Create `cropped.nc` and `unpacked.nc` in the current
directory. Several instances of script `inst_eddies.py` for different
slices should run in different directories.

We are reverting commit d4d05bc2. It was not true that we needed two
input fluxes in the Fortran program. `inst_eddies.py` can read the
file `config_nml.txt` and merge its content to stdin for the Fortran
program.

Always read coordinates from NetCDF file and create `grid_nml.txt`. Do
not try to read `grid_nml.txt`. Reverting part of commit c4410682. We
are trying to simplify the logic in program `inst_eddies`.

Add argument SHPC-dir to script `inst_eddies_Aviso.py`. We want to be
able to run `inst_eddies_Aviso` in parallel for several slices. Since
we write `used_config_nml.txt` to the current directory, we need to
run the parallel instances from different directories. So the current
directory cannot always be the directory containing the SHPC to be
appended to.

Add argument `SHPC_dir` to function `loop_inst_eddies`. We want to be
able to run `loop_inst_eddies` in parallel for several slices. Since
we write `used_config_nml.txt` to the current directory, we need to
run the parallel instances from different directories. So the current
directory cannot always be the directory containing the SHPC to be
appended to.

We are trying to simplify the logic in program `inst_eddies`. Also,
the program `inst_eddies` should not write `used_config_nml.txt` to
the top level of the SHPC directory since several instances could run
in parallel for several slices. So we are leaving it as a task for a
script over `inst_eddies` to create `used_config_nml.txt` at the top
level of the SHPC directory.

Do not try to read `used_config_nml.txt`. We are reverting commit
d9a67386, trying to simplify the logic in program `inst_eddies`. We
consider that using a single configuration for several runs of
`inst_eddies` is the problem of a script over `inst_eddies`, not the
problem of `inst_eddies`. Drawback: we write again
`used_config_nml.txt` in several runs of `inst_eddies`, but this is
not important.

We want to be able to run `inst_eddies` from a directory other than
the directory containing the SHPC to be appended to. Preparing to
write `grid_nml.txt` and `used_config_nml.txt` in the current
directory. To be able to do this in parallel for several slices, we
need to be running in different directories.

Makes more sense.

So the user can get the usage message more easily.

In program `examine_eddy`.

Change order of command line arguments of program
`examine_eddy`. Preparing to allow a variable number of NetCDF file
arguments.

Do not always specify uv-file when it is the same as ssh-file.

Instead of reading command line arguments in procedure `input_ssh`,
read them outside and pass file names to `input_ssh`. This allows
`input_ssh` to be called by programs with different number of command
line arguments, in different positions. Preparing to make the
specification of uv-file optional.

Lionel GUEZ authored 6 months ago and GUEZ Lionel committed 6 months ago

Reverting part of commit c4410682. We want to extend the program to a
non-uniform or non longitude-latitude grid. Checking equality of whole
longitude and latitude arrays, one or two-dimensional, seems a little
bit too much.

Useless since at least commit bff41cdd.

This was not useful since we do not need an array of snapshots in
`inst_eddies`. It is clearer without the integration in a snapshot
variable. The integration in a snapshot variable came from initial
commit, when there was only one program for detection of instantaneous
eddies and overlapping.

Replace argument `s` of `write_snapshot` by its component `list`.

Replace argument `s` of `set_all_extr` by its components. The idea is
to remove the structure `snapshot` from program `inst_edddies`.

We are circumventing a bug of the Intel Fortran compiler. This was
tested with both ifx `2023.1.0` and ifort `2021.9.0`. The bug occurs
on return from procedure `set_max_speed`: `free(): double free
detected in tcache 2` and crashes execution. The bug is revealed in
commit cc13fd5b. The GNU compiler does not have this bug.

To circumvent the Intel compiler bug, instead of an ssh component of
`cont_list_proj`, we have to use a separate array:
`cont_list_ssh`. This is maybe for the best because the component
`area` of `cont_list_proj` was not defined.

`n_points` can be deduced from previous print, and `n_extr` has been
printed too.