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long awaited PR with many different implementations

Bitbucket Importer requested to merge bitbucket/merged-pr-7 into branch/default

Created originally on Bitbucket by apatlpo (Aurelien LPO)

Was already merged in Bitbucket before import, marked as merged by the import user

  • take snapshot of work on APE and geostrophic initialization
  • APE diagnostic seems correct, low term decay of energy is attributed to the viscous nature of the time stepping
  • implement vortex initialization
  • fix omission of relevant files in previous commit
  • implement vortex grid
  • add initiation to rest
  • first pass at vertical mode documentation
  • fix typos in doc for vertical modes
  • computation of vertical normal modes implemented
  • start implementing forcing, broken for now
  • waveperiodic forcing seems debugged
  • first pass at qgvortices forcing implementation
  • start investigating disappearance of phys_fields with forcing
  • first pass at combining forcing, seems to be working
  • update doc on forcing
  • adjust the doc on wave forcing further, implements a better version of this forcing
  • start converging on forcing
  • Bug MPI in state.py (add bcast), Modification Combined class (to have periodicwaves + sponges)

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