public virtual void Compute(Universe.Nonbonded 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;
Compute(coords, ref energy, ref forces, ref hessian, pchij, pwfrc, pwspr);
}
public virtual void Compute(Universe.Nonbonded 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;
double radj = atom2.Rmin2;
double epsi = atom1.epsilon;
double epsj = atom2.epsilon;
Compute(nonbonded, coords, ref energy, ref forces, ref hessian, radi, radj, epsi, epsj, pwfrc, pwspr);
}
// electrostatic
public static PPotential Elec(Universe.Nonbonded 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));
}
// Lennard-Jones
public static PPotential LJ(Universe.Nonbonded 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;
double rad2 = atom2.Rmin2;
double eps1 = atom1.epsilon;
double eps2 = atom2.epsilon;
return(LJ(coord1, coord2, rad1, rad2, eps1, eps2));
}
public virtual void Compute(Universe.Nonbonded 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 radij = (atom1.Rmin2 + atom2.Rmin2);
if (divideRadijByTwo)
{
radij = radij / 2;
}
double epsij = Math.Sqrt(atom1.epsilon * atom2.epsilon);
Compute(coords, ref energy, ref forces, ref hessian, radij, epsij, pwfrc, pwspr);
}
public void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
Universe.Nonbonded nonbonded = (Universe.Nonbonded)info;
HDebug.Depreciated("check idx1 and idx2");
int idx1 = 0; // nonbonded.atoms[0].ID;
int idx2 = 1; // nonbonded.atoms[1].ID;
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);
pwidxs = null;
pwhessinfos = null;
return;
}
Vector diff = (coords[idx2] - coords[idx1]);
double dx = diff[0];
double dy = diff[1];
double dz = diff[2];
double pchi = atom1.Charge;
double pchj = atom2.Charge;
double ee = 80;
// !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
//
// V(rij) = (332 * pchij / ee) * rij^-1
// F(rij) = ( -1) * (332 * pchij / ee) * rij^-2
// K(rij) = (-2*-1) * (332 * pchij / ee) * rij^-3
// double pchij = pchi * pchj;
double rij2 = dx * dx + dy * dy + dz * dz;
double rij = Math.Sqrt(rij2);
double rij3 = rij2 * rij;
double fij = (-1) * (332 * pchij / ee) / rij2;
double kij = (-2 * -1) * (332 * pchij / ee) / rij3;
pwidxs = new Pair <int, int> [1];
pwidxs[0] = new Pair <int, int>(0, 1);
pwhessinfos = new PwIntrActInfo[1];
pwhessinfos[0] = new PwIntrActInfo(kij, fij);
}
public static bool GetPwEnrgFrcSprNbnd(bool vdW, bool elec
, Universe.Nonbonded nonbonded
, 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 = nonbonded.atoms[0];
Universe.Atom atom1 = nonbonded.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;
double rj0 = atom1.Rmin2;
double qi = atom0.Charge;
double qj = atom1.Charge;
double ei = atom0.epsilon;
double ej = atom1.epsilon;
GetPwEnrgFrcSprNbnd(vdW, elec
, coord0, ri0, qi, ei
, coord1, rj0, qj, ej
, D
, out Eij, out Fij, out Kij
);
return(true);
}
