danijonesocean / expose-tracer

Tracer distributions from passive tracer release experiments in Subantarctic Mode Water pools

expose-tracer

This repository contains code and data from a set of passive tracer experiments [Fig. 4, Jones et al. (2016)]. This figure has been included as part of a review paper on ventilation (Morrison et al., 2021)

Requirements for Matlab code

• Matlab 2018b
• M_Map v1.4k

Requirements for Jupyter notebook

• python 3.7.4
• matplotlib 3.1.1
• cartopy 0.17.0
• numpy 1.17.2
• xaray 0.16.2

Project Organization

├── colormaps                 <- Various colormaps used in these plots
├── data_in                   <- Tracer data from Jones et al. (2016)
├── data_pre                  <- Matlab code that was used to create the NetCDF file
├── notebooks                 <- Jupyter notebook for visualization
├── plots                     <- Plots from Matlab code
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├── LICENSE
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├── README.md                 <- Overall description
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├── tracer_histogram_plot.m   <- Matlab code to plot distribution 

References

Jones, D. C., Meijers, A. J. S., Shuckburgh, E., Sallée, J.-B., Haynes, P., McAufield, E. K., and Mazloff, M. R. (2016), How does Subantarctic Mode Water ventilate the Southern Hemisphere subtropics?, J. Geophys. Res. Oceans, 121, 6558– 6582, doi:10.1002/2016JC011680.

Morrison, A. K., Waugh, D. W., Hogg, A. McC., Jones, D. C., and Abernathey, R. P. (2021), Ventilation of the Southern Ocean pycnocline, under review

expose-tracer's Issues

Extend arrow not showing up on colorbar

I would like there to be an "extend" arrow on the colorbar, showing that the scale continues past 0.6. However, so far it will not display.

Convert tracer histogram files to NetCDF

I've located the original tracer histogram files on BAS HPC at this location:

/data/expose/archive/expose/analysis/tracer_runs/tracer_histogram/data_out/exposeOnSteady_v3

The goal is to (1) perform the time integration step, (2) convert to NetCDF, and (3) save in this new expose-tracer repository. This conversion will need to include relevant factors of the MITgcm grid. We may create a brief plotting notebook in this repository.

NetCDF data looks fine when read by Matlab but incorrect when read by Xarray

In this repository, I've collected various fields into a single NetCDF. I produced the file using Matlab. The resulting data, stored in NetCDF, looks okay when read back in using Matlab. However, when I use Xarray to read in the data, some values seem to be missing for some coordinate values.

The code used to create the NetCDF file in Matlab is here:
https://github.com/DanJonesOcean/expose-tracer/blob/main/data_pre/now_convert.m

And the notebook where the NetCDF file is read back in is here:
https://github.com/DanJonesOcean/expose-tracer/blob/main/Southern%20Ocean%20Thermocline%20Ventilation.ipynb

Advice is greatly appreciated.

Create Jupyter notebook plotting the tracer fields

There is a request to have the opacity/shading different for each one of the tracers. This might be easier in Python, possibly.