public static HessMatrix GetHessHydroBond(Universe univ, IList <Vector> coords, bool ignNegSpr, double?constSpr, double thres_energy)
{
int size = coords.Count;
double[,] hbond_kij = new double[size, size];
foreach (var hbond in univ.EnumHydroBondIrback09(coords))
{
Universe.Atom Ni = hbond.Ni;
Universe.Atom Hi = hbond.Hi;
Universe.Atom Oj = hbond.Oj;
Universe.Atom Cj = hbond.Cj;
double hbond_energy = hbond.energy;
double hbond_spring = hbond.spring; // spring between Hi..Oj
if (Math.Abs(hbond_energy) < thres_energy)
{
continue;
}
if (ignNegSpr && (hbond_spring < 0))
{
continue;
}
if (constSpr != null)
{
hbond_spring = constSpr.Value;
}
int i = Hi.ID;
int j = Oj.ID;
hbond_kij[i, j] = hbond_spring;
hbond_kij[j, i] = hbond_spring;
}
HessMatrix hess_hbond = GetHessAnm(coords, hbond_kij);
return(hess_hbond);
}
