public Mode[] GetModes()
{ // determine eigvals and eigvecs
if (_modes != null)
{
return(_modes.HClone <Mode>());
}
MatrixByArr hess = MatrixByArr.FromMatrixArray(this.hess);
_modes = HBioinfo.GetModes(hess, cachebase + "Modes.data");
return(_modes.HClone <Mode>());
}
public Anisou[] GetAnisous()
{
if (_anisous != null)
{
return(_anisous);
}
MatrixByArr hess = MatrixByArr.FromMatrixArray(this.hess);
_anisous = Anisou.FromHessian(hess, masses, scale: 10000000, cachepath: cachebase + "Anisous.data");
//_anisous = Bioinfo.GetAnisou(GetModes(), masses, scale: 10000000);
return(_anisous);
}
static void UpdateMassWeightedHess(Matrix hess, Vector mass)
{
if (HDebug.Selftest())
//if(GetMassWeightedHess_selftest1)
#region selftest
{
//HDebug.ToDo("replace examplt not to use blocked hessian matrix");
//GetMassWeightedHess_selftest1 = false;
MatrixByArr[,] _bhess = new MatrixByArr[2, 2];
_bhess[0, 0] = new double[3, 3] {
{ 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 }
};
_bhess[0, 1] = _bhess[0, 0] + 10;
_bhess[1, 0] = _bhess[0, 0] + 20;
_bhess[1, 1] = _bhess[0, 0] + 30;
Vector _mass = new double[2] {
2, 3
};
MatrixByArr _hess = MatrixByArr.FromMatrixArray(_bhess);
Matrix _mwhess = GetMassWeightedHess(_hess, _mass);
MatrixByArr[,] _mwbhess = GetMassWeightedHess(_bhess, _mass);
HDebug.AssertTolerance(0.00000001, MatrixByArr.FromMatrixArray(_mwbhess) - _mwhess.ToArray());
}
#endregion
HDebug.Exception(hess.ColSize == mass.Size);
HDebug.Assert(hess.ColSize == hess.RowSize);
HDebug.Assert(hess.ColSize % 3 == 0);
Vector mass05 = mass.ToArray().HSqrt();
// mass weighted hessian
// MH = M^(-1/2) * H * M^(-1/2)
// MH_ij = H_IJ * sqrt(M[i] * M[j])
{
// mass weighted block hessian
for (int i = 0; i < hess.ColSize; i++)
{
for (int j = 0; j < hess.RowSize; j++)
{
//if(i == j) continue;
hess[i, j] = hess[i, j] / (mass05[i] * mass05[j]);
//mbhess[i, i] -= mbhess[i, j];
}
}
}
}
public static MatrixByArr GetJ(Universe univ, Vector[] coords, List <RotableInfo> rotInfos, string option = null)
{
switch (option)
{
case "mine":
{
MatrixByArr[,] J = TNM_mine.GetJ(univ, coords, rotInfos, fnInv3x3: null);
double tolerance = 0.00001;
HDebug.Assert(CheckEckartConditions(univ, coords, rotInfos, J, tolerance: tolerance));
//if(Debug.IsDebuggerAttachedWithProb(0.1))
//{
// Matrix J0 = Matrix.FromBlockmatrix(J);
// Matrix J1 = Matrix.FromBlockmatrix(GetJ(univ, coords, rotInfos, option:"paper", useNamedLock:false));
// Debug.AssertTolerance(0.00000001, J0 - J1);
//}
return(MatrixByArr.FromMatrixArray(J));
}
case "paper":
{
MatrixByArr[,] J = TNM_paper.GetJ(univ, coords, rotInfos);
HDebug.Assert(CheckEckartConditions(univ, coords, rotInfos, J, 0.0000001));
return(MatrixByArr.FromMatrixArray(J));
}
case "mineopt":
{
MatrixByArr J = TNM_mineopt.GetJ(univ, coords, rotInfos);
if (HDebug.IsDebuggerAttached && univ.GetMolecules().Length == 1)
{
MatrixByArr J0 = TNM.GetJ(univ, coords, rotInfos, option: "paper");
MatrixByArr dJ = J - J0;
//double tolerance = dJ.ToArray().HAbs().HToArray1D().Mean();
//double maxAbsDH = dJ.ToArray().HAbs().HMax();
//if(tolerance == 0)
// tolerance = 0.000001;
HDebug.AssertTolerance(0.00000001, dJ);
}
return(J);
}
case null:
// my implementation has smaller error while checking Eckart conditions
goto case "mineopt";
}
return(null);
}
