fix bug in writing fesom.mesh.diag.nc

[patrickscholz]

• Raika tried to compute the density gradient in the channel sigma_xy in python like its done in fesom by using gradient_sca_x and gradient_sca_y from the fesom.mesh.diag.nc file and stepped into some issues.

• We found out that, like the code was written until now it exchanged the indices between gradient_sca_x[1,:] and gradient_sca_x[3,:] as well as gradient_sca_y[1,:] and gradient_sca_y[3,:] when it was written to the fesom.mesh.diag.nc file. The same is also valid for the arrays of gradient_vec_x and gradient_vec_y.

fesom2/src/io_mesh_info.F90

Lines 531 to 534 in 354fe9b

	do i=1, 3
	call gather_elem(gradient_sca(i, 1:myDim_elem2D), rbuffer, partit)
	call my_put_vara(ncid, gradient_sca_x_id, (/1, 4-i/), (/elem2D, 1/), rbuffer, partit) ! (4-i), NETCDF will permute otherwise
	end do

• its unclear to me why it was written in that way with (/1, 4-i/) which clearly writes the 3. index into 1st position and the 1. index into 3rd position, only index 2. is correctly located. However there is the comment " ! (4-i), NETCDF will permute otherwise", im not sure if there is here a hidden netcdf version issue or if its just plain wrong! Now with this bug fixed through ...

 do i=1, 3 
    call gather_elem(gradient_sca(i, 1:myDim_elem2D), rbuffer, partit) 
    call my_put_vara(ncid, gradient_sca_x_id, (/1, i/), (/elem2D, 1/), rbuffer, partit) ! (4-i), NETCDF will permute otherwise 
 end do 
...

... the outcome regarding sigma_xy looks now correct!

[koldunovn]

@vasmue you might then need to update your example :) https://github.com/FESOM/FESOM_examples/blob/main/gradients_div_curl/FESOM_example_gradients_div_curl.ipynb

[patrickscholz]

@koldunovn: Do we have a general channel to inform all fesom users? since this bug will affect a lot of fesom.mesh.diag.nc files and gradient analysis dependent on that file

[koldunovn]

We have FESOM mailing list at [email protected], but it is rarely (almost never :)) used, so I am not sure if it's a best channel. Otherwise - release notes :)