public static HessMatrix GetHessApproxAnm(Vector[] coords, HessMatrix hess, string option, ILinAlg ila)
{
int nresi = coords.Length;
HDebug.Assert(nresi * 3 == hess.ColSize);
HDebug.Assert(nresi * 3 == hess.RowSize);
double[,] Kij = new double[nresi, nresi];
for (int c = 0; c < nresi; c++)
{
for (int r = c + 1; r < nresi; r++)
{
HessMatrix anmCR = Hess.GetHessAnm(coords.HSelectByIndex(new int[] { c, r }));
//Matrix anmCR = anm.SubMatrix(new int[] { 0, 1, 2 }, new int[] { 3, 4, 5 });
int[] idxs = new int[] { c *3 + 0, c *3 + 1, c *3 + 2, r *3 + 0, r *3 + 1, r *3 + 2 };
HessMatrix hessCR = new HessMatrixDense {
hess = hess.SubMatrix(idxs, idxs)
};
hessCR = Hess.CorrectHessDiag(hessCR);
Vector vecHessCR = hessCR.GetColVectorList().ToVector();
Vector vecAnmCR = anmCR.GetColVectorList().ToVector();
double Kcr;
switch (option)
{
case "match magnitude": Kcr = vecHessCR.Dist / vecAnmCR.Dist; break;
case "least-mean square": Kcr = LinAlg.VtV(vecAnmCR, vecHessCR) / LinAlg.VtV(vecAnmCR, vecAnmCR); break;
default: throw new NotImplementedException();
}
if (Kcr < 0)
{
HDebug.Assert(false);
}
HDebug.Assert(Kcr >= 0);
double mag2cahessCR = vecAnmCR.Dist;
double mag2caAnmCR = vecHessCR.Dist;
double mag2caAnmCRx = (Kcr * anmCR).GetColVectorList().ToVector().Dist;
Kij[c, r] = Kij[r, c] = Kcr;
}
}
//return Kij;
return(Hess.GetHessAnm(coords, Kij));
throw new NotImplementedException();
}
public static HessMatrix GetHess(Universe univ)
{
Vector[] coords = univ.GetCoords();
HessMatrix hessian_spr = HessMatrixSparse.ZerosSparse(univ.size * 3, univ.size * 3);
Universe.Nonbondeds_v1 nonbondeds = new Universe.Nonbondeds_v1(univ.atoms, univ.size, 12);
nonbondeds.UpdateNonbondeds(coords, 0);
hessian_spr = STeM.GetHessBond(coords, univ.bonds, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with bond"));
hessian_spr = STeM.GetHessAngle(coords, univ.angles, true, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with angle"));
hessian_spr = STeM.GetHessImproper(coords, univ.impropers, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with improper"));
hessian_spr = STeM.GetHessDihedral(coords, univ.dihedrals, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with dihedral"));
hessian_spr = STeM.GetHessVdw(coords, univ.nonbonded14s.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw14"));
hessian_spr = STeM.GetHessElec(coords, univ.nonbonded14s.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec14"));
hessian_spr = STeM.GetHessVdw(coords, nonbondeds.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw"));
hessian_spr = STeM.GetHessElec(coords, nonbondeds.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec"));
//hessian_spr = GetHessSprElec(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
//hessian_spr = GetHessSprVdw(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
hessian_spr = Hess.CorrectHessDiag(hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr"));
return(hessian_spr);
}
public HessMatrix CorrectHessDiag()
{
return(Hess.CorrectHessDiag(this));
}
