Hi Carla,

Sorry, the halo finding call and import have changed. You now use the HaloCatalog for all halo finding, including rockstar. It should now look like this:

import yt
from yt.extensions.astro_analysis.halo_analysis import HaloCatalog

my_sim = yt.load_simulation('enzo_tiny_cosmology/32Mpc_32.enzo', 'Enzo')
hc = HaloCatalog(data_ds=my_sim, finder_method='rockstar',

                 finder_kwargs={"num_readers": 1, "num_writers": 1})
hc.create()

See the link below for more info

https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html

Britton

On Wed, Mar 24, 2021 at 9:57 AM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Hi Britton,

I updated my yt_astro_analysis package, but now I get this error: When trying to run

 from yt.extensions.astro_analysis.halo_finding.rockstar.api import RockstarHaloFinder

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/users/carla/yt/lib/python3.8/site-packages/yt/exthook.py", line 88, in load_module

    raise ImportError('No module named %s' % fullname)

ImportError: No module named yt.extensions.astro_analysis.halo_finding

My first thought was that yt_astro_analysis wasn't finding my installation of rockstar-galaxies, but I still have the file rockstar.cfg with the correct path to rockstar in my cloned repository of yt_astro_analysis. I am using the rockstar-galaxies repository from John Wise, which did not throw this error before I updated my yt_astro_analysis. Do you use the same repository or the one from Peter Behroozi?

Thanks,

Carla

Am Mo., 22. März 2021 um 17:15 Uhr schrieb Britton Smith <brittonsmith@gmail.com>:

Hi Carla,

Ok, this new version was only merged on Friday, so if you installed before then, you won't have it.

Britton

On Mon, Mar 22, 2021 at 4:09 PM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Hi Britton,

Thanks for clarifying. I installed yt_astro_analysis as part of the process of installing rockstar-galaxies, so I think this shouldn't be the issue. I did not have this installed in my previous version, so I did not need to worry about older versions getting in the way.

Cheers,

Carla

Am Mo., 22. März 2021 um 15:29 Uhr schrieb Britton Smith <brittonsmith@gmail.com>:

Hi Carla,

Ok, great. Just to be clear, though, it's not rockstar you need to update, but the yt_astro_analysis package. If you have cloned the repository, you would need to go into it and do:

git pull origin master

./clean.sh

pip install -e .

On Mon, Mar 22, 2021 at 2:12 PM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Hi Britton,

Thanks for the feedback. I updated rockstar-galaxies about a month ago, but I can try running with fof or hop and see if I get better results. Thanks.

Best,

Carla

Am Mo., 22. März 2021 um 14:00 Uhr schrieb Britton Smith <brittonsmith@gmail.com>:

Hi Carla,

I would have expected some smaller halos, too, but I have no reason to believe the halo finder is not doing what it should be. You might try using fof or hop instead to see if things change. By the way, the halo finders were very recently updated. I would suggest pulling in the latest changes. The documentation has also been substantially improved.

https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html

Britton

On Mon, Mar 22, 2021 at 9:36 AM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Hi Britton,

Thank you for your reply. Adding the keyword "min_halo_size" changed the parameter in my rockstar config file, but when I redid the analysis, the halo sizes were still larger than expected. With a Particle mass of 1.31418e+05 Msun/h and MIN_HALO_OUTPUT_SIZE = 10, I was expecting to get halos on the order of 1e7 Msun/h. The smallest halos I get now are 1.2e8 Msun/h. Is that reasonable to expect and if so, what do I need to change to see those smaller halos?

Thanks,

Carla

Am Di., 9. März 2021 um 17:08 Uhr schrieb Britton Smith <brittonsmith@gmail.com>:

Hi Carla,

It looks like RockstarHaloFinder accepts a keyword called "min_halo_size" which sets the minimum particle number for halos. The RockstarHaloFinder code writes its own config file, which is then passed to rockstar itself, so that's why modifying that file by hand doesn't do anything.

Britton

On Mon, Mar 8, 2021 at 9:29 AM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Dear yt and rockstar users,

I recently installed the newest version of rockstar-galaxies as I had been using a much older version. Although the output reports a particle mass of 1.31418e+05 Msun/h, I don't see any halos smaller than 1e+08 Msun/h. I was expecting to get the minimum masses an order of magnitude lower. 

I see in the config includes MIN_HALO_OUTPUT_SIZE = 25, set as a default. I tried to change this parameter to 10 and restart from the beginning, but I run rockstar within yt with RockstarHaloFinder (yt.extensions.astro_analysis.halo_finding.rockstar.api), but my config file was overwritten by the defaults. Is this even the right approach? If so, how do I restart rockstar (more detailed than just rh.run(restart=True), please) with customized parameters within yt's RockstarHaloFinder?

Thanks in advance,

--

Carla Bernhardt

PhD Student

Universität Heidelberg

ZAH Institut für Theoretische Astrophysik

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Carla Bernhardt

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Universität Heidelberg

ZAH Institut für Theoretische Astrophysik

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Carla Bernhardt

PhD Student

Universität Heidelberg

ZAH Institut für Theoretische Astrophysik

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Carla Bernhardt

PhD Student

Universität Heidelberg

ZAH Institut für Theoretische Astrophysik

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Carla Bernhardt

PhD Student

Universität Heidelberg

ZAH Institut für Theoretische Astrophysik

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