namelists and param

[rs028]

Some progress towards understanding the new features of the user interface (see #5).

The files in namelists/ are configuration files for each model run and apparently take the place of the src/istart file. However, istart still exists in src/ and it is not clear whether it is necessary or is completely superseded by implementation of the namelists.

The files in param are executable scripts. The model runs after modifying the directories in the param/scripts that point to input and output directories for a model run, as well as the correct namelist configuration file.

@pb866 : can you try this, when you have some time, and see if it works for you as well? If you manage to compile first of course (see suggestion in #10).

Things to consider:

• the names param and namelist are not very clear. We should consider renaming the directories.
• should the scripts and the configuration files be in the same directory instead of two different directories? Should the output directory also be the same so that for each run the configuration, the output and the related script are together?
• is src/istart still needed? Are there other files that have been made superfluous by the new user interface?

[rs028]

At the end of the param_example script, the command mv fort.* *.out *.nc rst*.dat *.asc $OUTDIR returns a warning message:

mv: cannot stat 'fort.*': No such file or directory
mv: cannot stat '*.asc': No such file or directory

The .asc files are from the nucleation module, not sure what should generate the fort. files.

As a temporary fix, the command has been changed to mv *.out *.nc rst*.dat $OUTDIR. This just means that, if generated, the files would remain where they are created, instead of being moved to the output subdirectory with all the other output files.