/// <summary>
/// load all parameters and symmetry operators
/// </summary>
public static void LoadSymOps(string symOpsFile)
{
symOps = new SymOps();
XmlSerializer xmlSerializer = new XmlSerializer(typeof(SymOps));
FileStream symOpsFileStream = new FileStream(symOpsFile, FileMode.Open);
symOps = (SymOps)xmlSerializer.Deserialize(symOpsFileStream);
}
private void FindDuplicateSpaceGroups(ref SymOps symOpList)
{
Dictionary <string, List <string> > sameSgHash = new Dictionary <string, List <string> > ();
string spaceGroup1 = "";
string spaceGroup2 = "";
for (int i = 0; i < symOpList.SymOpsInSpaceGroupList.Length - 1; i++)
{
spaceGroup1 = symOpList.SymOpsInSpaceGroupList[i].spaceGroup;
for (int j = i + 1; j < symOpList.SymOpsInSpaceGroupList.Length; j++)
{
spaceGroup2 = symOpList.SymOpsInSpaceGroupList[j].spaceGroup;
if (AreTwoSgStringsSame(symOpList.SymOpsInSpaceGroupList[i], symOpList.SymOpsInSpaceGroupList[j]))
{
// add spacegroup2 to the list of duplicate space group of sgMatrices1
if (sameSgHash.ContainsKey(spaceGroup1))
{
sameSgHash[spaceGroup1].Add(spaceGroup2);
}
else
{
List <string> sgList = new List <string> ();
sgList.Add(spaceGroup2);
sameSgHash.Add(spaceGroup1, sgList);
}
// add spacegroup1 to duplicate space group list of sg2
if (sameSgHash.ContainsKey(spaceGroup2))
{
sameSgHash[spaceGroup2].Add(spaceGroup1);
}
else
{
List <string> sgList = new List <string> ();
sgList.Add(spaceGroup1);
sameSgHash.Add(spaceGroup2, sgList);
}
}
}
}
foreach (SpaceGroupSymmetryMatrices sgMatrices in symOpList.SymOpsInSpaceGroupList)
{
if (sameSgHash.ContainsKey(sgMatrices.spaceGroup))
{
foreach (string sgString in sameSgHash[sgMatrices.spaceGroup])
{
sgMatrices.sameSgListString += (sgString + ";");
}
sgMatrices.sameSgListString = sgMatrices.sameSgListString.TrimEnd(';');
}
}
}
/// <summary>
/// load all parameters and symmetry operators
/// </summary>
public static void LoadSymOps()
{
if (!File.Exists(symOpsFile))
{
throw new Exception("Symmetry operators file not exist");
}
symOps = new SymOps();
XmlSerializer xmlSerializer = new XmlSerializer(typeof(SymOps));
FileStream symOpsFileStream = new FileStream(symOpsFile, FileMode.Open);
symOps = (SymOps)xmlSerializer.Deserialize(symOpsFileStream);
symOpsFileStream.Close();
}
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();
}
