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Actually, it's not based on that commit, sorry

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I'm gonna re-open another pull request and write commits in the bottom-up passion to emphasize the code changes and prevent any confusion from possible duplications of commits.

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Issues

  1. change to state-pairwise expression or give option.
  2. calculate decoherence term in shxf.py and give it to el_propagator, i.e. every nuclear time step, not electronic time step? (need change in all xf files).

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