SPINS MATLAB tools

Many versatile MATLAB functions have been written to easily read and analyze SPINS outputs. They are accessible for use on Belize and Boogaloo, and can also be pulled from github at https://github.com/ddeepwel/SPINSmatlab.git.

The main functionality are:

• parse spins.conf file into a matlab structure
• automatic calculation of secondary grid parameters (spacing, expansion type, ...)
• easy reading of grid
• easy cross-sectional plotting
• plotting of spins diagnostics
• functions for calculating characteristics (amplitude, wavelength) of waves
• SPINS resize

The first three are organized into the spins_gridparams function. The plotting is accomplished by spins_plot2d which has many optional arguments for making plots with very little work. See David Deepwell (ddeepwel@uwaterloo.ca) or the github page for more information on usage, making bug reports, or suggesting other options or functions to add.

SPINSmatlab has a host of useful functions. Some are very general, while some are specialized. Below is a list of every function included in SPINSmatlab (as of October 2021), as well as a short description of what the function does. In parentheses is the directory in which the described script is located.

Following the description of the scripts, a list of "MUST KNOW" scripts is included. These scripts are the most widely used on the day-to-day and fluency in them is imperative to a smooth workflow.

1. gdpar = spins_gridparams(); split_gdpar; par2var;

spins_reader()

spins_reader() is the function one uses to read in SPINS output into a MATLAB array. The basic functionality comes rom specifying the field name as a character vector, as well as the output index. As an example, if one would like to import the file rho.14 (i.e. the density field at the 14th output), they could write my_rho = spins_reader('rho',14).

For larger datasets, it is often impractical to load the entire dataset into MATLAB. To this end, the user can specify certain subsets of the data they wish to import. This is done by specifying index ranges in the $x$ dimension (xrange), $y$ dimension (yrange), and/or $z$ dimension (zrange). Each of the range arguments take an index or set of indices and return the field values at those indices. To access this functionality, one could write my_rho = spins_reader('rho',14,xstart:xend,y_slice_ind,[]). For the $x$ dimension, a custom range of indices beginning at xstart and ending at xend was used. For the $y$ dimension, the field was sliced at a single location indicated by y_slice_ind. Finally, the entire $z$ dimension was imported by using [].

If data is two-dimensional, accessing custom subsets of the data is done by ignoring the fifth argument. When only four arguments are supplied, spins_reader() assumes that the data only has an $x$ and $z$ dimension and no $y$ dimension.

clean_diagnostics

plot_diagnos()

cmocean()

cmocean() is a package of perceptually uniform colourmaps(Add Thyng reference). These colourmaps should be used whenever possible, as they avoid artificial gradients created by using some other colourmaps.

To access the colourmaps within the package, when writing the colormap command, write colormap(cmocean(my_colourmap)) where my_colourmap(character vector) is any of the available colourmaps found by typing help cmocean.

print_figure()

resize_all()

extend_all()

1. ind = nearest_index(x1d,xi)
2. diagnos = plot_diagnos(make_plots,do_filter)
3. clean_diagnostics
4. print_figure(filename, 'opt1', val1, 'opt2', val2, ...)
5. cmocean
6. resize_all(out,[Nx_new, Ny_new, Nz_new])
7. extend_all(out,Ly,Ny)