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There is a bug in file opencdf.F of the plotting package when processing the variable spherical in the grid NetCDF file. We need to use ID ncgrd instead of ncid1.

Many thanks to Simon Spagnol for ​reporting this typo.

Updated file hbackground.F for ROMS plotting package to add the new changes for common block mapcm1 in the NCAR's library version 5.2.0. I can believe that they continue making changes to this common block once in a while. It is annoying because the library is not backward compatible.

A new cpp option NCARG520 is introduced in the makefile to allow compiling with this version of the library.

Many thanks to Simon Spagnol for ​providing us his updated hbackground.F for this new version of the libray.

I am also using the logical flag lmask in mskcle.F to avoid land/sea masking, if wanted, when lmask=0 even if there is a land/sea masking array in the input NetCDF. In this way, the user may utilize this standard input parameter for land/sea masking behaviors in the plot. This is useful when plotting the raw bathymetry with the gebco palettes. It allows to color land with the appropriate values of the topography. The lmask=1 paints the land with a solid color. Of course, the hraw variable, record 1, needs to have positive values in the land and negative values in the water. Recall that the bathymetry used in ROMS, variable h, has the water values positive and the land is cropped to a constant positive value greater than zero. The variable hraw is never used in ROMS. Many users ignore this variable. I always like to write in record 1, the original topography before cropping and smoothing. In this way we save the starting raw topography for future reference.

I updated the matlab repository and included several new scripts and improved others.

The new scripts are:

• 4dvar/c_observations.m: creates 4D-Var observation NetCDF file.

• 4dvar/d_observations.m: driver template to process 4D-Var observation NetCDF file.

• 4dvar/d_ssh_obs.m: driver template to extract SSH observations for AVISO, create and write observation file. Then, it computes super observations and creates and writes super observations NetCDF file.

• 4dvar/inside.m: checks if a point is strictly inside of the region defined by a polygon. This is an old Matlab function which is not longer supported. It is very useful to find outliers observations.

• 4dvar/load_ssh_data.m: extracts AVISO sea level anomaly for the period of interest and specified region from ROMS Grid file.

• 4dvar/plot_super.m: sample script to compute and plot super observations from specified 4D-Var observations NetCDF file.

• 4dvar/obs_ijpos.m: computes observations locations in ROMS fractional coordinates. It uses the inside deprecated Matlab function.

• 4dvar/obs_read.m: reads observation NetCDF file and load all data into a structure array.

• 4dvar/obs_write.m: writes all observation data in structure array into an existing NetCDF file.

• 4dvar/super_obs.m: checks the provided observation data (4D-Var NetCDF file or structure) and creates super observations if there is more than one datum of the same observation type per grid cell.

• boundary/c_boundary.m: creates ROMS open boundary conditions NetCDF file.

• boundary/d_mercator.m: driver template to extract open boundary conditions from Mercator dataset. It creates open boundary conditions NetCDF file, interpolates data to application grid, and writes out data.

• boundary/obc_mercator.m: interpolates requested variable open boundary conditions from Mercator to ROMS grid boundary edges.

• grid/c_grid.m: creates or modifies a ROMS grid NetCDF file.

• initial/c_biology.m: defines ROMS biology variables to an existing initial conditions or climatology NetCDF file.

• initial/mercator2roms.m: interpolates requested variable data from Mercator to ROMS grid.

• utility/roms_vectors: processes vector data for either the full grid for boundary edges. The strategy is to get any horizontal vector field at RHO-points for the event that a rotation to ROMS curvilinear grid is needed. Then, they are computed at the appropriate Arakawa C-grid location.

• utility/uv_barotropic: computes vertically integrated velocity components for ROMS full grid or boundaries.

I also updated various existing scripts. I highly recommend users to update this repository.

Notice that two new directories were added: boundary and grid. Therefore, the startup.m was also modified to include the path of these directories.