/// <summary>
/// two space group sym OPs are same
/// </summary>
/// <param name="sgMatrices1"></param>
/// <param name="sgMatrices2"></param>
/// <returns></returns>
private bool AreTwoSgStringsSame(SpaceGroupSymmetryMatrices sgMatrices1, SpaceGroupSymmetryMatrices sgMatrices2)
{
string fullSymOpString1 = GetFullSymOpStringForAllSymOps(sgMatrices1);
string fullSymOpString2 = GetFullSymOpStringForAllSymOps(sgMatrices2);
if (string.Compare(fullSymOpString1, fullSymOpString2) == 0)
{
return(true);
}
return(false);
}
/// <summary>
///
/// </summary>
/// <param name="sgOpMatrices"></param>
/// <returns></returns>
private string GetFullSymOpStringForAllSymOps(SpaceGroupSymmetryMatrices sgOpMatrices)
{
string[] fullSymOpListStrings = new string [sgOpMatrices.SymmetryOpList.Length];
for (int i = 0; i < fullSymOpListStrings.Length; i++)
{
fullSymOpListStrings[i] = sgOpMatrices.SymmetryOpList[i].fullSymmetryString;
}
Array.Sort(fullSymOpListStrings);
string fullSymOpString = "";
foreach (string symOpString in fullSymOpListStrings)
{
fullSymOpString += symOpString;
}
return(fullSymOpString);
}
public void ParseSymOpsFile(string fileName)
{
SymOps symOpList = new SymOps();
string line = "";
int symOpNum = 0;
int dimNum = 3;
int vectNum = 2;
SpaceGroupSymmetryMatrices sgSymMatrices = null;
StreamReader fileReader = new StreamReader(fileName);
string preSg = "";
string currentSg = "";
while ((line = fileReader.ReadLine()) != null)
{
// skip notation
line = line.Trim();
if (line == "" ||
line.ToLower().IndexOf("space_group") > -1 ||
line.ToLower().IndexOf("loop") > -1)
{
continue;
}
// skip comments
if (line[0] == '#')
{
continue;
}
// remove space
currentSg = line.Substring(line.IndexOf("'") + 1, line.LastIndexOf("'") - line.IndexOf("'") - 1);
line = line.Substring(line.LastIndexOf("'") + 1, line.Length - line.LastIndexOf("'") - 1).Trim();
// start new space group,
// add previous one
if (currentSg != preSg)
{
// add symmetry operations of a space group
if (sgSymMatrices != null)
{
symOpList.Add(sgSymMatrices);
}
sgSymMatrices = new SpaceGroupSymmetryMatrices();
sgSymMatrices.spaceGroup = currentSg;
}
SymOpMatrix symOpMatrix = new SymOpMatrix();
string[] fields = ParseHelper.SplitPlus(line, ' ');
symOpMatrix.symmetryOpNum = fields[0];
symOpNum = Convert.ToInt32(fields[0]);
symOpMatrix.symmetryString = symOpNum.ToString() + "_555";
// set 3*3 matrix
int i = 1;
for (; i < 10; i++)
{
symOpMatrix.Add((int)Math.Floor((double)(i - 1) / (double)dimNum), (i - 1) % dimNum, Convert.ToDouble(fields[i]));
}
// set matrix vector
string denominator = "";
string nominator = "";
int dim = 0;
for (; i < fields.Length; i += vectNum)
{
denominator = fields[i];
nominator = fields[i + 1];
if (nominator == "0")
{
symOpMatrix.Add(dim, 3, 0);
}
else
{
symOpMatrix.Add(dim, 3, Convert.ToDouble(denominator) / Convert.ToDouble(nominator));
}
dim++;
}
// format full symmetry string from symmetry matrix
symOpMatrix.fullSymmetryString = symOpMatrix.ToFullSymString();
sgSymMatrices.Add(symOpMatrix);
symOpMatrix = new SymOpMatrix();
preSg = currentSg;
}
if (sgSymMatrices != null)
{
// add the last space group
symOpList.Add(sgSymMatrices);
}
FindDuplicateSpaceGroups(ref symOpList);
XmlSerializer xmlSerializer = new XmlSerializer(symOpList.GetType());
TextWriter symOpWriter = new StreamWriter("symOps.xml", false);
xmlSerializer.Serialize(symOpWriter, symOpList);
symOpWriter.Close();
}
