// 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);
}
private void findBonds(object argument)
{
List <int> threadAtoms = (List <int>)argument;
foreach (int atomIndex in threadAtoms)
{
Atom atom = atoms[atomIndex];
KdTreeNode <float, int>[] bondAtoms = tree.RadialSearch(new float[] { atom.Position.x, atom.Position.y, atom.Position.z }, BondLengths.MaximumLengthAllElements, BondLengths.MaxBondsPerAtom);
foreach (KdTreeNode <float, int> bondAtomNode in bondAtoms)
{
// atom can't bond to itself
// (tree search always finds the supplied atom as well since it's only searching from a position, not an atom)
if (atomIndex == bondAtomNode.Value)
{
continue;
}
string bondKey = getBondKey(atom.Index, bondAtomNode.Value);
// check it hasn't been added previously (i.e. bond in reverse).
if (!addedBonds.Contains(bondKey))
{
Atom bondAtom = atoms[bondAtomNode.Value];
// get the maximum bond length for this bond
// first try a lookup
float maxBondLength;
if (!maxBondLengths.TryGetValue(new ElementPair(atom.Element, bondAtom.Element), out maxBondLength))
{
// if lookup fails use defaults
if (atom.Element == Element.H || bondAtom.Element == Element.H)
{
maxBondLength = BondLengths.MaximumLengthHydrogen;
}
else
{
maxBondLength = BondLengths.MaximumLengthAllElements;
}
}
// if the maxBondLength is lower than the search radius in the KDTree search
// then calculate the bond length between the atoms and check it doesn't exceed maxBondLength
if (maxBondLength < BondLengths.MaximumLengthAllElements)
{
if (atomDistance(atom, bondAtom) > maxBondLength)
{
continue;
}
}
lock (bondAddLock) {
bonds.Add(++bondID, new Bond(atomIndex, bondAtomNode.Value));
addedBonds.Add(bondKey);
//addBond(atom.Index, bondAtomNode.Value);
}
}
}
}
}