numerical_mixing contains information needed to reproduce figures shown in Schlichting et al. (2023) JAMES. If you want to access the TXLA model output, see the directory "TXLA ROMS nested model for SUNRISE" at https://hafen.geos.tamu.edu/thredds/catalog/catalog.html.
If you work in Python, we recommend creating a custom conda environment so package version control can be managed easily. To run scripts/notebooks in this repository, an environment can be installed by running
conda install --file copano_env_revised.yml
The environment used for initial submission can be installed with copano_env_initial.yml. The yaml file for the revised submission is copano_env_revised.yml. The crux of the work done here relies on xroms. See https://github.com/xoceanmodel for more information. xroms is not required for analysis but it will substantially shorten cumbersome calculations like Jacobians or the nonlinear equation of state for seawater density. xroms has undergone significant development since creation of this repository, so be wary of version control issues!
/analysis_scripts/: Contains scripts used to generate data for non-tracer budget figures (i.e. histograms)
depth_integrated.py: computes depth and time-integrated numerical and physical mixing for coarse/fine simulationshistograms_fronts_whole.py: histograms for whole water column sorted by fronts only, i.e., normalized relative vorticity, divergence, strain, and horizontal salinity gradient magnitude as described in Section 3.histograms_fronts_surface.py: histograms for surface water column sorted by fronts.
/budget_scripts/: Contains scripts used to generate each term in the tracer budgets. Each script subsets the variable of interest one day (or less) at a time in a for loop to avoid limitations with HPRC resources.
tendency_new.py: Calculates all integrated tracer tendency termsadvection.py: Calculates volume integrated tracer advection termsmixing.py: Calculates volume integrated physical and numerical mixingsurface.py: Calculates volume integrated surface fluxeshmix_diffusion.py: Calculates horizontal physical mixing and horizontal diffusive boundary fluxessbar.py: Calculates volume-averaged salinity
/figures/: Contains Jupyter notebooks used to generate all manuscript figures. Notebooks are named numerically.latex_backups/: Contains backup of overleaft LaTex files for manuscript./quality_control/: Contains a mix of notebooks and scripts to debug and verify several calculations. Also includes checks for calculations that came up during the review process.
histograms_*_test.py: scripts used to check that discreetly computing PDFs by chunking in time is identical to computing all at once withxhistogram'sdensity=Truesyntax.grid_sanity_check.ipynb: notebook to verify location of parent/child grids match.QC_diffusion.ipynb: notebook to ensure horizontal diffusion terms are computed correctly.QC_tendency.ipynb: notebook to ensure volume-integrated time rate of change terms for tracers are computed correctly.QC_advection.ipynb: notebook to ensure horizontal advective boundary fluxes are computed correctly, verifies math in Section 2.3.QC_surface.ipynb: notebook to ensure surface diffusive boundary fluxes are computed correctly, verifies math in Section 2.2-2.3.histogram_surface_stats.py: computes statistics for histogram variables of surface values used in Table 1.thomas_angle.py: Computes instability metric$\phi_{Rib}$ as described in Thomas et al. DSR II (2013): Symmetric instability in the Gulf Stream. This is used in Section 5.2 to verify whether new dynamical processes have emerged in fine simulation. Not shown in main text of manuscript.