Reorganize code

[malihass]

• add setup Reorganize the repo #22
• Swap json for yaml Reorganize the repo #22
• See if we need the constraint on scipy version Reorganize the repo #22
• Check which os to run on Reorganize the repo #22
• Make sure ci passes Reorganize the repo #22
• Modules
  • Meshing
    • block cylindrical meshing Reorganize the repo #22
    • stl meshing Reorganize the repo #22
    • Stir tank Reorganize the repo #22
    • Airlift reactor (use yaml for input) in /bird/meshing (follow example of stir tank reactor) then add an interface in applications/(also follow the stir tank example)
  • Inverse modeling
    • NN Surrogate bayesian calibration Reorganize the repo #22
  • Openfoam solvers
    • Multiphase models: Grace, Higbie, (efficiency models) Reorganize the repo #22
    • Applications: BDOfoam (multiphase Euler + sub cycling chemistry for microbial reactions) OFsolvers/applications
  • Case
    • Flat panel reactors papers/
    • Loop reactor papers/
    • BDOfoam papers/
  • Post processing
    • Get rid of plotsUtil in favor of the prettyPlot package Reorganize the repo #22
    • Early prediction Reorganize the repo #22
    • conditional mean Reorganize the repo #22
    • pv script for gh, concentration and outlet composition bird/postProcess
  • Pre processing
    • Surf 2 patch utils Surf patch bc #27