yt-users November 2018

yt-users@python.org

12 participants
22 discussions

by Elizabeth Harper-Clark

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

1 month, 2 weeks

Variance in phase/profiles

by david collins

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.

1 year, 9 months

3-D Mass power spectra

by 梁家豪

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

2 years, 7 months

CURVE FITS FOR MULTIPLE 1D PROFILES

by Vadlamani Samhitha

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

3 years, 2 months

Ramses star- dark matter particle filter

by Vadlamani Samhitha

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.

3 years, 2 months

ERROR IN PARTICLE FILTER

by Vadlamani Samhitha

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?

3 years, 2 months

Re: Merger trees

by Nick Gnedin

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> >

3 years, 2 months

How can I set a value with its units to derived_field?

by lianxiaoli87＠sjtu.edu.cn

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).

3 years, 2 months

Re: Merger trees

by 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 <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>

3 years, 2 months

Re: Merger trees

by Nick Gnedin

Nathan, I added rockstar to my yt installation, and it works, but only one snapshot at a time. I.e, when I try running the halo finder in the loop: for set in sets: d = yt.load(set) hc = HaloCatalog(data_ds=d,finder_method='rockstar',finder_kwargs={'dm_only':True,'particle_type':'N-BODY'}) hc.create() if(yt.is_root()): print('Memory: ',yt.funcs.get_memory_usage()) it runs once, but at the second loop iteration gives the following error. I checked the memory use, it is very small for this small simulation, so the segfault is most likely the result of the network failure. This was run with 1 reader and 1 writer on a single node: mpirun -n 3 python3 hfc-rs.py but I also tried more ranks, the error occurs independently of the number of ranks used. This is not critical, since I can run the script for each snapshot separately, but it would be nice to be able to run all of them at once. Perhaps, some network connections are not properly cleaned - I heard that rockstar does something weird with networking. Nick ------------- error messages ------------------------------ ... P001 yt : [WARNING ] 2018-11-21 10:54:13,109 Total Particle Count: 1.342e+08 [ 0s] Accepting connections... [ 0s] Accepted all reader / writer connections. [Warning] Network IO Failure (PID 146476): Connection reset by peer [Warning] Network IO Failure (PID 146476): Success [Network] Packet receive retry count at: 1 [Warning] Connection attempt 1 to nanna.uchicago.edu:59013 failed: : Connection refused [Warning] Network IO Failure (PID 146477): Connection reset by peer [Warning] Network IO Failure (PID 146477): Success [Network] Packet receive retry count at: 1 [Warning] Connection attempt 1 to nanna.uchicago.edu:59013 failed: : Connection refused ===================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES ===================================================================================== APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) On 11/19/18 4:12 PM, Nathan Goldbaum wrote: > Hi Nick, > > See the installation docs here, in particular the section titled > “installing support for the rockstar halo finder”: > > http://yt-project.org/doc/installing.html > <https://urldefense.proofpoint.com/v2/url?u=http-3A__yt-2Dproject.org_doc_in…> > > Nathan > > On Mon, Nov 19, 2018 at 2:47 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Britton, > > How would I install Rockstar for yt to use? Your webpage mentions > install-script.sh, but my from-source installation lacks it: > > ~/ART/yt >ls > appveyor.yml CONTRIBUTING.rst MANIFEST.in setup.cfg yt.egg-info > benchmarks COPYING.txt nose.cfg setupext.py > build CREDITS __pycache__ setup.py > CITATION doc README.md tests > clean.sh docker scripts yt > > I downloaded it as the help recommends, but then the script tries to > download and install yet another yt installation. > > I need to use my clone, since I made some changes to it that I haven't > yet submitted in a pull request. > > > > > > On 10/5/2018 12:23 PM, Britton Smith wrote: > > Hi Nick, > > > > Ok, good luck. It should be noted that the version of Rockstar > that runs > > with yt is not the latest version of Rockstar, known as > > Rockstar-Galaxies. yt's Rockstar does not support multi-mass > > simulations. You may also find different i/o performance between > the two > > versions, so it's worth experimenting, if both options are available. > > > > Britton > > > > On Fri, Oct 5, 2018 at 10:10 AM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote: > > > > > > Britton, > > > > Thank you very much, I will try Rockstar first. > > > > n > > > > > > On 10/5/2018 7:06 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>> > > > <mailto:gnedin@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…> > > > > > > <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>> > > > <mailto:yt-users@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>> > > > <mailto:yt-users-leave@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…> > > > <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=…> > > > <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…> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsig…>> > > > > > > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > _______________________________________________ > 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> >

3 years, 2 months

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yt-users November 2018