// Returns atom interactions between groups of atoms. Will ignore interactions between atoms within each group.
// Uses KDTree to find atoms within a certain distance and then calculates the forces on those atoms.
public List <AtomInteraction> GetAllInteractions(List <Atom> molecule1Atoms, List <Vector3> molecule1AtomPositions, List <Atom> molecule2Atoms, List <Vector3> molecule2AtomPositions, Gradient repulsiveGradient, Gradient strongAttractiveGradient, Gradient weakAttractiveGradient, int processorCores = 1)
{
if (molecule1Atoms == null || molecule1AtomPositions == null || molecule1Atoms.Count != molecule1AtomPositions.Count)
{
Debug.Log("Interactions calculator, Molecule 1 atoms count and molecule 1 atom positions count don't match");
return(new List <AtomInteraction>());
}
if (molecule2Atoms == null || molecule2AtomPositions == null || molecule2Atoms.Count != molecule2AtomPositions.Count)
{
Debug.Log("Interactions calculator, Molecule 2 atoms count and molecule 2 atom positions count don't match");
return(new List <AtomInteraction>());
}
KdTree <float, int> molecule2AtomTree = new KdTree <float, int>(3, new FloatMath());
for (int i = 0; i < molecule2Atoms.Count; i++)
{
Vector3 molecule2AtomPosition = molecule2AtomPositions[i];
molecule2AtomTree.Add(new float[] { molecule2AtomPosition.x, molecule2AtomPosition.y, molecule2AtomPosition.z }, i);
}
List <AtomInteraction> interactions = new List <AtomInteraction>();
for (int i = 0; i < molecule1Atoms.Count; i++)
{
Atom atom = molecule1Atoms[i];
Vector3 atomPosition = molecule1AtomPositions[i];
KdTreeNode <float, int>[] interactingAtoms = molecule2AtomTree.RadialSearch(new float[] { atomPosition.x, atomPosition.y, atomPosition.z }, maxInteractionDistance, maxInteractionsPerAtom);
foreach (KdTreeNode <float, int> node in interactingAtoms)
{
Atom interactingAtom = molecule2Atoms[node.Value];
Vector3 interactingAtomPosition = molecule2AtomPositions[node.Value];
// get distance between atoms
float deltaX = interactingAtomPosition.x - atomPosition.x;
float deltaY = interactingAtomPosition.y - atomPosition.y;
float deltaZ = interactingAtomPosition.z - atomPosition.z;
float distance = (float)Math.Sqrt(deltaX * deltaX + deltaY * deltaY + deltaZ * deltaZ);
AtomInteraction interaction = new AtomInteraction()
{
Atom1 = atom,
Atom2 = interactingAtom,
Distance = distance,
};
SetLennardJonesPotential(interaction);
SetElecrostaticEnergy(interaction);
SetInteractionType(interaction, repulsiveGradient, strongAttractiveGradient, weakAttractiveGradient);
interactions.Add(interaction);
}
}
return(interactions);
}
// Sets a colour calculated on distance compared to atom sigmas
public void SetInteractionType(AtomInteraction interaction, Gradient repulsiveGradient, Gradient strongAttractiveGradient, Gradient weakAttractiveGradient)
{
float weakAttractiveMaxDistance = 2.5f * (float)interaction.SumOfAtomicRadii;
if (interaction.Distance >= weakAttractiveMaxDistance)
{
interaction.InteractionType = null;
return;
}
float strongAttractiveMaxDistance = 1.5f * (float)interaction.SumOfAtomicRadii;
float repulsiveMaxDistance = 0.9f * (float)interaction.SumOfAtomicRadii;
if (interaction.Distance >= strongAttractiveMaxDistance)
{
interaction.InteractionType = InteractionType.Attractive;
float weakForce = (interaction.Distance - strongAttractiveMaxDistance) / (weakAttractiveMaxDistance - strongAttractiveMaxDistance);
interaction.InteractionColour = weakAttractiveGradient.Evaluate(weakForce);
}
else if (interaction.Distance >= repulsiveMaxDistance)
{
interaction.InteractionType = InteractionType.Stable;
float strongForce = (interaction.Distance - repulsiveMaxDistance) / (strongAttractiveMaxDistance - repulsiveMaxDistance);
interaction.InteractionColour = strongAttractiveGradient.Evaluate(strongForce);
}
else
{
interaction.InteractionType = InteractionType.Repulsive;
float repulsiveForce = interaction.Distance / repulsiveMaxDistance;
interaction.InteractionColour = repulsiveGradient.Evaluate(repulsiveForce);
}
}
// Calculates the Lennard-Jones Potential for two atoms
public void SetLennardJonesPotential(AtomInteraction interaction)
{
// distance and sigma/epsilon need to be both in nanometres
// interaction distance is in Nanometres
if (interaction.Distance >= 8d)
{
return;
}
// get sigma/epsilon in nanometres
AtomSigmaEpsilon atom1SigmaEpsilon = InteractionForces.GetAtomSigmaEpsilonAngstroms(interaction.Atom1);
AtomSigmaEpsilon atom2SigmaEpsilon = InteractionForces.GetAtomSigmaEpsilonAngstroms(interaction.Atom2);
interaction.SumOfAtomicRadii = ((double)atom1SigmaEpsilon.Sigma + (double)atom2SigmaEpsilon.Sigma) / 2d;
double energyWellDepth = Math.Sqrt((double)atom1SigmaEpsilon.Epsilon * (double)atom2SigmaEpsilon.Epsilon);
double distanceBetweenAtoms6 = Math.Pow(interaction.Distance, 6);
double distanceBetweenAtoms12 = Math.Pow(interaction.Distance, 12);
double sumOfAtomicRadii6 = Math.Pow(interaction.SumOfAtomicRadii, 6);
double sumOfAtomicRadii12 = Math.Pow(interaction.SumOfAtomicRadii, 12);
double score = energyWellDepth * ((sumOfAtomicRadii12 / distanceBetweenAtoms12) - (2d * sumOfAtomicRadii6 / distanceBetweenAtoms6));
interaction.LennardJonesPotential = Double.IsPositiveInfinity(score) ? Double.MaxValue : score;
}
// Calulates the Coulombs force between two atoms
public void SetElecrostaticEnergy(AtomInteraction interaction)
{
double coulombsConstant = 138.7848663d;
double distance = interaction.Distance;
double chargeAtom1 = (double)interaction.Atom1.Charge;
double chargeAtom2 = (double)interaction.Atom2.Charge;
double electrostaticForce = coulombsConstant * ((chargeAtom1 * chargeAtom2) / distance);
interaction.ElectrostaticEnergy = electrostaticForce;
}