void AngleBendContrib::getGrad(double *pos,double *grad) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
double dist[2] = {
dp_forceField->distance(d_at1Idx, d_at2Idx, pos),
dp_forceField->distance(d_at2Idx, d_at3Idx, pos)
};
RDGeom::Point3D p1(pos[3 * d_at1Idx],
pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
RDGeom::Point3D p2(pos[3 * d_at2Idx],
pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
RDGeom::Point3D p3(pos[3 * d_at3Idx],
pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
double *g[3] = {
&(grad[3 * d_at1Idx]),
&(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx])
};
RDGeom::Point3D r[2] = {
(p1 - p2) / dist[0],
(p3 - p2) / dist[1]
};
double cosTheta = r[0].dotProduct(r[1]);
double sinThetaSq = 1.0 - cosTheta * cosTheta;
double sinTheta = std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
//std::cerr << "GRAD: " << cosTheta << " (" << acos(cosTheta)<< "), ";
//std::cerr << sinTheta << " (" << asin(sinTheta)<< ")" << std::endl;
// use the chain rule:
// dE/dx = dE/dTheta * dTheta/dx
// dE/dTheta is independent of cartesians:
double dE_dTheta=getThetaDeriv(cosTheta,sinTheta);
Utils::calcAngleBendGrad(r, dist, g, dE_dTheta, cosTheta, sinTheta);
}
void AngleBendContrib::getGrad(double *pos,double *grad) const {
PRECONDITION(dp_forceField,"no owner");
PRECONDITION(pos,"bad vector");
PRECONDITION(grad,"bad vector");
double dist1=this->dp_forceField->distance(this->d_at1Idx,this->d_at2Idx,pos);
double dist2=this->dp_forceField->distance(this->d_at2Idx,this->d_at3Idx,pos);
//std::cout << "\tAngle("<<this->d_at1Idx<<","<<this->d_at2Idx<<","<<this->d_at3Idx<<") " << dist1 << " " << dist2 << std::endl;
RDGeom::Point3D p1(pos[3*this->d_at1Idx],
pos[3*this->d_at1Idx+1],
pos[3*this->d_at1Idx+2]);
RDGeom::Point3D p2(pos[3*this->d_at2Idx],
pos[3*this->d_at2Idx+1],
pos[3*this->d_at2Idx+2]);
RDGeom::Point3D p3(pos[3*this->d_at3Idx],
pos[3*this->d_at3Idx+1],
pos[3*this->d_at3Idx+2]);
double *g1=&(grad[3*this->d_at1Idx]);
double *g2=&(grad[3*this->d_at2Idx]);
double *g3=&(grad[3*this->d_at3Idx]);
RDGeom::Point3D p12=p1-p2;
RDGeom::Point3D p32=p3-p2;
double cosTheta = p12.dotProduct(p32)/(dist1*dist2);
double sinTheta = std::max(sqrt(1.0-cosTheta*cosTheta),1e-8);
//std::cerr << "GRAD: " << cosTheta << " (" << acos(cosTheta)<< "), ";
//std::cerr << sinTheta << " (" << asin(sinTheta)<< ")" << std::endl;
// use the chain rule:
// dE/dx = dE/dTheta * dTheta/dx
// dE/dTheta is independent of cartesians:
double dE_dTheta=getThetaDeriv(cosTheta,sinTheta);
// -------
// dTheta/dx is trickier:
double dCos_dS1=1./dist1 * (p32.x/dist2 - cosTheta*p12.x/dist1);
double dCos_dS2=1./dist1 * (p32.y/dist2 - cosTheta*p12.y/dist1);
double dCos_dS3=1./dist1 * (p32.z/dist2 - cosTheta*p12.z/dist1);
double dCos_dS4=1./dist2 * (p12.x/dist1 - cosTheta*p32.x/dist2);
double dCos_dS5=1./dist2 * (p12.y/dist1 - cosTheta*p32.y/dist2);
double dCos_dS6=1./dist2 * (p12.z/dist1 - cosTheta*p32.z/dist2);
g1[0] += dE_dTheta*dCos_dS1/(-sinTheta);
g1[1] += dE_dTheta*dCos_dS2/(-sinTheta);
g1[2] += dE_dTheta*dCos_dS3/(-sinTheta);
g2[0] += dE_dTheta*(-dCos_dS1 - dCos_dS4)/(-sinTheta);
g2[1] += dE_dTheta*(-dCos_dS2 - dCos_dS5)/(-sinTheta);
g2[2] += dE_dTheta*(-dCos_dS3 - dCos_dS6)/(-sinTheta);
g3[0] += dE_dTheta*dCos_dS4/(-sinTheta);
g3[1] += dE_dTheta*dCos_dS5/(-sinTheta);
g3[2] += dE_dTheta*dCos_dS6/(-sinTheta);
}
