private static Dictionary <Orbital, IVertex <Atom> > MapBondOrbitalToNeighborVertex(
List <Orbital> filledOuterOrbitals, AtomWithOrbitals currentAtom, List <IVertex <Atom> > adjacentVertices)
{
var orbitalNeighborVertexMap = filledOuterOrbitals
.Where(o => o.IsPartOfBond)
.ToDictionary(
o => o,
o => {
var bond = o.AssociatedBond;
var neighborAtom = bond.Atom1.Equals(currentAtom) ? bond.Atom2 : bond.Atom1;
return(adjacentVertices.Single(v => v.Object.Equals(neighborAtom)));
});
return(orbitalNeighborVertexMap);
}
private static IEnumerable <Point3D> GetAtomSpherePoints(AtomWithOrbitals currentAtom, IEnumerable <IVertex <Atom> > adjacentVertices)
{
var positionedNeighbors = adjacentVertices
.Where(v => v.Object.IsPositioned || v.Object.IsPositionFixed)
.ToList();
var existingPoints = positionedNeighbors
.Select(v => v.Object)
.Select(a => currentAtom.Position.VectorTo(a.Position))
.ToList();
var neighborAndLonePairCount = currentAtom.OuterOrbitals.Count(o => o.IsFull);
var evenlyDistributedPoints = SpherePointDistributor.EvenlyDistributePointsOnSphere(
1.0,
neighborAndLonePairCount - existingPoints.Count,
existingPoints);
return(evenlyDistributedPoints);
}
public static List <Orbital> Generate(AtomWithOrbitals atom, int maximumPeriod)
{
var orbitals = new List <Orbital>();
for (var period = 1; period <= maximumPeriod; period++)
{
// s-orbital
orbitals.Add(new Orbital(atom, period, OrbitalType.s));
if (period == 1)
{
continue;
}
// p-orbitals
for (var i = 0; i < 3; i++)
{
orbitals.Add(new Orbital(atom, period, OrbitalType.p));
}
if (period == 2)
{
continue;
}
// d-orbitals
for (var i = 0; i < 5; i++)
{
orbitals.Add(new Orbital(atom, period, OrbitalType.d));
}
if (period == 3)
{
continue;
}
// f-orbitals
for (int i = 0; i < 7; i++)
{
orbitals.Add(new Orbital(atom, period, OrbitalType.f));
}
//if(period == 4)
// continue;
}
return(orbitals);
}
private static IEnumerable <OrbitalBond> CreateOrbitalBonds(AtomWithOrbitals atom1, AtomWithOrbitals atom2, int bondCount)
{
if (!atom1.OrbitalsAvailableForBonding.Any())
{
throw new ChemistryException($"Cannot bond to noble gas {atom1.Element}");
}
if (!atom2.OrbitalsAvailableForBonding.Any())
{
throw new ChemistryException($"Cannot bond to noble gas {atom2.Element}");
}
var bonds = new List <OrbitalBond>();
for (int bondIdx = 1; bondIdx <= bondCount; bondIdx++)
{
var orbital1 = atom1.OrbitalsAvailableForBonding.MinimumItem(o => o.Energy.In(Unit.ElectronVolts));
var orbital2 = atom2.OrbitalsAvailableForBonding.MinimumItem(o => o.Energy.In(Unit.ElectronVolts));
var bond = new OrbitalBond(atom1, orbital1, atom2, orbital2);
bonds.Add(bond);
}
return(bonds);
}
public static UnitValue Calculate(AtomWithOrbitals atom1, Orbital orbital1, AtomWithOrbitals atom2, Orbital orbital2)
{
return(-5.To(Unit.ElectronVolts));
}
public static UnitValue CalculateOrbitalEnergy(AtomWithOrbitals atom, Orbital orbital)
{
return(-(1.0 / (OrbitalComparer.CalculateOrbitalOrder(orbital) + 1)).To(Unit.ElectronVolts));
}
public static UnitValue Calculate(AtomWithOrbitals atom1, Orbital orbital1, AtomWithOrbitals atom2, Orbital orbital2)
{
return(1.0 * (atom1.Radius + atom2.Radius));
}