I actually haven't gotten the plot yet that Brian made due to my HaloProfiler problem (which I'm about to start working on). I have got his list of haloes reproduced. The plot I made earlier was with a threshold=160.0, and Brian ran at 80.0. He also ran with a lower minimum group size in regroup (2 versus 20), which is something that is currently hard coded in yt-hop. So the lower threshold and the lower minimum group size is what I needed.
The hop website says two things of note here:
""" -mingroup int Only groups with this many particles or more will be outputted. Default: 10
Remember that HOP is biased against finding groups smaller than N_dens or N_hop; hence, setting -mingroup to be tiny is usually pointless. """
I'll make this a parameter, but I am going to leave it at -1 for default, which sets it to 10. This is what it's been doing... I've also set the dsaddle by default to be what Greg suggested, 2.5*threshold.
So in summary, I see what you're saying. I'd then add at minimum, the minimum group size, and -dsaddle.
Done, changeset is on bitbucket:
Strictly speaking I don't need to set self.mingroupsize and self.dsaddle in the HaloFinder, but that's not a big deal. HopOutput.py doesn't need these changes because they're optional arguments.