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Added functionality to use reinitialization

Andreas Baer requested to merge dev-reinit into main

Reinitialization is now possible:

  • added a job for preparing simulation output/input between simulations
  • initialization input files need to be created prior to the experiment
  • added a template REINIT-CHEM that runs a reinitialization

Documentation is added here and in the changelog.

Closes #19 (closed) .

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