// same as above method but allows for custom max bond lengths
public Dictionary <int, Bond> CalculateBonds(Dictionary <int, Atom> atoms, Dictionary <ElementPair, float> maxBondLengths, int processorCores)
{
this.atoms = atoms;
this.maxBondLengths = maxBondLengths;
bonds = new Dictionary <int, Bond>();
tree = new KdTree <float, int>(3, new FloatMath());
addedBonds = new HashSet <string>();
bondID = 0;
UnityEngine.Debug.Log("Generating Atom Tree");
Stopwatch watch = new Stopwatch();
watch.Start();
foreach (KeyValuePair <int, Atom> atom in atoms)
{
tree.Add(new float[] { atom.Value.Position.x, atom.Value.Position.y, atom.Value.Position.z }, atom.Key);
}
watch.Stop();
UnityEngine.Debug.Log("Generated Atom Tree: " + watch.ElapsedMilliseconds.ToString("N2"));
watch.Reset();
watch.Start();
//for each atom find all linked atoms
List <Thread> threadList = new List <Thread>();
List <int> atomIndexes = atoms.Keys.ToList();
int threadCount = processorCores - 1;
if (threadCount <= 0)
{
threadCount = 1;
}
int maxAtomsPerThread = Mathf.Max(1, atomIndexes.Count / threadCount);
for (int i = 0; i < atomIndexes.Count; i += maxAtomsPerThread)
{
int threadAtomCount = maxAtomsPerThread;
if (i > atomIndexes.Count - threadAtomCount - 1)
{
threadAtomCount = atomIndexes.Count - i - 1;
}
List <int> threadAtoms = atomIndexes.GetRange(i, threadAtomCount);
Thread newThread = new Thread(findBonds);
newThread.Start(threadAtoms);
threadList.Add(newThread);
}
foreach (var thread in threadList)
{
thread.Join();
}
watch.Stop();
UnityEngine.Debug.Log("Generated Bond Results: " + watch.ElapsedMilliseconds.ToString("N2"));
watch.Reset();
return(bonds.ToDictionary(entry => entry.Key, entry => entry.Value));
}