yt-users November 2018

yt-users@python.org

12 participants
23 discussions

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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CURVE FITS FOR MULTIPLE 1D PROFILES
by Vadlamani Samhitha 29 Nov '18

29 Nov '18

Hi, I've been looking for a way to overplot fits for multiple 1D profiles? Is there a way in yt to do this?

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Ramses star- dark matter particle filter
by Vadlamani Samhitha 29 Nov '18

29 Nov '18

Hi, I would like to know if it’s possible to have a particle filter based on the mass resolutions of the particles. I am using RAMSES data where I can distinguish stars and dark matter only from their mass resolutions (no particle_type). Any help is highly appreciated.

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ERROR IN PARTICLE FILTER
by Vadlamani Samhitha 28 Nov '18

28 Nov '18

Hi, I am trying to make a particle filter for just the old stars for which my simulation requires pruning with two fields "particle_mass" and "particle_age". def old(pfilter, data): > > age = data["all", "particle_age"] > > old_only = data["all", "particle_mass"] > > filter = np.logical_and(age.in_units('Myr') = 0, > old_only.in_units('Msun') < 4e6) > > return filter > > > But I encounter an error: File "new-old-stars.py", line 14 > filter = np.logical_and(age.in_units('Myr') = 0, > old_only.in_units('Msun') < 4e6) > ^ > SyntaxError: keyword can't be an expression Could someone please point out what the issue here could be? Can I not use a filter with two different fields?

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Re: Merger trees
by Nick Gnedin 27 Nov '18

27 Nov '18

Britton, Thank you very much for the instructions, Rockstar seems to work well with a time series dataset. Could you briefly tell me what the difference is between the two methods for building merger trees: (1) using consistent-trees and (2) using ytree directrly with ytree.load("out_0.list")? What would ytree use for making a merger tree? n On 11/25/18 12:02 PM, Britton Smith wrote: > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_yt-2Dprojec…> 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://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>. > > 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 <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > 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 <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <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_a…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dproject.org_doc_a…>) > > > > 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(a)python.org > <mailto:yt-users@python.org> > > <mailto:yt-users@python.org <mailto:yt-users@python.org>> > > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>> > > > > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > Virus-free. www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com&d=DwMFaQ&c=…> > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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How can I set a value with its units to derived_field?
by lianxiaoli87＠sjtu.edu.cn 25 Nov '18

25 Nov '18

Hi, all: I need an initial value of CMB magnetic to derive a new field in plugins python file. How can I set the unit of "gauss " to this value? For I can not carry on my calculation between CMB magnetic strength (dimensionless) and the outputs of Enzo (in units of gauss).

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Re: Merger trees
by Nick Gnedin 25 Nov '18

25 Nov '18

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 <gnedin(a)fnal.gov > <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_a…>) > > 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(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> > Virus-free. www.avg.com > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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yt-users November 2018