public void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
HDebug.Depreciated("check idx1 and idx2");
int idx1 = 0; // nonbonded.atoms[0].ID;
int idx2 = 1; // nonbonded.atoms[1].ID;
Universe.Atom atom1 = info.atoms[0];
Universe.Atom atom2 = info.atoms[1];
Vector diff = (coords[idx2] - coords[idx1]);
double dx = diff[0];
double dy = diff[1];
double dz = diff[2];
double radi = double.NaN;
double radj = double.NaN;
double epsi = double.NaN;
double epsj = double.NaN;
if (typeof(Universe.Nonbonded14).IsInstanceOfType(info))
{
radi = atom1.Rmin2_14; radi = (double.IsNaN(radi) == false) ? radi : atom1.Rmin2;
radj = atom2.Rmin2_14; radj = (double.IsNaN(radj) == false) ? radj : atom2.Rmin2;
epsi = atom1.eps_14; epsi = (double.IsNaN(epsi) == false) ? epsi : atom1.epsilon;
epsj = atom2.eps_14; epsj = (double.IsNaN(epsj) == false) ? epsj : atom2.epsilon;
}
if (typeof(Universe.Nonbonded).IsInstanceOfType(info))
{
radi = atom1.Rmin2;
radj = atom2.Rmin2;
epsi = atom1.epsilon;
epsj = atom2.epsilon;
}
HDebug.Assert(double.IsNaN(radi) == false, double.IsNaN(radj) == false, double.IsNaN(epsi) == false, double.IsNaN(epsj) == false);
// !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(r) = epsij * r0^12 * rij^-12 - 2 * epsij * r0^6 * rij^-6
// F(r) = -12 * epsij * r0^12 * rij^-13 - -6*2 * epsij * r0^6 * rij^-7
// K(r) = -13*-12 * epsij * r0^12 * rij^-14 - -7*-6*2 * epsij * r0^6 * rij^-8
double r = (radi + radj);
double r6 = Math.Pow(r, 6);
double r12 = Math.Pow(r, 12);
double rij2 = (dx * dx + dy * dy + dz * dz);
double rij = Math.Sqrt(rij2);
double rij7 = Math.Pow(rij2, 3) * rij;
double rij8 = Math.Pow(rij2, 4);
double rij13 = Math.Pow(rij2, 6) * rij;
double rij14 = Math.Pow(rij2, 7);
double epsij = epsi * epsj;
double fij = (-12) * epsij * r12 / rij13 - (-6 * 2) * epsij * r6 / rij7;
double kij = (-13 * -12) * epsij * r12 / rij14 - (-7 * -6 * 2) * epsij * r6 / rij8;
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 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 virtual void Compute(Universe.AtomPack nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian
, double radi, double radj, double epsi, double epsj, double[,] pwfrc = null, double[,] pwspr = null)
{
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
Vector pos0 = coords[0];
Vector pos1 = coords[1];
double rmin = (radi + radj);
double epsij = Math.Sqrt(epsi * epsj);
double lenergy, forceij, springij;
Compute(coords, out lenergy, out forceij, out springij, epsij, rmin);
double abs_forceij = Math.Abs(forceij);
if (pwfrc != null)
{
pwfrc[0, 1] = pwfrc[1, 0] = forceij;
}
if (pwspr != null)
{
pwspr[0, 1] = pwspr[1, 0] = springij;
}
///////////////////////////////////////////////////////////////////////////////
// energy
energy += lenergy;
///////////////////////////////////////////////////////////////////////////////
// force
if (forces != null)
{
Vector frc0, frc1;
GetForceVector(pos0, pos1, forceij, out frc0, out frc1);
forces[0] += frc0;
forces[1] += frc1;
}
///////////////////////////////////////////////////////////////////////////////
// hessian
if (hessian != null)
{
hessian[0, 1] += GetHessianBlock(coords[0], coords[1], springij, forceij);
hessian[1, 0] += GetHessianBlock(coords[1], coords[0], springij, forceij);
}
}
public void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
Universe.Bond bond = (Universe.Bond)info;
double Kb = bond.Kb;
double b0 = bond.b0;
HDebug.Assert(coords.Length == 2);
Vector pos1 = coords[0];
Vector pos2 = coords[1];
Vector r12 = pos1 - pos2;
double r = r12.Dist;
double kij = 2 * Kb;
double fij = (2 * Kb) * (r - b0);
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 void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
pwidxs = null;
pwhessinfos = null;
//Universe.Improper improper = (Universe.Improper)info;
//double Kpsi = improper.Kpsi;
////int n = improper.param.n;
//double psi0 = improper.psi0;
//Vector a = coords[0];
//Vector b = coords[1];
//Vector c = coords[2];
//Vector d = coords[3];
//Pair<double, double> fij_kij = GetFijKij(Kpsi, psi0, a, b, c, d);
//double fij = fij_kij.first;
//double kij = fij_kij.second;
//
//Debug.Assert(coords.Length == 4);
//pwidxs = new Pair<int, int>[1];
//pwidxs[0] = new Pair<int, int>(0, 3);
//pwhessinfos = new PwIntrActInfo[1];
//pwhessinfos[0] = new PwIntrActInfo(kij, fij);
}
public void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
Universe.Angle angle = (Universe.Angle)info;
double Ktheta = angle.Ktheta;
double Theta0 = angle.Theta0;
double Kub = angle.Kub;
double S0 = angle.S0;
Vector pos1 = coords[0]; // const Vector *pos1 = coords + angle->atom1;
Vector pos2 = coords[1]; // const Vector *pos2 = coords + angle->atom2;
Vector pos3 = coords[2]; // const Vector *pos3 = coords + angle->atom3;
double a = (pos2 - pos1).Dist;
double b = (pos3 - pos2).Dist;
double c = (pos3 - pos1).Dist;
ValueTuple <double, double> fij_kij = GetFijKij(a, b, c, Ktheta, Theta0);
double fij = fij_kij.Item1;
double kij = fij_kij.Item2;
HDebug.Assert(coords.Length == 3);
pwidxs = new Pair <int, int> [1];
pwidxs[0] = new Pair <int, int>(0, 2);
pwhessinfos = new PwIntrActInfo[1];
pwhessinfos[0] = new PwIntrActInfo(kij, fij);
}
public void BuildHess4PwIntrAct(Universe.AtomPack info, Vector[] coords, out Pair <int, int>[] pwidxs, out PwIntrActInfo[] pwhessinfos)
{
Universe.Improper improper = (Universe.Improper)info;
double Kchi = improper.Kpsi;
int n = improper.n;
double delta = improper.psi0;
//Vector pos1 = coords[0]; // const Vector *pos1 = coords + angle->atom1;
//Vector pos2 = coords[1]; // const Vector *pos2 = coords + angle->atom2;
//Vector pos3 = coords[2]; // const Vector *pos3 = coords + angle->atom3;
//double a = (pos2-pos1).Dist;
//double b = (pos3-pos2).Dist;
//double c = (pos3-pos1).Dist;
//Pair<double,double> fij_kij = GetFijKij(a, b, c, Ktheta, Theta0);
//double fij = fij_kij.first;
//double kij = fij_kij.second;
/// A
/// / B
/// a .../. c /
/// \ / / \ /
/// \ / /\
/// \ / / \
/// b ..... d
///
/// a
/// |\ /
/// | \ /T
/// | \ ----- A ----+----
/// | \ /
/// | \ B
/// p l /
/// | \ \ /
/// |T \ \
/// | \ \
/// \ \
/// \\
/// d
///
/// A = (b-a) x (c-b)
/// B = (c-b) x (d-c)
/// (A x B) ⊥ (Δ adp)
/// p ∈ bc
/// T + ∠apd = π
///
/// V = K0 (T - T0)^2
/// F = dV/dT = 2 K0 (T - T0)
/// K = (d^2 V)/(d T^2) = 2 K0
/// return { dV/dl, (d^2 V)/(d l^2) }
Vector a = coords[0];
Vector b = coords[1];
Vector c = coords[2];
Vector d = coords[3];
Vector A = LinAlg.CrossProd(a - b, b - c);
Vector B = LinAlg.CrossProd(b - c, c - d);
Vector AxB = LinAlg.CrossProd(A, B);
double ad = (a - d).Dist;
Vector p = Geometry.Point4LinePlaneIntersect(a, d, a + A, b, c);
double ap = (a - p).Dist;
double pd = (p - d).Dist;
ValueTuple <double, double> fij_kij = MindyAngle.GetFijKij(ap, pd, ad, Kchi, delta, -1, +1, -1);
double fij = fij_kij.Item1;
double kij = fij_kij.Item2;
HDebug.Assert(coords.Length == 4);
pwidxs = new Pair <int, int> [1];
pwidxs[0] = new Pair <int, int>(0, 3);
pwhessinfos = new PwIntrActInfo[1];
pwhessinfos[0] = new PwIntrActInfo(kij, fij);
}
public virtual void Compute(Universe.AtomPack nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian
, double radi, double radj, double epsi, double epsj, double[,] pwfrc = null, double[,] pwspr = null)
{
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];
Vector diff = (coords[idx2] - coords[idx1]);
double dx = diff[0];
double dy = diff[1];
double dz = diff[2];
//double radi = atom1.Rmin2;
//double radj = atom2.Rmin2;
//double epsi = atom1.epsilon;
//double epsj = atom2.epsilon;
///////////////////////////////////////////////////////////////////////////////
// energy
energy += EnergyVdw(dx, dy, dz, radi, radj, epsi, epsj);
///////////////////////////////////////////////////////////////////////////////
// force
if (forces != null)
{
Vector f12 = ForceVdw(dx, dy, dz, radi, radj, epsi, epsj);
forces[idx1] += f12;
forces[idx2] += -f12;
}
///////////////////////////////////////////////////////////////////////////////
// hessian
if (hessian != null)
{
//string option = "Spring+Force";
//Vector diff01 = (coords[1] - coords[0]);
//Vector diff10 = (coords[0] - coords[1]);
//hessian[0, 1] += SprngVdw(diff01, radi, radj, epsi, epsj, option);
//hessian[1, 0] += SprngVdw(diff10, radi, radj, epsi, epsj, option);
{
// !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(r) = epsij * r0^12 * rij^-12 - 2 * epsij * r0^6 * rij^-6
// F(r) = -12 * epsij * r0^12 * rij^-13 - -6*2 * epsij * r0^6 * rij^-7
// K(r) = -13*-12 * epsij * r0^12 * rij^-14 - -7*-6*2 * epsij * r0^6 * rij^-8
double r = (radi + radj);
double r6 = Math.Pow(r, 6);
double r12 = Math.Pow(r, 12);
double rij2 = (dx * dx + dy * dy + dz * dz);
double rij = Math.Sqrt(rij2);
double rij7 = Math.Pow(rij2, 3) * rij;
double rij8 = Math.Pow(rij2, 4);
double rij13 = Math.Pow(rij2, 6) * rij;
double rij14 = Math.Pow(rij2, 7);
double epsij = epsi * epsj;
double fij = (-12) * epsij * r12 / rij13 - (-6 * 2) * epsij * r6 / rij7;
double kij = (-13 * -12) * epsij * r12 / rij14 - (-7 * -6 * 2) * epsij * r6 / rij8;
fij *= optHessianForceFactor;
//Matrix Hij = ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[0, 1] += ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[1, 0] += ForceField.GetHessianBlock(coords[1], coords[0], kij, fij);
}
}
}
