Hi Dietmar,
It looks like Micael made a change to GitHub - COSIMA/topogtools: Tools related to changing ocean model topography and regenerating dependent model inputs. in late 2022 (post when I wrote that tutorial, which was quite a while ago) that has caused this. Specifically, he added a frac input to the topog2mask.py code (Add two new tools: one automatically fixes non-advective cells found … · COSIMA/topogtools@03cfc66 · GitHub) that seems to have broken backward compatibility. I’ll put an issue on that repository.
In the mean time, I think you can most likely fix this by just using an older version of the code. Can you try again checking out an older commit - specifically, in the git directory that you created when you did git clone https://github.com/COSIMA/topogtools.git try doing
git checkout 952cbb16ba7cf8cf55c4aad425f33e2edeb62fe5
and then run it again.
With regards to the second question: It depends on what you’re doing (i.e. do you want geothermal heating to change, although I’m pretty sure geothermal heating is not on in ACCESS-OM2 anyway)? However, if you’re not worried about these things and all you want to change is the topography and land-sea mask, then I don’t think so. Those files aren’t masked and the values look reasonable:
I hope that helps. My memory of that process is a bit fuzzy, but happy to try and help if you run into any other issues.