Where in the source code is the density built?

ser3na · March 16, 2022, 7:05pm

Avogadro can plot densities out of molden files. An electron density is the square of two vectors of molecular orbitals. I was wondering where in the source code the electron density is built such that I am able to tinker around with how this is done. Specifically I am looking to replace certain d-orbitals in one of the MO vectors iff in the other MO vector is a p-orbital, etc. I’d imagine there to be a big loop structure somewhere in the source code where it is looped over all GTOs but I didn’t find it. If I have that, recompiling it and running it should be doable.

Thanks for the help!

ghutchis · March 16, 2022, 10:23pm

See, for example in Avo2:

github.com

OpenChemistry/avogadrolibs/blob/09d379440fe0c449fcb967f64c2b4118cf5995c7/avogadro/core/gaussiansettools.cpp#L82

      
        
            
            
bool GaussianSetTools::calculateElectronDensity(Cube& cube) const
            {
              for (size_t i = 0; i < cube.data()->size(); ++i) {
                Vector3 pos = cube.position(i);
                cube.setValue(i, calculateElectronDensity(pos));
              }
              return true;
            }
            
            
double GaussianSetTools::calculateElectronDensity(const Vector3& position) const
            {
              const MatrixX& matrix = m_basis->densityMatrix();
              int matrixSize(static_cast<int>(m_basis->moMatrix().rows()));
              if (matrix.rows() != matrixSize || matrix.cols() != matrixSize) {
                return 0.0;
              }
            
            
  vector<double> values(calculateValues(position));
            
            
  // Now calculate the value of the density at this point in space

system · March 21, 2022, 9:25pm

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