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);
}
internal void oldFindAtoms(WannierData retval)
{
for (int i = 0; i < 3; i++)
{
if (lattice[i].Magnitude == 0)
throw new InvalidOperationException("Lattice vectors have not been read.");
}
if (sites.Count == 0)
throw new InvalidOperationException("Atom sites have not been read.");
for (int i = 0; i < retval.Atoms.Count; i++)
{
Atom a = retval.Atoms[i];
Vector3 red = ReduceRealSpace(a.Position);
double minDist = double.MaxValue;
Atom minSite = null;
for (int j = 0; j < sites.Count; j++)
{
Vector3 site_red = ReduceRealSpace(sites[j].Position);
Vector3 diff = red - site_red;
for (int k = 0; k < 3; k++)
{
if (Math.Abs(diff[k] - 1) < 1e-5)
diff[k] = 0;
}
if (diff.Magnitude < minDist)
{
minDist = diff.Magnitude;
minSite = sites[j];
}
}
if (minDist > 1e-6)
throw new Exception(string.Format("Could not find atom {0}.", i));
a.Element = minSite.Element;
}
}
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);
}
private void WriteData(WannierData data)
{
foreach (var wan in data.WannierFunctions)
{
string filename = string.Format("wan{0}.xsf", wan.Name);
filename = filename.Replace(" ", "_");
Grid grid = data.Grid;
Console.WriteLine("Writing data to {0}", filename);
using (StreamWriter wr = new StreamWriter(filename))
{
wr.WriteLine("CRYSTAL");
wr.WriteLine("PRIMVEC");
for (int i = 0; i < 3; i++)
{
Vector3 span = grid.SpanVectors[i] * bohrToAng;
wr.WriteLine("{0} {1} {2}", span.X, span.Y, span.Z);
}
wr.WriteLine("PRIMCOORD");
wr.WriteLine("{0} 1", data.Atoms.Count);
foreach (var atom in data.Atoms)
{
Vector3 pos = atom.Position * bohrToAng;
wr.WriteLine("{0} {1} {2} {3}", atom.AtomicNumber, pos.X, pos.Y, pos.Z);
}
wr.WriteLine("BEGIN_BLOCK_DATAGRID3D");
wr.WriteLine("Wannier");
wr.WriteLine("BEGIN_DATAGRID_3D_Wannier");
wr.WriteLine("{0} {1} {2}", grid.GridSize[0], grid.GridSize[1], grid.GridSize[2]);
//wr.WriteLine("{0} {1} {2}", grid.Origin.X * bohrToAng, grid.Origin.Y * bohrToAng, grid.Origin.Z * bohrToAng);
wr.WriteLine("{0} {1} {2}", 0, 0, 0);
for (int i = 0; i < 3; i++)
{
Vector3 span = grid.SpanVectors[i] * bohrToAng;
wr.WriteLine("{0} {1} {2}", span.X, span.Y, span.Z);
}
int count = 0;
for (int k = 0; k < wan.Data.Depth; k++)
{
for (int j = 0; j < wan.Data.Height; j++)
{
for (int i = 0; i < wan.Data.Width; i++)
{
wr.Write("{0} ", wan.Data[i, j, k]);
count++;
if (count == 3)
{
wr.WriteLine();
count = 0;
}
}
}
}
wr.WriteLine("END_DATAGRID_3D");
wr.WriteLine("END_BLOCK_DATAGRID3D");
}
}
}
private void ReadWFnames(StreamReader reader, WannierData retval, int count)
{
while (retval.WannierFunctions.Count < count)
retval.WannierFunctions.Add(new WannierFunction());
for (int i = 0; i < count; i++)
{
string name = ReadNextLine(reader);
if (name.StartsWith("\"") && name.EndsWith("\""))
name = StripQuotes(name);
retval.WannierFunctions[i].Name = name;
}
}
private void ReadWFdata(StreamReader reader, WannierData retval, int count, int number)
{
List<double> data = new List<double>();
int lineCount = 0;
while (data.Count < count)
{
string line = ReadNextLine(reader);
string[] text = SplitLine(line);
double[] thisdata = ParseStringArray(text);
data.AddRange(thisdata);
lineCount++;
}
ReadToComment(reader);
WannierFunction fn = retval.WannierFunctions[number];
int index = 0;
for (int x = 0; x < fn.Data.Width; x++)
{
for (int y = 0; y < fn.Data.Height; y++)
{
for (int z = 0; z < fn.Data.Depth; z++)
{
fn.Data[x, y, z] = data[index];
index++;
}
}
}
}
private void ReadPositions(StreamReader reader, WannierData retval, string[] list)
{
int len = list.Length;
int xgrid = int.Parse(list[len - 3]);
int ygrid = int.Parse(list[len - 2]);
int zgrid = int.Parse(list[len - 1]);
for (int i = 0; i < retval.WannierFunctions.Count; i++)
{
retval.WannierFunctions[i].Data = new VolumeData(xgrid, ygrid, zgrid);
}
retval.Grid = new Grid();
retval.Grid.GridSize[0] = xgrid;
retval.Grid.GridSize[1] = ygrid;
retval.Grid.GridSize[2] = zgrid;
string[] text = SplitLine(ReadNextLine(reader));
retval.Grid.Origin = Vector3.Parse(text[1], text[2], text[3]);
for (int i = 0; i < 3; i++)
{
text = SplitLine(ReadNextLine(reader));
retval.Grid.Delta[i] = Vector3.Parse(text[1], text[2], text[3]);
}
ReadToComment(reader);
}
private void ReadJunkObject(StreamReader reader, WannierData retval, int count)
{
for (int i = 0; i < count; i++)
ReadNextLine(reader);
ReadNextLine(reader);
}
private void ReadFploInfo(StreamReader reader, WannierData retval)
{
Fplo8Data data = new Fplo8Data();
int count = 0;
while (reader.EndOfStream == false)
{
string line = reader.ReadLine();
if (line.StartsWith("lattice vectors"))
{
data.ReadLatticeVectors(reader, data);
}
if (line.StartsWith("Number of sites :"))
{
count = int.Parse(line.Substring(line.Length - 3));
}
if (line.StartsWith("No. Element WPS"))
{
data.ReadAtomSites(reader, data, count);
}
}
data.FindAtoms(retval);
}
private void ReadDXObject(StreamReader reader, string line, WannierData retval)
{
string[] list = GetMatches(line);
System.Diagnostics.Debug.Assert(list[0] == "object");
int shape = -1;
int count = -1;
for (int i = 2; i < list.Length; i++)
{
if (list[i] == "shape")
{
shape = int.Parse(list[i + 1]);
}
if (list[i] == "data")
{
count = int.Parse(list[i - 1]);
}
}
System.Diagnostics.Debug.Assert(list[1].StartsWith("\"") && list[1].EndsWith("\""));
string name = StripQuotes(list[1]);
int number;
string theclass = list[3];
if (int.TryParse(name.Substring(name.Length - 3, 3), out number))
{
name = name.Substring(0, name.Length - 3);
number--;
}
switch (theclass)
{
case "array":
switch (name)
{
case "wfnames":
Console.WriteLine("Reading names");
ReadWFnames(reader, retval, count);
break;
case "wfdata":
Console.WriteLine("Reading data for WF {0}", number);
ReadWFdata(reader, retval, count, number);
break;
case "atompositions":
Console.WriteLine("Reading atom positions for WF {0}", number);
ReadAtomPositions(reader, retval, count, number);
break;
case "dataradius":
case "datacolor":
case "atom":
Console.WriteLine("Skipping {0} {1}", name, number);
ReadToComment(reader);
break;
}
break;
case "gridpositions":
Console.WriteLine("Reading grid positions");
ReadPositions(reader, retval, list);
break;
case "series":
case "gridconnections":
case "field":
Console.WriteLine("Skipping {0}", name);
ReadToComment(reader);
break;
}
}
private WannierData ReadData()
{
WannierData retval = new WannierData();
InitRegex();
using (StreamReader reader = new StreamReader("opendxWF.dx"))
{
while (reader.EndOfStream == false)
{
string line = ReadNextLine(reader);
if (line.StartsWith("object"))
{
ReadDXObject(reader, line, retval);
}
else
throw new InvalidDataException("Could not understand line.");
}
}
using (StreamReader reader = new StreamReader("out"))
{
ReadFploInfo(reader, retval);
}
return retval;
}
