Multilevel molecule

[slamavl]

Add possibility to use multilevel molecules

• Improved molecule class which supports multiple states within single excitation band
• Agrregate build system from multilevel molecules including the right automatic band assignment
• Possibility to include magnetic transition dipole moment either directly or through transition electronic dipole in velocity gauge
• !No interaction between different exciton bands! - this will be added in a future

Spectroscopy:

• Improved calculation of linear spectra (absorption, fluorescence and CD are calculated all together)
• Definition of excitonic corelation function and reorganization energy for multilevel molecules
• Fixed the possibility to use relaxation rate matrix also for higher excitonic states
• Fixed CD spectra and added possibility to use full definition of the rotatory strength including the transition magnetic dipole moment
• Pump-probe spectra calculation (as a separate module in pumpprobe2.py which might be merged with the actual one in pumpprobe.py).
• Added relaxation pathways which corresponds to the relaxation to the ground state.
• Fixed ground state populations in liuville pathways when using non-zero temperatures

NOTES:

• Four tests failed because now it is not possible to define coupling in aggregate without molecules and couplings in aggregate are stored in "resonance_coupling_vec" instead of "resonance_coupling"
• In my OS I had a problem with loading units and representation definition, therefore I set it in the manager without loading the setting file (this probably should not be merged)