Discrepancy between elements in structure and in the hamiltonian section do not cause an abort

**Is your feature request related to a problem? Please describe.**
When running multiple systems, sometime input files are copied by hand. In this case, the structure had 3 elements (C, N, H), but the Hamiltonian had only 2 elements. The code ran normally with the wrong energy.

**Describe the solution you'd like**
To run a check if all elements in structure are defined in hamiltonian section. (Or at least a warning)

**Describe alternatives you've considered**
An alternative would be to not run things by hand but we are still in early stage testing of many features.. sometimes, by hand is the only solution.

**Additional context**
Add any other context or screenshots about the feature request here.