private void PossiblySetCellParams(double a, double b, double c, double alpha, double beta, double gamma)
{
if (a != 0.0 && b != 0.0 && c != 0.0 && alpha != 0.0 && beta != 0.0 && gamma != 0.0)
{
Trace.TraceInformation("Found and set crystal cell parameters");
var axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
}
public void TestRoundTrip()
{
Crystal crystal = new Crystal();
double a = 3.0;
double b = 5.0;
double c = 7.0;
double alpha = 90.0;
double beta = 110.0;
double gamma = 100.0;
var axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
// serialazing
StringWriter sWriter = new StringWriter();
ShelXWriter resWriter = new ShelXWriter(sWriter);
resWriter.Write(crystal);
resWriter.Close();
string resContent = sWriter.ToString();
// deserialazing
ShelXReader resReader = new ShelXReader(new StringReader(resContent));
ICrystal rCrystal = (ICrystal)resReader.Read(new Crystal());
// OK, do checking
Assert.IsNotNull(rCrystal);
Assert.AreEqual(crystal.A.X, rCrystal.A.X, 0.001);
Assert.AreEqual(crystal.A.Y, rCrystal.A.Y, 0.001);
Assert.AreEqual(crystal.A.Z, rCrystal.A.Z, 0.001);
Assert.AreEqual(crystal.B.X, rCrystal.B.X, 0.001);
Assert.AreEqual(crystal.B.Y, rCrystal.B.Y, 0.001);
Assert.AreEqual(crystal.B.Z, rCrystal.B.Z, 0.001);
Assert.AreEqual(crystal.C.X, rCrystal.C.X, 0.001);
Assert.AreEqual(crystal.C.Y, rCrystal.C.Y, 0.001);
Assert.AreEqual(crystal.C.Z, rCrystal.C.Z, 0.001);
}
private ICrystal ReadCrystal(ICrystal crystal)
{
string line = input.ReadLine();
bool end_found = false;
while (line != null && !end_found)
{
/* is line continued? */
if (line.Length > 0 && line.Substring(line.Length - 1).Equals("=", StringComparison.Ordinal))
{
/* yes, line is continued */
line = line + input.ReadLine();
}
/* determine ShelX command */
string command;
try
{
command = line.Substring(0, 4);
}
catch (ArgumentOutOfRangeException)
{
// disregard this line
break;
}
Debug.WriteLine($"command: {command}");
var u_command = command.ToUpperInvariant();
if (u_command.StartsWith("REM", StringComparison.Ordinal))
{
/* line is comment, disregard */
/* 7.1 Crystal data and general instructions */
}
else if (u_command.StartsWith("END", StringComparison.Ordinal))
{
end_found = true;
}
else
{
switch (u_command)
{
case "TITL":
break;
case "CELL":
{
// example: CELL 1.54184 23.56421 7.13203 18.68928 90.0000
// 109.3799 90.0000 CELL 1.54184 7.11174 21.71704 30.95857
// 90.000 90.000 90.000
var st = Strings.Tokenize(line);
//st[0]; // string command_again
//st[1]; // string wavelength
string sa = st[2];
string sb = st[3];
string sc = st[4];
string salpha = st[5];
string sbeta = st[6];
string sgamma = st[7];
Debug.WriteLine($"a: {sa}");
Debug.WriteLine($"b: {sb}");
Debug.WriteLine($"c: {sc}");
Debug.WriteLine($"alpha: {salpha}");
Debug.WriteLine($"beta : {sbeta}");
Debug.WriteLine($"gamma: {sgamma}");
double a = FortranFormat.Atof(sa);
double b = FortranFormat.Atof(sb);
double c = FortranFormat.Atof(sc);
double alpha = FortranFormat.Atof(salpha);
double beta = FortranFormat.Atof(sbeta);
double gamma = FortranFormat.Atof(sgamma);
Vector3[] axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
break;
case "ZERR":
case "LATT":
case "SYMM":
case "SFAC":
case "DISP":
case "UNIT":
case "LAUE":
case "REM ":
case "MORE":
case "TIME":
/* 7.2 Reflection data input */
case "HKLF":
case "OMIT":
case "SHEL":
case "BASF":
case "TWIN":
case "EXTI":
case "SWAT":
case "HOPE":
case "MERG":
/* 7.3 Atom list and least-squares constraints */
case "SPEC":
case "RESI":
case "MOVE":
case "ANIS":
case "AFIX":
case "HFIX":
case "FRAG":
case "FEND":
case "EXYZ":
//case "EXTI":
case "EADP":
case "EQIV":
/* 7.4 The connectivity list */
case "CONN":
case "PART":
case "BIND":
case "FREE":
/* 7.5 Least-squares restraints */
case "DFIX":
case "DANG":
case "BUMP":
case "SAME":
case "SADI":
case "CHIV":
case "FLAT":
case "DELU":
case "SIMU":
case "DEFS":
case "ISOR":
case "NCSY":
case "SUMP":
/* 7.6 Least-squares organization */
case "L.S.":
case "CGLS":
case "BLOC":
case "DAMP":
case "STIR":
case "WGHT":
case "FVAR":
/* 7.7 Lists and tables */
case "BOND":
case "CONF":
case "MPLA":
case "RTAB":
case "HTAB":
case "LIST":
case "ACTA":
case "SIZE":
case "TEMP":
case "WPDB":
/* 7.8 Fouriers, peak search and lineprinter plots */
case "FMAP":
case "GRID":
case "PLAN":
break;
case "MOLE":
/* NOT DOCUMENTED BUT USED BY PLATON */
break;
case "SPGR":
{
// Line added by PLATON stating the spacegroup
var st = Strings.Tokenize(line);
//st[0]; // string command_again
string spacegroup = st[1];
crystal.SpaceGroup = spacegroup;
}
break;
case " ":
{
Debug.WriteLine($"Disrgarding line assumed to be added by PLATON: {line}");
/* All other is atom */
}
break;
default:
{
//Debug.WriteLine($"Assumed to contain an atom: {line}");
// this line gives an atom, because all lines not starting with
// a ShelX command is an atom (that sucks!)
var st = Strings.Tokenize(line);
string atype = st[0];
//st[1]; // string scatt_factor
string sa = st[2];
string sb = st[3];
string sc = st[4];
// skip the rest
if (char.IsDigit(atype[1]))
{
// atom type has a one letter code
atype = atype.Substring(0, 1);
}
else
{
var sb2 = new StringBuilder();
sb2.Append(atype[1]);
atype = atype.Substring(0, 1) + sb2.ToString().ToLowerInvariant();
}
double[] frac = new double[3];
frac[0] = FortranFormat.Atof(sa); // fractional coordinates
frac[1] = FortranFormat.Atof(sb);
frac[2] = FortranFormat.Atof(sc);
Debug.WriteLine("fa,fb,fc: " + frac[0] + ", " + frac[1] + ", " + frac[2]);
if (string.Equals(atype, "Q", StringComparison.OrdinalIgnoreCase))
{
// ingore atoms named Q
}
else
{
Trace.TraceInformation("Adding atom: " + atype + ", " + frac[0] + ", " + frac[1] + ", " + frac[2]);
IAtom atom = crystal.Builder.NewAtom(atype);
atom.FractionalPoint3D = new Vector3(frac[0], frac[1], frac[2]);
crystal.Atoms.Add(atom);
Debug.WriteLine($"Atom added: {atom}");
}
}
break;
}
}
line = input.ReadLine();
}
return(crystal);
}
