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// Parameters:
// bar : neigboring high charge atom
// ionPos : original ionPosition or cordinates
// normal : unit normal vector
// firstNeighDist: nearest neigbour
// thetaDeg : the polar angle in degrees.
// phiDeg : the azimuth angle in degrees.
Vect rollUpSpherical(const Vect &ionPos, const Vect &bar, const Vect &normal,
double firstNeighDist, double thetaDeg, double phiDeg)
{
// Rolled-up ion position
Vect ionPos_r = bar + normal * firstNeighDist;
// Direction Vector from original ionPos to rolled-up ionPos
Vect dirVec = ionPos_r - ionPos;
// Its magnitude
double r = magnitude(dirVec);
// Defining the new z_local-axis as normalized direction vector
Vect zLocal = normalize(dirVec);
// Construct a local orthonormal frame (xLocal, yLocal, zLocal) where:
// - zLocal is as defined above.
// - xLocal is chosen by crossing an arbitrary reference vector with zLocal.
Vect reference(1.0, 0.0, 0.0);
if (std::fabs(dot(zLocal, reference)) > 0.99)
{
reference = Vect(0.0, 1.0, 0.0);
}
Vect xLocal = normalize(cross(reference, zLocal));
Vect yLocal = normalize(cross(zLocal, xLocal));
double theta = toRadians(thetaDeg);
double phi = toRadians(phiDeg);
// Calculatecomponents of the rotated direction vector (in the local frame).
// - Component along zPrime: r * cos(theta)
// - Component in the perpendicular (x'y' plane): r * sin(theta), further split using phi.
double compX = r * sin(theta) * cos(phi);
double compY = r * sin(theta) * sin(phi);
double compZ = r * cos(theta);
// Transform the local vector components in local coord sys to the global coordinate system.
Vect rotatedDirVec{
compX * xLocal.x + compY * yLocal.x + compZ * zLocal.x,
compX * xLocal.y + compY * yLocal.y + compZ * zLocal.y,
compX * xLocal.z + compY * yLocal.z + compZ * zLocal.z};
// Add rotatedDirVec to the original ionPos.
Vect rotatedIonPos = ionPos + rotatedDirVec;
return rotatedIonPos;
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