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 GetHessSbNMA
(Universe univ
, IList <Vector> coords
, double nbondMaxDist // =12
, double?maxAbsSpring
, bool b_bonds
, bool b_angles
, bool b_impropers
, bool b_dihedrals
, bool b_nonbondeds
, bool b_nonbonded14s
, double?sca_bonds
, double?sca_angles
, double?sca_impropers
, double?sca_dihedrals
, double?sca_nonbondeds
, double?sca_nonbonded14s
, Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorBond
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorAngle
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorImproper
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorDihedral
, Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorNonbonded
, Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorNonbonded14
, Func <HessSpr.CustomKijInfo, double> GetCustomKij = null
, params string[] options
)
{
IEnumerable <Universe.Nonbonded> nonbondeds = null;
IEnumerable <Universe.Nonbonded14> nonbonded14s = univ.nonbonded14s.GetEnumerable();
if (options.Contains("TIP3P: tetrahedral hydrogen bonds"))
{
nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist, ListTip3pTetraHBond, options);
}
else if (options.Contains("TIP3P: near waters"))
{
nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist, ListTip3pNears, options);
}
else
{
nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist);
}
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)
double?K_r = null; // null for sbNMA, and 340.00 for ssNMA
double?K_theta = null; // null for sbNMA, and 45.00 for ssNMA
double?K_ub = null; // null for sbNMA, and 10.00 for ssNMA
double?K_psi = null; // null for sbNMA, and 70.00 for ssNMA
double?K_chi = null; // null for sbNMA, and 1.00 for ssNMA
double?n = null; // null for sbNMA, and 1 for ssNMA
string K_nbnd = null; // null for sbNMA, and "Unif" for ssNMA
if (options.Contains("TIP3P: (vdW+elec) for OH,OO,HH"))
{
K_nbnd = "TIP3P: (vdW+elec) for OH,OO,HH";
}
if (options.Contains("TIP3P: (vdW+elec) for OH"))
{
K_nbnd = "TIP3P: (vdW+elec) for OH";
}
if (options.Contains("vdW:L79"))
{
K_nbnd = "L79";
}
if (options.Contains("vdW:UnifSgn"))
{
K_nbnd = "UnifSgn";
}
if (options.Contains("K_chi:1"))
{
K_chi = 1;
}
HessMatrix hess = null;
if (b_bonds)
{
hess = STeM.GetHessBond(coords, univ.bonds, K_r: K_r, hessian: hess, collector: collectorBond);
}
if (b_angles)
{
hess = STeM.GetHessAngle(coords, univ.angles, true, K_theta: K_theta, K_ub: K_ub, hessian: hess, collector: collectorAngle);
}
if (b_impropers)
{
hess = STeM.GetHessImproper(coords, univ.impropers, K_psi: K_psi, hessian: hess, useArnaud96: true, collector: collectorImproper);
}
if (b_dihedrals)
{
hess = STeM.GetHessDihedral(coords, univ.dihedrals, K_chi: K_chi, n: n, hessian: hess, useAbsSpr: true, useArnaud96: true, collector: collectorDihedral);
}
if (b_nonbondeds)
{
hess = HessSpr.GetHessNonbond(coords, nonbondeds, D, K_nbnd: K_nbnd, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring, collector: collectorNonbonded, GetCustomKij: GetCustomKij);
}
if (b_nonbonded14s)
{
hess = HessSpr.GetHessNonbond(coords, nonbonded14s, D, K_nbnd: K_nbnd, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring, collector: collectorNonbonded14, GetCustomKij: GetCustomKij);
}
if (sca_bonds != null)
{
if (sca_bonds.Value != 1)
{
hess += (sca_bonds.Value - 1) * STeM.GetHessBond(coords, univ.bonds, K_r: K_r, hessian: null);
}
}
if (sca_angles != null)
{
if (sca_angles.Value != 1)
{
hess += (sca_angles.Value - 1) * STeM.GetHessAngle(coords, univ.angles, true, K_theta: K_theta, K_ub: K_ub, hessian: null);
}
}
if (sca_impropers != null)
{
if (sca_impropers.Value != 1)
{
hess += (sca_impropers.Value - 1) * STeM.GetHessImproper(coords, univ.impropers, K_psi: K_psi, hessian: null, useArnaud96: true);
}
}
if (sca_dihedrals != null)
{
if (sca_dihedrals.Value != 1)
{
hess += (sca_dihedrals.Value - 1) * STeM.GetHessDihedral(coords, univ.dihedrals, K_chi: K_chi, n: n, hessian: null, useAbsSpr: true, useArnaud96: true);
}
}
if (sca_nonbondeds != null)
{
if (sca_nonbondeds.Value != 1)
{
hess += (sca_nonbondeds.Value - 1) * HessSpr.GetHessNonbond(coords, nonbondeds, D, K_nbnd: K_nbnd, hessian: null, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
}
}
if (sca_nonbonded14s != null)
{
if (sca_nonbonded14s.Value != 1)
{
hess += (sca_nonbonded14s.Value - 1) * HessSpr.GetHessNonbond(coords, nonbonded14s, D, K_nbnd: K_nbnd, hessian: null, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring);
}
}
//Hess.UpdateHessNaN(hess, coords);
{
foreach (var bc_br_bval in hess.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
var bval = bc_br_bval.Item3;
if (coords[bc] == null)
{
throw new HException("have hess block for null-coord");
}
if (coords[br] == null)
{
throw new HException("have hess block for null-coord");
}
if (bval == null)
{
throw new HException();
}
for (int c = 0; c < bval.ColSize; c++)
{
for (int r = 0; r < bval.RowSize; r++)
{
double val = bval[c, r];
if (double.IsNaN(val))
{
throw new HException("hess has nan element");
}
if (double.IsPositiveInfinity(val))
{
throw new HException("hess has pos-inf element");
}
if (double.IsNegativeInfinity(val))
{
throw new HException("hess has neg-inf element");
}
}
}
}
}
return(new HessInfo
{
hess = hess,
mass = univ.GetMasses(),
atoms = univ.atoms.ToArray(),
coords = coords.HCloneVectors().ToArray(),
numZeroEigval = 6,
});
}