public bool CheckModeWithHess(MatrixByArr hess, double[] masses, ILinAlg la, Mode[] modes = null, double tolerance = 0.00001)
{
if (modes == null)
{
modes = ToModes(masses);
}
HessMatrix ohess = new HessMatrixDense
{
hess = modes.GetHessian(masses, la),
};
double corr = HMath.HCorr(hess.ToArray().HToArray1D(), ohess.ToArray().HToArray1D());
System.Console.Write("corr(TestHess,HessVibr:{0} ", corr);
{
HDebug.Assert(hess.ColSize == ohess.ColSize);
HDebug.Assert(hess.RowSize == ohess.RowSize);
double ltolerance = hess.ToArray().HAbs().HMax() * tolerance;
ltolerance = tolerance;
for (int c = 0; c < ohess.ColSize; c++)
{
for (int r = 0; r < ohess.RowSize; r++)
{
double v = hess[c, r];
double mwv = ohess[c, r];
double diff = Math.Abs(v - mwv);
if (diff >= ltolerance)
{
return(false);
}
}
}
}
//{
// Matrix vhess = hess / hess.ToArray().HToArray1D().HVar();
// Matrix vohess = ohess / ohess.ToArray().HToArray1D().HVar();
//
// HDebug.Assert(hess.ColSize == ohess.ColSize);
// HDebug.Assert(hess.RowSize == ohess.RowSize);
// HDebug.Assert(vhess.Size == vohess.Size);
// for(int c=0; c<vhess.ColSize; c++)
// for(int r=0; r<vhess.RowSize; r++)
// {
// double v = vhess[c,r];
// double vo = vohess[c,r];
// double diff = Math.Abs(v - vo);
// if(diff >= tolerance)
// {
// HDebug.Assert(false);
// return false;
// }
// }
//}
return(true);
}
public static double[] GetRotAngles(Universe univ
, Vector[] coords
, Vector[] dcoords
, MatrixByArr J = null
, Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = null
, List <Universe.RotableInfo> univ_rotinfos = null
, Vector[] dcoordsRotated = null
)
{
if (J == null)
{
if (univ_rotinfos == null)
{
if (univ_flexgraph == null)
{
univ_flexgraph = univ.BuildFlexibilityGraph();
}
univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
}
J = TNM.GetJ(univ, coords, univ_rotinfos);
}
double[] dangles;
using (new Matlab.NamedLock("TEST"))
{
Matlab.Clear("TEST");
Matlab.PutVector("TEST.R", Vector.FromBlockvector(dcoords));
Matlab.PutMatrix("TEST.J", J.ToArray(), true);
Matlab.PutVector("TEST.M", univ.GetMasses(3));
Matlab.Execute("TEST.M = diag(TEST.M);");
Matlab.Execute("TEST.invJMJ = inv(TEST.J' * TEST.M * TEST.J);");
Matlab.Execute("TEST.A = TEST.invJMJ * TEST.J' * TEST.M * TEST.R;"); // (6) of TNM paper
dangles = Matlab.GetVector("TEST.A");
if (dcoordsRotated != null)
{
HDebug.Assert(dcoordsRotated.Length == dcoords.Length);
Matlab.Execute("TEST.dR = TEST.J * TEST.A;");
Vector ldcoordsRotated = Matlab.GetVector("TEST.dR");
HDebug.Assert(ldcoordsRotated.Size == dcoordsRotated.Length * 3);
for (int i = 0; i < dcoordsRotated.Length; i++)
{
int i3 = i * 3;
dcoordsRotated[i] = new double[] { ldcoordsRotated[i3 + 0], ldcoordsRotated[i3 + 1], ldcoordsRotated[i3 + 2] };
}
}
Matlab.Clear("TEST");
}
return(dangles);
}
public static void ToFile(string filepath
, IList <Atom> atoms
, IList <Vector> coords = null
, IList <MatrixByArr> anisous = null
, double?anisouScale = null
, IList <double> bfactors = null
, bool append = false
, IList <string> headers = null
, int?modelidx = null
)
{
List <string> lines = new List <string>();
int size = atoms.Count;
if (coords != null)
{
HDebug.Assert(size == coords.Count);
}
if (anisous != null)
{
HDebug.Assert(size == anisous.Count);
}
//if(anisouScale != null) Debug.Assert(size == anisouScale.Count);
if (headers != null)
{
lines.AddRange(headers);
}
{
// 1 2 3 4 5 6 7 8
// 12345678901234567890123456789012345678901234567890123456789012345678901234567890
// "MODEL 1 "
string line = "MODEL 1 ";
if (modelidx != null)
{
line.Replace("1", modelidx.Value.ToString());
}
line = line.Substring(0, 80);
lines.Add(line);
}
for (int i = 0; i < size; i++)
{
Atom atom = atoms[i];
if (atom == null)
{
continue;
}
{
if (coords != null)
{
double x = coords[i][0];
double y = coords[i][1];
double z = coords[i][2];
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
}
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[i]));
}
lines.Add(atom.line);
}
{
if (anisous != null)
{
MatrixByArr U = anisous[i];
if (anisouScale != null)
{
U = U * anisouScale.Value;
}
Anisou anisou = Anisou.FromAtom(atom, U.ToArray().HToInt());
string line = anisou.line; //anisou.GetUpdatedU(anisous[i])
lines.Add(line);
}
}
}
lines.Add("ENDMDL ");
//int idx = 0;
//foreach(Element element in elements)
//{
// string line = element.line;
// if(typeof(Atom).IsInstanceOfType(element))
// {
// double x = coords[idx][0];
// double y = coords[idx][1];
// double z = coords[idx][2];
// Atom atom = (Atom)element;
// line = atom.GetUpdatedLine(x, y, z);
// idx++;
// }
// lines.Add(line);
//}
if (append == false)
{
HFile.WriteAllLines(filepath, lines);
}
else
{
StringBuilder text = new StringBuilder();
foreach (string line in lines)
{
text.AppendLine(line);
}
HFile.AppendAllText(filepath, text.ToString());
}
}
