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;
}
}
}
public static ForceCalculatorResult CalculateForces(Molecule molecule, AtomNeighborhoodMap neighborhoodMap = null)
{
if (!molecule.IsPositioned)
{
molecule.PositionAtoms();
}
if (neighborhoodMap == null)
{
neighborhoodMap = new AtomNeighborhoodMap(molecule);
}
var graph = molecule.MoleculeStructure;
var forceLookup = CalculateBondForces(graph);
//CalculateIonicForces(molecule, forceLookup, neighborhoodMap);
CalculateAtomShellRepulsion(molecule, forceLookup, neighborhoodMap);
var lonePairForceLookup = CalculateLonePairRepulsion(graph, forceLookup);
if (forceLookup.Values.Any(v => v.X.IsNaN()))
{
throw new Exception("Force cannot be 'NaN'");
}
if (lonePairForceLookup.Values.Any(v => v.X.IsNaN()))
{
throw new Exception("Lone pair repulsion cannot be 'NaN'");
}
return(new ForceCalculatorResult(forceLookup, lonePairForceLookup, neighborhoodMap));
}
public ForceCalculatorResult(Dictionary <uint, Vector3D> forceLookup,
Dictionary <Orbital, Vector3D> lonePairForceLookup,
AtomNeighborhoodMap neighborhoodMap)
{
ForceLookup = forceLookup;
LonePairForceLookup = lonePairForceLookup;
NeighborhoodMap = neighborhoodMap;
}
private void RunSimulation(CancellationToken cancellationToken)
{
if (!Molecule.IsPositioned)
{
Molecule.PositionAtoms();
}
var currentAtomPositions = Molecule.MoleculeStructure.Vertices
.ToDictionary(vertex => vertex.Id, vertex => Molecule.GetAtom(vertex.Id).Position);
var lastNeighborhoodUpdate = 0.To(Unit.Second);
var atomNeighborhoodMap = new AtomNeighborhoodMap(Molecule);
for (var t = 0.To(Unit.Second); t < simulationSettings.SimulationTime; t += simulationSettings.TimeStep)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
if (t - lastNeighborhoodUpdate > 400.To(SIPrefix.Femto, Unit.Second))
{
atomNeighborhoodMap.Update();
}
var forces = ForceCalculator.CalculateForces(Molecule, atomNeighborhoodMap);
AddCustomForces(Molecule, t, forces.ForceLookup, customAtomForces);
ApplyAtomForces(Molecule, t, forces, simulationSettings);
ApplyLonePairRepulsion(forces);
// TODO: Redistribute electrons (either here or as a step after molecule is fully connected
//WriteDebug(molecule);
var newAtomPositions = Molecule.MoleculeStructure.Vertices
.ToDictionary(vertex => vertex.Id, vertex => Molecule.GetAtom(vertex.Id).Position);
if (simulationSettings.StopSimulationWhenAtomAtRest && t > simulationSettings.ForceRampUpPeriod)
{
var maximumPositionChange = currentAtomPositions.Keys
.Select(atom => currentAtomPositions[atom].DistanceTo(newAtomPositions[atom]).In(SIPrefix.Pico, Unit.Meter))
.Max();
if (maximumPositionChange / simulationSettings.TimeStep.Value < simulationSettings.MovementDetectionThreshold.Value)
{
break;
}
}
currentAtomPositions = newAtomPositions;
OnTimestepCompleted(new SimulationTimestepCompleteEventArgs(t, Molecule));
}
OnSimulationFinished();
}
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;
}
}
}