Hello, if you are reading this you are viewing the repository which contains the code used to study parametric subharmonic instability in the oceanic bottom boundary layer. The important files which made this possible and general organization are described below:\

1. To run the full nonlinear simulations, there are two options:
   • To run all the simulations in the parameter space, run the shell script run_all.sh which will automatically run the simulations using run_all.py, full_code_diagnostics_stblty_comp.jl, and aux_pbs_psi.sh for the parameters defined in parameters.jl.
   • To run a single simulation, modify full_code_diagnostics.jl and run the shell script sub.sh.
2. The linear stability analysis over the parameter space is contained in the code stability_analysis_full_run.py where submitting the shell script stability.sh will execute the code.
   • Note that the jupyter notebook stability_analysis_output_reader.ipynb allow us to read the stability analysis output
3. The Result_Calculations folder contains the jupyter notebooks used to analyze outputs from the nonlinear simulations. The individual scripts and their functions are listed below:
   • BFLUx_GSP_comp.ipynb is the jupyter notebook where the comparison of integrated BFLUX and GSP
   • time_series_and_fourier_transform.ipynb has the code for the quasi-lagrangian time series of velocity along with power spectrum
   • TKE_terms_velocity_comparison.ipynb generates figure showing velocities and TKE terms over 2 modified inertial periods
   • TKE_terms.ipynb generates the TKE budget plots that are the basis for other figures and the growth rate
   • velocity_visualization.ipynb generates plots of the instability in the domain