void TorsionAngleContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
RDGeom::Point3D r[4] = {iPoint - jPoint, kPoint - jPoint, jPoint - kPoint,
lPoint - kPoint};
RDGeom::Point3D t[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
double d[2] = {t[0].length(), t[1].length()};
if (isDoubleZero(d[0]) || isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
clipToOne(cosPhi);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
double sin2Phi = 2.0 * sinPhi * cosPhi;
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
// dE/dPhi is independent of cartesians:
double dE_dPhi =
0.5 * (-(d_V1)*sinPhi + 2.0 * d_V2 * sin2Phi - 3.0 * d_V3 * sin3Phi);
#if 0
if(dE_dPhi!=dE_dPhi){
std::cout << "\tNaN in Torsion("<<d_at1Idx<<","<<d_at2Idx<<","<<d_at3Idx<<","<<d_at4Idx<<")"<< std::endl;
std::cout << "sin: " << sinPhi << std::endl;
std::cout << "cos: " << cosPhi << std::endl;
}
#endif
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm =
-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
double TorsionAngleContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
return Utils::calcTorsionEnergy(
d_V1, d_V2, d_V3,
Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
}
void OopBendContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
pos[3 * d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
pos[3 * d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
pos[3 * d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g1 = &(grad[3 * d_at1Idx]);
double *g2 = &(grad[3 * d_at2Idx]);
double *g3 = &(grad[3 * d_at3Idx]);
double *g4 = &(grad[3 * d_at4Idx]);
RDGeom::Point3D rJI = iPoint - jPoint;
RDGeom::Point3D rJK = kPoint - jPoint;
RDGeom::Point3D rJL = lPoint - jPoint;
double dJI = rJI.length();
double dJK = rJK.length();
double dJL = rJL.length();
if (isDoubleZero(dJI) || isDoubleZero(dJK) || isDoubleZero(dJL)) {
return;
}
rJI /= dJI;
rJK /= dJK;
rJL /= dJL;
RDGeom::Point3D n = (-rJI).crossProduct(rJK);
n /= n.length();
double const c2 = MDYNE_A_TO_KCAL_MOL * DEG2RAD * DEG2RAD;
double sinChi = rJL.dotProduct(n);
clipToOne(sinChi);
double cosChiSq = 1.0 - sinChi * sinChi;
double cosChi = std::max(((cosChiSq > 0.0) ? sqrt(cosChiSq) : 0.0), 1.0e-8);
double chi = RAD2DEG * asin(sinChi);
double cosTheta = rJI.dotProduct(rJK);
clipToOne(cosTheta);
double sinThetaSq = std::max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta =
std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
double dE_dChi = RAD2DEG * c2 * d_koop * chi;
RDGeom::Point3D t1 = rJL.crossProduct(rJK);
RDGeom::Point3D t2 = rJI.crossProduct(rJL);
RDGeom::Point3D t3 = rJK.crossProduct(rJI);
double term1 = cosChi * sinTheta;
double term2 = sinChi / (cosChi * sinThetaSq);
double tg1[3] = {(t1.x / term1 - (rJI.x - rJK.x * cosTheta) * term2) / dJI,
(t1.y / term1 - (rJI.y - rJK.y * cosTheta) * term2) / dJI,
(t1.z / term1 - (rJI.z - rJK.z * cosTheta) * term2) / dJI};
double tg3[3] = {(t2.x / term1 - (rJK.x - rJI.x * cosTheta) * term2) / dJK,
(t2.y / term1 - (rJK.y - rJI.y * cosTheta) * term2) / dJK,
(t2.z / term1 - (rJK.z - rJI.z * cosTheta) * term2) / dJK};
double tg4[3] = {(t3.x / term1 - rJL.x * sinChi / cosChi) / dJL,
(t3.y / term1 - rJL.y * sinChi / cosChi) / dJL,
(t3.z / term1 - rJL.z * sinChi / cosChi) / dJL};
for (unsigned int i = 0; i < 3; ++i) {
g1[i] += dE_dChi * tg1[i];
g2[i] += -dE_dChi * (tg1[i] + tg3[i] + tg4[i]);
g3[i] += dE_dChi * tg3[i];
g4[i] += dE_dChi * tg4[i];
}
}
void TorsionAngleContrib::getGrad(double *pos, double *grad) const
{
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
RDGeom::Point3D iPoint(pos[3 * this->d_at1Idx],
pos[3 * this->d_at1Idx + 1], pos[3 * this->d_at1Idx + 2]);
RDGeom::Point3D jPoint(pos[3 * this->d_at2Idx],
pos[3 * this->d_at2Idx + 1], pos[3 * this->d_at2Idx + 2]);
RDGeom::Point3D kPoint(pos[3 * this->d_at3Idx],
pos[3 * this->d_at3Idx + 1], pos[3 * this->d_at3Idx + 2]);
RDGeom::Point3D lPoint(pos[3 * this->d_at4Idx],
pos[3 * this->d_at4Idx + 1], pos[3 * this->d_at4Idx + 2]);
double *g1 = &(grad[3 * this->d_at1Idx]);
double *g2 = &(grad[3 * this->d_at2Idx]);
double *g3 = &(grad[3 * this->d_at3Idx]);
double *g4 = &(grad[3 * this->d_at4Idx]);
RDGeom::Point3D r1 = iPoint - jPoint;
RDGeom::Point3D r2 = kPoint - jPoint;
RDGeom::Point3D r3 = jPoint - kPoint;
RDGeom::Point3D r4 = lPoint - kPoint;
RDGeom::Point3D t1 = r1.crossProduct(r2);
RDGeom::Point3D t2 = r3.crossProduct(r4);
double d1 = t1.length();
t1 /= d1;
double d2 = t2.length();
t2 /= d2;
if (isDoubleZero(d1) || isDoubleZero(d2)) {
return;
}
double cosPhi = t1.dotProduct(t2);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
double sin2Phi = 2.0 * sinPhi * cosPhi;
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
// dE/dPhi is independent of cartesians:
double dE_dPhi = 0.5 * (-(this->d_V1) * sinPhi + 2.0
* this->d_V2 * sin2Phi - 3.0 * this->d_V3 * sin3Phi);
#if 0
if(dE_dPhi!=dE_dPhi){
std::cout << "\tNaN in Torsion("<<this->d_at1Idx<<","<<this->d_at2Idx<<","<<this->d_at3Idx<<","<<this->d_at4Idx<<")"<< std::endl;
std::cout << "sin: " << sinPhi << std::endl;
std::cout << "cos: " << cosPhi << std::endl;
}
#endif
// -------
// dTheta/dx is trickier:
double dCos_dT1 = 1.0 / d1 * (t2.x - cosPhi * t1.x);
double dCos_dT2 = 1.0 / d1 * (t2.y - cosPhi * t1.y);
double dCos_dT3 = 1.0 / d1 * (t2.z - cosPhi * t1.z);
double dCos_dT4 = 1.0 / d2 * (t1.x - cosPhi * t2.x);
double dCos_dT5 = 1.0 / d2 * (t1.y - cosPhi * t2.y);
double dCos_dT6 = 1.0 / d2 * (t1.z - cosPhi * t2.z);
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm = -dE_dPhi * (isDoubleZero(sinPhi)
? (1.0 / cosPhi) : (1.0 / sinPhi));
g1[0] += sinTerm * (dCos_dT3 * r2.y - dCos_dT2 * r2.z);
g1[1] += sinTerm * (dCos_dT1 * r2.z - dCos_dT3 * r2.x);
g1[2] += sinTerm * (dCos_dT2 * r2.x - dCos_dT1 * r2.y);
g2[0] += sinTerm * (dCos_dT2 * (r2.z - r1.z)
+ dCos_dT3 * (r1.y - r2.y) + dCos_dT5 * (-1.0 * r4.z) + dCos_dT6 * (r4.y));
g2[1] += sinTerm * (dCos_dT1 * (r1.z - r2.z)
+ dCos_dT3 * (r2.x - r1.x) + dCos_dT4 * (r4.z) + dCos_dT6 * (-1.0 * r4.x));
g2[2] += sinTerm * (dCos_dT1 * (r2.y - r1.y)
+ dCos_dT2 * (r1.x - r2.x) + dCos_dT4 * (-1.0 * r4.y) + dCos_dT5 * (r4.x));
g3[0] += sinTerm * (dCos_dT2 * (r1.z) + dCos_dT3 * (-1.0 * r1.y) +
dCos_dT5 * (r4.z - r3.z) + dCos_dT6 * (r3.y - r4.y));
g3[1] += sinTerm * (dCos_dT1 * (-1.0 * r1.z) + dCos_dT3 * (r1.x) +
dCos_dT4 * (r3.z - r4.z) + dCos_dT6 * (r4.x - r3.x));
g3[2] += sinTerm * (dCos_dT1 * (r1.y) + dCos_dT2 * (-1.0 * r1.x) +
dCos_dT4 * (r4.y - r3.y) + dCos_dT5 * (r3.x - r4.x));
g4[0] += sinTerm * (dCos_dT5 * r3.z - dCos_dT6 * r3.y);
g4[1] += sinTerm * (dCos_dT6 * r3.x - dCos_dT4 * r3.z);
g4[2] += sinTerm * (dCos_dT4 * r3.y - dCos_dT5 * r3.x);
}
