public void FindAtoms(WannierData retval)
{
const int size = 4;
Vector3 origin = retval.Grid.Origin;
Vector3[] span = retval.Grid.SpanVectors;
oldFindAtoms(retval);
List<Atom> atoms = new List<Atom>();
foreach (Atom atom in sites)
{
for (int k = -size; k <= size; k++)
{
for (int j = -size; j <= size; j++)
{
for (int i = -size; i <= size; i++)
{
Vector3 v = i * lattice[0] + j * lattice[1] + k * lattice[2];
Vector3 loc = atom.Position + v;
loc -= origin;
bool bad = false;
for (int l = 0; l < 3; l++)
{
double dot = span[l].DotProduct(loc);
double dist = dot / span[l].Magnitude;
if (dot < 0) bad = true;
if (dist > span[l].Magnitude) bad = true;
}
if (bad)
continue;
Atom a = new Atom();
a.Element = atom.Element;
a.Position = loc;
atoms.Add(a);
}
}
}
}
retval.Atoms.Clear();
retval.Atoms.AddRange(atoms);
}
private void ReadAtomPositions(StreamReader reader, WannierData retval, int count, int number)
{
if (number > 0)
{
ReadToComment(reader);
return;
}
for (int i = 0; i < count; i++)
{
Vector3 p = Vector3.Parse(ReadNextLine(reader));
Atom a = new Atom();
a.Position = p;
retval.Atoms.Add(a);
}
ReadToComment(reader);
}
int AtomSorter(Atom a, Atom b)
{
if (a.Element != b.Element)
return a.Element.CompareTo(b.Element);
int val = a.Position.Z.CompareTo(b.Position.Z);
val = (val == 0) ? a.Position.Y.CompareTo(b.Position.Y) : val;
val = (val == 0) ? a.Position.X.CompareTo(b.Position.X) : val;
return val;
}
internal void ReadAtomSites(System.IO.StreamReader reader, Fplo8Data data, int count)
{
if (count == 0)
throw new ArgumentException("Number of sites can't be zero.");
for (int i = 0; i < count; i++)
{
string line = reader.ReadLine().Trim();
string[] text = line.Split(new char[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
Atom a = new Atom();
a.Element = text[1];
int len = text.Length;
a.Position = Vector3.Parse(text[len - 3], text[len - 2], text[len - 1]);
sites.Add(a);
}
}
