* Math.Exp(Math.Min(1e12 * (atomRadiusSum - distance), 0)))
* r.Normalize().ToVector3D();
forceLookup[vertex] += shellRepulsionForce;
forceLookup[neighborVertex] += -shellRepulsionForce;
}
}
}