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* change nodata_value to -99999 in topotools Previous value -9999 did not have enough digits since new etopo 2022 data has this as an actual topography value in the Mariana Trench (when written with `Z_format='%.0f'`). * Fix bug related to tracking pressure at gauges * simplify make_fgout_animation.py use of update_artists These do not need to be passed into update, unpacked, and repacked, since the objects created in the script will be used into update. If blit==False then they are not needed at all. * use image backend Agg in make_fgout_animation.py so animation size agrees with specified figure size * set blit=False and auto-detect number of fgout frames * clean up make_fgout_animation.py * added new chile2010_fgmax-fgout/make_fgout_animation_with_transect.py * Add dZ_format parameter to DTopography.write function The default is now '%.3f', millimeter resolution, making smaller dtopo files than previously. * handle 0 radius * fix type on set_pressure * fix duplicate r * make comparison fp-safe * handle underflow * avoid underflow in wind setting too * point to riemann/src for Riemann solvers * Remove Riemann solvers from src/2d/bouss, Makefile.common points to riemann/src Note that rpn2_geoclaw.f and geoclaw_riemann_utils.f were update in riemann/src to handle 5 waves and rpt2_geoclaw_sym.f was discarded in favor of standard rpt2.f, which works fine with 5 waves. * Initial CI GitHub action script * Update testing.yml * Add checking out of clawpack and geoclaw * Add lint and testing to CI * Disable linting for the time being * Re-enable linting but only for geoclaw * Exclude old_topotools.py Do not want to touch the old topotools file for reference. * initial commit of xarray backends and example use file * remove extra words * relax assumption of where command is issued (no longer needs to be in run directory). * Fix up gauge plotting for storm surge Includes a couple of minor bugs related to gauge plotting. Major change involves how we now plot the gauge data. * Add dry gauge plotting * create gauge filenames that allow more than 5 digits in gauge number If fewer than 5 digits, still add zero padding e.g. gauge00012.txt but no longer throws an error for large gauge numbers, e.g. gauge1234567.txt * cleaner way to zero pad only if fewer than 5 digits using I0.5 format * Cleanup and reimplement reading of ATCF and writing of GeoClaw storms * Minor string comparison bug fix * Extract name of storm from file name * Minor tweaks and fixes * Fix missing comma * AutoPEP8 surge code * add more information about rioxarray * better import error for rioxarray * add B and level * add fgout output_style parameter and support for array of output_times * remove trailing whitespaces in fgout_module.f990 * Refactor fgout_module.f90 so it works for either GeoClaw or D-Claw and support in fgout_tools.py for new dclaw attribute dclaw to set in setrun.py to indicate D-Claw, in which case 7 components of q are output instead of 4. Support for eventually indicating fewer components to output. * Use geoclaw module rho * Remove module level parameters that were not needed or were specific These mostly pertained to the CLE code. * Initial implementation of rotation control * Minor bugfixes and rearranging * Fix bugs in the non-spherical coordinates for storms" * fix fgout_tools.FGoutGrid.read_fgout_grids_data for time array Now that `output_style==2` is supported for fgout grids (an array of times, see clawpack#617), the function fgout_tools.FGoutGrid.read_fgout_grids_data needs to be fixed to properly read in the new format of `fgout_grids.data`, also note that `nout` now comes before `tstart` and `tend` for `output_style==1`. * Add kwargs to Topography reading * Add radii to plotting options * Add plotting of storm tracks * add clip example * return ds * Allow specifying which components of q to output on each fgout grid Modifications to fgout_module.f90 and fgout_tools.py, primarily. Can now set `fgout.q_out_vars` to a list of which components of q to output for each fgout frame (Fortran indexing). The default is `fgout.q_out_vars = [1,2,3,4]` for all components of q[1:3] and also eta (4), consistent with the previous behavior. The user could also/instead ask to output the topo B as component 5. (If two out of three of h, eta, B are output then the other can be computed from these.) Note that this list is written out to `fgout_grids.data` rather than a boolean list of True/False values for each possible component as is done in other places in GeoClaw. * working on dclaw variables * Fix fgout_tools.py to support fgout.q_out_vars also for Boussinesq or D-Claw When instantiating fgout_tools.FGoutGrid object, new qmap parameter can be set to 'geoclaw', 'geoclaw-bouss', 'dclaw', or a custom dictionary. (Eventually add 'dclaw-bouss' option also). This dictionary has the form `{'h':1, 'hu':2, etc}` with mapping from fgout variable names to Fortran indices of q in the code creating the fgout output. * Update topo_module.f90 The `character` variables that were storing variable names and IDs for NetCDF topography reading were only length 10. This just makes them 64 characters long. Probably too long but not really a big deal. * fix data_file -> data_path * add FGoutGrid.read_fgout_grids_data_pre511 for reading legacy fgout_grids.data from before v5.11 * add to doc string for pre511 * print more helpful error msg if fgout_grids.data seems to be pre511 * force user to call read_fgout_grids_data before read_frame * Fix chiles2010_fgmax-fgout scripts to make fgout animations Now need to call fgout_grid.read_fgout_grids_data() explicitly, but do not need to set format. * Leave output_format as an argument to FGoutGrids.__init__ but not that this is ignored since it is read from fgout_grids.data. Also properly handle output_format == 2 for binary32. * fix qmap=='geoclaw-bouss' mapping * wip * first pass at using revised fgout data structure with backends. * add a few more comments. * name updates * bdiff->bdif * remove vestigial _qelements * Add example that should work with/without dask * improve drytol handling (now tested for both absence of h, and absence of h, eta, and B) * don't specify error type. * switch from hard coded drytol to user-specified drytol * update use of dry_tolerance * fix exceptions. * update examples/tsunami/chile2010/setplot.py Improve this by using new options added in recent releases so the plots look better and this can better serve as a template for other problems. * Fix src/bouss/amr2.f90 call to set_fgout, adding nvar This was modified in the shallow/amr2.f90 code to support more fgout flexibility in clawpack#624, and this change is also required in the bouss version. Also enhanced the examples/bouss README files a bit. --------- Co-authored-by: Randy LeVeque <rjl@uw.edu> Co-authored-by: Kyle Mandli <kyle.Mandli@gmail.com> Co-authored-by: Barnhart, Katherine (Katy) Ruth <krbarnhart@usgs.gov>
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