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DFTQuantumDot
Density Functional Theory with plane waves basis, applied on a 'quantum dot'. Volumetric visualization of orbitals with VTK
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A density functional theory project that could be extended to use non-local pseudopotentials to compute a molecule: https://github.com/aromanro/DFTQuantumDot (there is an example in there on how to compute a molecule but without pseudo potentials, so it works only on simple ones like H2 or so, for an example with a pseudo-potential - but a simple local one - check out the python repository).
DFT in real space, but only for an atom: https://github.com/aromanro/DFTAtom (for a molecule it's much harder, you cannot go with 1D as in that project).
You could also go with Quantum Monte Carlo, here is one such project, but limited to max 2 atoms: https://github.com/aromanro/VQMCMolecule (the general case is more difficult).