[Avogadro-devel] Eigen3 migration

[Kirill O. <kir...@gm...>]

Dear Avogadro developers,

I want to use Avogadro in my project to visualize molecules and crystal 
structures. In my project, I'm using Eigen3 library, so I decide to get 
into Avogadro code and change it to support Eigen3 API.

I did step-by-step migration, like described here.
http://eigen.tuxfamily.org/dox/Eigen2SupportModes.html and came to stage 
EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS, meaning that new code 
should follow 100%  Eigen3 API, but in old code still function 
compatible with eigen2 exists ("eigen2_" prefix)

I have only one part of code, which is not working like before. 
computeGeomInfo() in molecule.cpp

In Eigen3 library LeastSquares module was excluded, so I should write 
the code for the fitting by myself. The investigation of the code showed 
one problematic part.

void Molecule::computeGeomInfo() const
{
...
     d->center.setZero();
... //some code not affecting d->center variable

     // compute radius and the farthest atom
     d->radius = std::numeric_limits<double>::min();
     foreach (Atom *atom, m_atomList) {
       double distanceToCenter = (*atom->pos() - 
d->center).squaredNorm();  //!!! center is Zero
           if(distanceToCenter > d->radius) {
             d->radius = distanceToCenter;
             d->farthestAtom = atom;
           }
         }
         d->radius = sqrt(d->radius);

         ...... // Calculation of the center after

         // Calculate the center of the molecule too
         foreach (Atom *atom, m_atomList) {
           Vector3d *pos = &(*m_atomPos)[atom->id()];
           d->center += *pos;
           atomPositions[i++] = pos;
         }
         d->center /= static_cast<double>(nAtoms);

         ...

I just want to ask some questions.

1) Are you interesting in the contribution (eigen2->eigen3).
2) What should I do with geometry info procedure. Should I change the 
radius calculations.

Best regards,
Kirill.