Britton, I am still confused about making merger trees with yt. I ran rockstar on my snapshots, but the ytree doc page says it is only able to make trees from Gadget FoF/Subfind halo finders. I could use Consistent Trees, but it needs halo catalogs in rockstar native format, not in h5 format that is produced by yt. Nick On 10/5/2018 12:06 PM, Britton Smith wrote:
HI Nick,
Sadly, yt's FoF and HOP finders don't output member particle information for the halos, so it might not be possible to use those catalogs to make merger trees. ytree's merger-tree creation works with FoF catalogs generated by the inline Gadget halo finder, for which yt supports extracting member particle information. If you're looking to make merger-trees, the best route currently is probably Rockstar/consistent-trees, the outputs of which can be loaded by ytree.
It is probably a week's worth of work to fix up yt's HOP/FoF finders to output particle information and then to add support for loading that into yt.
Britton
On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin
mailto:gnedin@fnal.gov> wrote: Folks,
I am confused about how to compute merger trees with yt. Documentation (https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.html?... https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_analyzing_analysis-5Fmodules_halo-5Fmerger-5Ftree.html-3Fhighlight-3Dmerger-2520tree&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=zeRRll5QvyPrOQIZHiEPcx7nJk84AGxCHVY_xIV4OZ8&s=JcesVppFFSFwh2Hj4CdmDhGC6m2PJwj6igNfcC-vblA&e=)
refers to ytree package, but that package documentation seems to indicate that only FoF or Subfind halo catalogs can be converted into a merger tree, while the halo finder in yt is HOP.
I have run HOP for several snapshots from a simulation. What would you recommend to use to make a merger tree from such a data set?
Thank you,
Nick Gnedin
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Hi Nick,
Sorry for the long delay. Lots of travel this past week.
After reading through this discussion, I have two comments that might help.
First, to get rockstar to run on multiple datasets, you need to create a
time series object and pass that directly to the RockstarHaloFinder. For
example,
import yt
yt.enable_parallelism()
from yt.extensions.astro_analysis.halo_finding.rockstar.api import \
RockstarHaloFinder
ts = yt.DatasetSeries(LIST_OF_FILES)
rh = RockstarHaloFinder(ts, num_readers=1, num_writers=1)
rh.run()
Note, I'm using the yt_astro_analysis
https://github.com/yt-project/yt_astro_analysis package, where all these
tools have now moved for future development. I think the installation docs
are also a bit clearer there. The halo finding part of the documentation
definitely needs improvement. I'll try to do this within yt_astro_analysis
docs https://yt-astro-analysis.readthedocs.io/en/latest/.
Second, if you've now got all of the rockstar catalogs and don't want to
use consistent-trees, what you'll need are the out_*.list files that get
made. There will be one for each snapshot. You should find these within the
rockstar_halos directory. If you have those, you can feed the first one,
usually out_0.list, straight to ytree and it will assemble the merger trees.
import ytree
a = ytree.load("out_0.list")
Britton
On Wed, Nov 21, 2018 at 11:43 AM Nick Gnedin
Britton,
I am still confused about making merger trees with yt. I ran rockstar on my snapshots, but the ytree doc page says it is only able to make trees from Gadget FoF/Subfind halo finders.
I could use Consistent Trees, but it needs halo catalogs in rockstar native format, not in h5 format that is produced by yt.
Nick
On 10/5/2018 12:06 PM, Britton Smith wrote:
HI Nick,
Sadly, yt's FoF and HOP finders don't output member particle information for the halos, so it might not be possible to use those catalogs to make merger trees. ytree's merger-tree creation works with FoF catalogs generated by the inline Gadget halo finder, for which yt supports extracting member particle information. If you're looking to make merger-trees, the best route currently is probably Rockstar/consistent-trees, the outputs of which can be loaded by ytree.
It is probably a week's worth of work to fix up yt's HOP/FoF finders to output particle information and then to add support for loading that into yt.
Britton
On Fri, Oct 5, 2018 at 6:07 AM Nick Gnedin
mailto:gnedin@fnal.gov> wrote: Folks,
I am confused about how to compute merger trees with yt. Documentation ( https://yt-project.org/doc/analyzing/analysis_modules/halo_merger_tree.html?... < https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_analyzing_analysis-5Fmodules_halo-5Fmerger-5Ftree.html-3Fhighlight-3Dmerger-2520tree&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=zeRRll5QvyPrOQIZHiEPcx7nJk84AGxCHVY_xIV4OZ8&s=JcesVppFFSFwh2Hj4CdmDhGC6m2PJwj6igNfcC-vblA&e= )
refers to ytree package, but that package documentation seems to indicate that only FoF or Subfind halo catalogs can be converted into a merger tree, while the halo finder in yt is HOP.
I have run HOP for several snapshots from a simulation. What would you recommend to use to make a merger tree from such a data set?
Thank you,
Nick Gnedin
_______________________________________________ yt-users mailing list -- yt-users@python.org mailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org mailto:yt-users-leave@python.org
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participants (2)
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Britton Smith
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Nick Gnedin