// ! Wildcards used to minimize memory requirements
// NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
// CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5
// !
// !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
// !
// !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
// !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
// !
// !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
// !
// HT 0.0 -0.0460 0.2245 ! TIP3P
// HN1 0.0 -0.0460 0.2245
// CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
// CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
// ...
/////////////////////////////////////////////////////////////
public virtual void Compute(Universe.Nonbonded14 nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
double radi = atom1.Rmin2_14; radi = (double.IsNaN(radi) == false) ? radi : atom1.Rmin2;
double radj = atom2.Rmin2_14; radj = (double.IsNaN(radj) == false) ? radj : atom2.Rmin2;
double epsi = atom1.eps_14; epsi = (double.IsNaN(epsi) == false) ? epsi : atom1.epsilon;
double epsj = atom2.eps_14; epsj = (double.IsNaN(epsj) == false) ? epsj : atom2.epsilon;
Compute(nonbonded, coords, ref energy, ref forces, ref hessian, radi, radj, epsi, epsj, pwfrc, pwspr);
}
public static PPotential Elec(Universe.Nonbonded14 nonbonded, Vector[] coords, double ee)
{
Universe.Atom atom1 = nonbonded.atoms[0]; Vector coord1 = coords[atom1.ID];
Universe.Atom atom2 = nonbonded.atoms[1]; Vector coord2 = coords[atom2.ID];
//double ee = 1; // 80
double pch1 = atom1.Charge;
double pch2 = atom2.Charge;
return(Elec(coord1, coord2, pch1, pch2, ee));
}
public static PPotential LJ(Universe.Nonbonded14 nonbonded, Vector[] coords)
{
Universe.Atom atom1 = nonbonded.atoms[0]; Vector coord1 = coords[atom1.ID];
Universe.Atom atom2 = nonbonded.atoms[1]; Vector coord2 = coords[atom2.ID];
double rad1 = atom1.Rmin2_14; rad1 = (double.IsNaN(rad1) == false) ? rad1 : atom1.Rmin2;
double rad2 = atom2.Rmin2_14; rad2 = (double.IsNaN(rad2) == false) ? rad2 : atom2.Rmin2;
double eps1 = atom1.eps_14; eps1 = (double.IsNaN(eps1) == false) ? eps1 : atom1.epsilon;
double eps2 = atom2.eps_14; eps2 = (double.IsNaN(eps2) == false) ? eps2 : atom2.epsilon;
return(LJ(coord1, coord2, rad1, rad2, eps1, eps2));
}
public static bool GetPwEnrgFrcSprNbnd(bool vdW, bool elec
, Universe.Nonbonded14 nonbonded14
, IList <Vector> coords
, double D // = 80 // dielectric constant
, out double Eij
, out double Fij
, out double Kij
)
{
Eij = Fij = Kij = double.NaN;
Universe.Atom atom0 = nonbonded14.atoms[0];
Universe.Atom atom1 = nonbonded14.atoms[1];
int id0 = atom0.ID; if (coords[id0] == null)
{
return(false);
}
int id1 = atom1.ID; if (coords[id1] == null)
{
return(false);
}
Vector coord0 = coords[id0];
Vector coord1 = coords[id1];
double ri0 = atom0.Rmin2_14; if (double.IsNaN(ri0))
{
ri0 = atom0.Rmin2;
}
double rj0 = atom1.Rmin2_14; if (double.IsNaN(rj0))
{
rj0 = atom1.Rmin2;
}
double qi = atom0.Charge;
double qj = atom1.Charge;
double ei = atom0.eps_14; if (double.IsNaN(ei))
{
ei = atom0.epsilon;
}
double ej = atom1.eps_14; if (double.IsNaN(ej))
{
ej = atom1.epsilon;
}
GetPwEnrgFrcSprNbnd(vdW, elec
, coord0, ri0, qi, ei
, coord1, rj0, qj, ej
, D
, out Eij, out Fij, out Kij
);
return(true);
}
public virtual void Compute(Universe.Nonbonded14 nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
double pchij = atom1.Charge * atom2.Charge;
if (double.IsNaN(pchij))
{
HDebug.Assert(false);
return;
}
Compute(coords, ref energy, ref forces, ref hessian, pchij, pwfrc, pwspr);
}
public virtual void Compute(Universe.Nonbonded14 nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
double radi = atom1.Rmin2_14; radi = (double.IsNaN(radi) == false) ? radi : atom1.Rmin2;
double radj = atom2.Rmin2_14; radj = (double.IsNaN(radj) == false) ? radj : atom2.Rmin2;
double epsi = atom1.eps_14; epsi = (double.IsNaN(epsi) == false) ? epsi : atom1.epsilon;
double epsj = atom2.eps_14; epsj = (double.IsNaN(epsj) == false) ? epsj : atom2.epsilon;
double radij = (radi + radj);
if (divideRadijByTwo)
{
radij = radij / 2;
}
double epsij = Math.Sqrt(epsi * epsj);
if (double.IsNaN(radij) || double.IsNaN(epsij))
{
HDebug.Assert(false);
return;
}
Compute(coords, ref energy, ref forces, ref hessian, radij, epsij, pwfrc, pwspr);
}
public virtual void Compute(Universe.Nonbonded14 nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
Compute(atom1, atom2, coords, ref energy, ref forces, ref hessian, pwfrc, pwspr);
}