public static HessInfo GetHessSsNMA
(Universe univ
, IList <Vector> coords
, IEnumerable <Universe.Bond> bonds
, IEnumerable <Universe.Angle> angles
, IEnumerable <Universe.Improper> impropers
, IEnumerable <Universe.Dihedral> dihedrals
, IEnumerable <Universe.Nonbonded> nonbondeds
, IEnumerable <Universe.Nonbonded14> nonbonded14s
, double?maxAbsSpring = null
, double?K_r = 340.00
, double?K_theta = 45.00
, double?K_ub = 10.00
, double?K_psi = 70.00
, double?K_chi = 1.00
, double?n = 1
, string k_vdW = "Unif"
//, bool setNanForEmptyAtom // =true
)
{
bool vdW = true; // use vdW
bool elec = false; // ignore electrostatic
double D = double.PositiveInfinity; // dielectric constant for Tinker is "1"
bool ignNegSpr = true; // ignore negative spring (do not add the spring into hessian matrix)
//maxAbsSpring = Math.Pow(10, 9);
HessMatrix hess = null;
hess = STeM.GetHessBond(coords, bonds, K_r, hessian: hess);
hess = STeM.GetHessAngle(coords, angles, true, K_theta, K_ub, hessian: hess);
hess = STeM.GetHessImproper(coords, impropers, K_psi, hessian: hess, useArnaud96: true);
hess = STeM.GetHessDihedral(coords, dihedrals, K_chi, n, hessian: hess, useAbsSpr: true, useArnaud96: true);
hess = HessSpr.GetHessNonbond(coords, nonbondeds, D, k_vdW, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
hess = HessSpr.GetHessNonbond(coords, nonbonded14s, D, k_vdW, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
//if(setNanForEmptyAtom)
Hess.UpdateHessNaN(hess, coords);
return(new HessInfo
{
hess = hess,
mass = univ.GetMasses(),
atoms = univ.atoms.ToArray(),
coords = coords.HCloneVectors().ToArray(),
numZeroEigval = 6,
});
}
public static HessInfo GetHessEAnm
(Universe univ
, IList <Vector> coords
, IEnumerable <Tuple <int, int, double> > enumKij
, bool b_bonds
, bool b_angles
, bool b_impropers
, bool b_dihedrals
)
{
//bool vdW = true; // use vdW
//bool elec = false; // ignore electrostatic
//double D = double.PositiveInfinity; // dielectric constant for Tinker is "1"
//bool ignNegSpr = true; // ignore negative spring (do not add the spring into hessian matrix)
HessMatrix hess = null;
hess = Hess.GetHessAnm(coords, enumKij);
if (b_bonds)
{
hess = STeM.GetHessBond(coords, univ.bonds, 340.00, hessian: hess);
}
if (b_angles)
{
hess = STeM.GetHessAngle(coords, univ.angles, true, 45.00, 10.00, hessian: hess);
}
if (b_impropers)
{
hess = STeM.GetHessImproper(coords, univ.impropers, 70.00, hessian: hess, useArnaud96: true);
}
if (b_dihedrals)
{
hess = STeM.GetHessDihedral(coords, univ.dihedrals, 1.00, 1, hessian: hess, useAbsSpr: true, useArnaud96: true);
}
Hess.UpdateHessNaN(hess, coords);
return(new HessInfo
{
hess = hess,
mass = univ.GetMasses(),
atoms = univ.atoms.ToArray(),
coords = coords.HCloneVectors().ToArray(),
numZeroEigval = 6,
});
}
public static void UpdateHessNaN(HessMatrix hess, IList <Vector> coords)
{
int[] idxNaN = coords.HIndexOfNull();
Hess.UpdateHessNaN(hess, idxNaN);
}
