GitLab

Update the documentation to reflect new functions. Also add a dependency graph for the functions in the toolbox

Flip the order of the vertical levels in the POLCOMS data to match its depth array values (i.e. go from the seabed to the surface instead of the other way around). This changes means the POLCOMS data matches the convention in the FVCOM arrays (where the surface is the first index) and in the POLCOMS depth data. Also change the 1D interpolation to use the pchip interpolation method (shape-preserving piecewise cubic interpolation) instead of linear interpolation. The original change from pchip to linear was because I thought pchip didn't do extrapolation, but since we're scaling the POLCOMS vertical profiles to the FVCOM depths, it doesn't matter. Finally, some miscellaneous changes (moving the creation of the open boundary nodes array to outside the loops and tidying up some of the whitespace/figures code

Change the way the open boundary nodes are obtained to match that which is in the code which generates Casename_obc.dat. This should stop problems with ordering values in the input arrays where the manner in which the list of open boundary nodes are generated in different ways resulting in different output orders

Add a couple of diagnostic figures at the end of the function for sanity checking the function. Also change the way the open boundary nodes are index by using the same approach as is in the code to generate the Casename_obc.dat file. This should avoid problems where the interpolated arrays store the data in a different order from how FVCOM is expecting it (I am assuming here that FVCOM assumes the order of boundary nodes specified in Casename_obc.dat will be common across all input data which use the open boundary nodes. This seems sensible to me)

Add check to avoid setting nodes as river nodes when that node is part of only one element. If this is not added, then the model fills up the element without moving the water out of that element, eventually leading to a crash, which is obviously not ideal. The fix searches for another node in the element which is part of at least two elements, thereby avoiding the "element filling" issue

Add the beginnings of a unit test file for the get_POLCOMS_tsobc function to make sure it returns the same data as a 'known good' verison. This is by no means complete yet

Add a data directory (with a brief document outlining the data types). This repository omits the actual data files as they are too large, but the files may be made available elsewhere (and a note to that effect added to the README)

    - The number of nodes and elements in the returned arrays against the reference arrays.
    - The number of time steps in the returned arrays.
    - The range of values in the arrays (both nodal and element arrays).

Add some (simple) unit tests to make sure the results of the toolbox functions are maintained between changes.

At the moment, this is only a simple check against an existing result, so it is not particularly comprehensive, but it should sound alarm bells if something has broken catastrophically.

The data against which grid2fvcom is compared is not included in the toolbox as it is too large (and this whole testing thing might be moved to a separate repository if it makes more sense that way).

Add the matlabpool code to actually open the workers rather than letting MATLAB try to figure out that it should do it itself

Make the interpolation of the regularly gridded data to the unstructured grid occur in parallel. So far as I can tell (and have tested) this has not changed the results of the interpolation, but the speedup is significant (from almost interminable to over in the blink of an eye). Getting the loop to be able to be parallelised required refactoring the code a bit (mainly through the creation of intermediate arrays), but as I said, it seems to have improved things speed-wise

Add parallel loop support in the loop through the positions in the regular grid. This function only interpolates the regularly gridded POLCOMS vertical grid onto the FVCOM vertical grid; horizontal gridding happens afterwards in interp_POLCOMS2FVCOM. Also update the comments to better reflect what is actually being done in this function

Add support for parallel execution of the vertical sigma layer interpolations. In addition to this function being launched in parallel, the subfunction grid_vert_interp.m is also parallelised. Although, now that I think about it, that might mean the two functions are competing for the workers in the pool and thus might be suboptimal. I will have to run some tests to see if that is the case

Make the construction of the combined struct be a little less complicated whilst maintaining the same functionality

Add minor syntax changes (extra spaces here and there). Also move the verbose statments to after the return so they actually get run!

Add the required fields to the Mobj help. Also add an example usage section. Finally, tidy up some of the fprintf statements

Fix the precipitation and evaporation case statements to use either the original prate and pevpr (the latter is probably wrong since its units are W/m^{2} whereas FVCOM wants m/s) or P_E or Et (which are probably better choices). Also improve the help at the beginning by adding required fields in Mobj and adding an example usage section

Fix the evaporation to use pevpr rather than P_E (which is actually the precipitation minus the calculated evaporation). Remove some old code which was commented out anyway. Add some more verbose output to better clarify what is actually being written and when. Other minor changes to the formatting (e.g. fprintf statements)

Add the beginnings of a child function to actually convert the pp files to something more sensible (e.g. NetCDF)

Add the first steps in producing a function to automatically download the Met Office Unified Model outputs

Remove section warning against polygons in the map file. Add a note saying that if polygons have been created in FVCOM, then the effect is that it is a lot easier to handle islands within the domain as SMS has done the hard work of groups different arcs into islands and coastline sections

Fix some remaining FORTRAN code (do loop and float function) to MATLAB. Also add a function description to match the format of the other tools in the toolbox. Also reformat the code to MATLAB standard format (indentation etc.).