Mailman 3 October 2014 - yt-users

Fwd: [gadget-list] universal reader for python
by Nathan Goldbaum Oct. 26, 2014

Oct. 26, 2014

This might be of interest here. ---------- Forwarded message ---------- From: *Robert Thompson* <rthompsonj(a)gmail.com> Date: Sunday, October 26, 2014 Subject: [gadget-list] universal reader for python To: gadget-list(a)mpa-garching.mpg.de Gadget community, I wanted to share a tool that I’ve been developing for the past several years called pyGadgetReader. It is a universal gadget snapshot reader for python that supports type-1, type-2, HDF5, and TIPSY binary outputs (also supports binaries from FoF, P-StarGroupFinder, Rockstar, & Rockstar-Galaxies). I finally got around to polishing up the documentation and now believe it to be ready for public consumption. Happy simulating! https://bitbucket.org/rthompson/pygadgetreader -Robert Thompson

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empty field_list when loading old enzo output (possibly v1.5)
by Wing-Kit Lee Oct. 23, 2014

Oct. 23, 2014

Hi all, I have some outputs from an unknown (private) branch of Enzo (possibly as early as version 1.5). I believe there was no big change on the output structure vs actual Enzo 1.5. When loaded it with yt (3.0.2), I got an empty field list. Can someone point me to where I can look at? Thanks a lot! Best, Kit -- Wing Kit Lee Postdoc Fellow Academia Sinica, Institute of Astronomy and Astrophysics

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particle generator and update issues
by Elizabeth Tasker Oct. 22, 2014

Oct. 22, 2014

Hi everyone, I've hit a couple of problems trying to generate a particle distribution. I'm following the code here: http://blog.yt-project.org/post/ParticleGenerator.html (at the moment exactly: http://pastebin.com/JFnWeXqM ) The first issue was CICDeposit_3 doesn't seem to exist, but from the source code, it looks like it is now CICSample_3 via "from yt.utilities.lib.CICDeposit import CICSample_3". I switched this but then hit a different error: In [1]: execfile("particle_generator.py") yt : [INFO ] 2014-10-14 17:51:59,895 Parameters: current_time = 0.0 yt : [INFO ] 2014-10-14 17:51:59,895 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2014-10-14 17:51:59,895 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-10-14 17:51:59,896 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2014-10-14 17:51:59,897 Parameters: cosmological_simulation = 0.0 --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/tasker/yt-3/src/yt-hg/scripts/iyt in <module>() ----> 1 execfile("particle_generator.py") /home/tasker/yt-3/src/yt-hg/scripts/iyt in <module>() 39 'particle_position_y':y, 40 'particle_position_z':z} ---> 41 particles1 = FromListParticleGenerator(ug, num_particles1, pdata) 42 particles1.assign_indices() 43 particles1.apply_to_stream() /home/tasker/yt-3/src/yt-hg/yt/utilities/particle_generator.pyc in __init__(self, ds, num_particles, data) 227 228 field_list = data.keys() --> 229 x = data.pop(("io", "particle_position_x")) 230 y = data.pop(("io", "particle_position_y")) 231 z = data.pop(("io", "particle_position_z")) KeyError: ('io', 'particle_position_x') I tried updating the code, but 'yt update' then seemed to pull me back from yt-3.0 which I thought I was running (is branch 'yt' now yt-3?) to yt 2: tasker@schiehallion:~/yt-3/bin$ yt update yt : [INFO ] 2014-10-14 17:48:23,618 Loading plugins from /home/tasker/.yt/my_plugins.py yt module located at: /home/tasker/yt-new/src/yt-hg The current version and changeset for the code is: --- Version = 2.6.1 Changeset = f7c69809dbd0 (stable) --- This installation CAN be automatically updated. Reading configuration from /home/tasker/yt-new/src/yt-hg/.hg/hgrc Could someone give me a shove back onto the right track with those two issues? Thanks! Elizabeth

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API change for data_collection
by Chris Malone Oct. 21, 2014

Oct. 21, 2014

Hi all, If any of you happen to be using a data_collection object [1] for any purposes, please note that API has changed on the yt branch, according this this issue [2]. In particular, the 'center' argument is no longer required, but can still be passed as a keyword argument. Chris [1] http://yt-project.org/docs/3.0/analyzing/objects.html?highlight=data_collec… [2] https://bitbucket.org/yt_analysis/yt/issue/872/data-collection-object-requi…

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Re: [yt-users] streamlines and volume rendering
by Sam Skillman Oct. 21, 2014

Oct. 21, 2014

Hi Kiki, Thanks for the compliments on the volume rendering in yt. As of right now there isn't a simple way to add streamlines in the same figure. However, we are really close! There is a current work-in-progress [WIP] pull request https://bitbucket.org/yt_analysis/yt/pull-request/1256/wip-volume-rendering… where we are adding such a capability. What I'd suggest is to keep your ears open for new requests for testing the new framework and check back soon. I hope that by the end of the week we'll have some examples up on the pull request that would give you enough of a head start to try it out. I will try to remember to cc you when i send out requests for beta-testers. Cheers, Sam On Mon, Oct 20, 2014 at 6:02 PM, Dionysopoulou K. < K.Dionysopoulou(a)soton.ac.uk> wrote: > Dear Sir or Madam, > > I recently came across the yt libraries for python and was impressed by > its capabilities and the speed of the volume renderer in particular. The > library creates superior quality figures and I would like to use it for my > papers. The problem I have for now is that I would like to have volume > rendering plus streamlines of a vector field in the same figure and I > haven’t figured out how one could do that. Is there a way to achieve this > in yt? > > Thanking you in advance. > > All the best, > > Kiki > > Kyriaki Dionysopoulou > ======================================================= > Mathematical Sciences > University of Southampton > Southampton, SO17 1BJ, UK > K.Dionysopoulou(a)soton.ac.uk<mailto:K.Dionysopoulou@soton.ac.uk> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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derived field with Grackle?
by Brian O'Shea Oct. 21, 2014

Oct. 21, 2014

Hi folks, I am attempting to create a derived field from a cosmological simulation dataset using Grackle. Specifically, I have a simulation that was run with Grackle, but which unfortunately did not output the cooling time. Ergo, I'd like to create that as a derived field. Does anybody have an example of a Grackle-based derived field in yt that I can use as a model? I would note that I looked at the "run_from_yt.py" example in the Grackle distro, but it isn't quite what I need. Thanks! --Brian _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Halo Analysis in 3.0
by John Regan Oct. 20, 2014

Oct. 20, 2014

Hi All, I was testing out the new HaloCatalog infrastructure and I got stuck pretty quickly :) When trying to access the halo mass I tried to do so using the all_data() function and then the particle mass field e.g. hc = HaloCatalog(data_ds=data_ds, finder_method='hop') hc.create() ad = hc.all_data() masses = ad['particle_mass'][:] but the script failed on trying to access the all_data function - see traceback below. What is the best way to get at the Halo properties? Cheers, John yt : [INFO ] 2014-10-20 15:54:11,353 Loaded species (109 new fields) /homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/units/yt_array.py:739: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__div__(ro)) yt : [INFO ] 2014-10-20 15:54:11,450 Saving halo catalog (2 halos) to halo_catalogs/catalog/catalog. Traceback (most recent call last): File "BasicHaloFinder.py", line 12, in <module> ad = hc.all_data() AttributeError: 'HaloCatalog' object has no attribute 'all_data' _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Postdoc positions at NCSA
by Matthew Turk Oct. 14, 2014

Oct. 14, 2014

Hi everyone, The astro group at NCSA is in the process of hiring postdocs: http://www.ncsa.illinois.edu/about/jobs/postdoc_astro Postdocs in this group will have the opportunity to work on computational tools, especially yt, and to apply those tools both to astrophysics as well as other domains of science. I've attached a PDF copy of the ad, and I would encourage you to forward this on to any colleagues or groups that may be interested. Please email me at mturk(a)ncsa.illinois.edu if you have any questions! Best, Matt

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colorbar in AxesGrid of yt slices
by Morgan MacLeod Oct. 14, 2014

Oct. 14, 2014

Hi all, I have a question related to saving multipanel figures generated with the AxesGrid toolkit as ".eps". I've made a few plots in which I *very* closely follow this example: http://yt-project.org/doc/cookbook/multiplot_2x2_time_series.py Except I replace the save line with plt.savefig('my_figure.eps',format='eps') I am hoping to fix this issue (where the colorbar has thin lines in it): http://stackoverflow.com/questions/15003353/why-does-my-colorbar-have-lines… with a line like: cbar.solids.set_rasterized(True) I haven't been able to figure out, though, how to access the colorbar object itself within the context of the AxesGrid. In the example script, we access the colorbar axes, which is close, but not quite what is needed, I think. Thank you in advance for the help, Morgan

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Rockstar and RAMSES (DM only run). Rockstar appears to run, but no halo information is written.
by Ben Thompson Oct. 14, 2014

Oct. 14, 2014

P.S sorry if I sent the same email twice.. this is the actual email... accidental press send before I sent the email out. Hello everyone. I am currently using YT to run rockstar on my simulation. I have been following the instructions which are around and about and have managed to write a script to run rockstar via MPI readers = int(ncpu/4.) #Reserve one cpu for the server writers = ncpu - readers - 1 print 'Running rockstar with %i writers and %i readers'%(writers, readers) rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers, particle_type="dark_matter", dm_only=True) rh.run() using a particle filter on the datasets @yt.particle_filter("dark_matter", requires=[('particle_mass')]) def dark_matter(pfilter, data): if ('all', 'particle_age') in data.ds.field_list: return data[("all", "particle_age")] == 0.0 else: arr = np.zeros(len(data['particle_mass'])) return arr == 0.0 def setup_ds(ds): #Return only dark matter particles, and assert that the filter holds print 'Here' assert(ds.add_particle_filter("dark_matter")) It seems to run fine.... e.g [ 111s] Sending projection requests... [ 112s] Transferring particles to writers... [ 116s] Analyzing for FoF groups... [ 116s] Transferring boundary particles between writers... [ 117s] Linking boundary particles... [ 117s] Analyzing for halos / subhalos... [ 119s] Loading merger tree information... [ 120s] Constructing merger tree... [ 121s] [Success] Done with snapshot 7. [ 121s] Reading 6 blocks for snapshot 8... P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins. P002 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins. P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded angular_momentum (8 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded astro (14 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded cosmology (20 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded fluid (56 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded fluid_vector (88 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded geometric (102 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded local (102 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded magnetic_field (108 new fields) P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded species (108 new fields) P006 yt : [INFO ] 2014-10-03 16:19:28,127 Loading field plugins. P005 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins. P003 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins. P004 yt : [INFO ] 2014-10-03 16:19:28,135 Loading field plugins. [ 129s] Sending projection requests... [ 130s] Transferring particles to writers... [ 132s] Analyzing for FoF groups... [ 133s] Transferring boundary particles between writers... [ 133s] Linking boundary particles... [ 134s] Analyzing for halos / subhalos... [ 137s] Loading merger tree information... [ 138s] Constructing merger tree... [ 139s] [Success] Done with snapshot 8. [ 139s] Reading 6 blocks for snapshot 9... [ 143s] Sending projection requests... [ 144s] Transferring particles to writers... [ 146s] Analyzing for FoF groups... [ 147s] Transferring boundary particles between writers... [ 147s] Linking boundary particles... [ 148s] Analyzing for halos / subhalos... [ 150s] Loading merger tree information... [ 151s] Constructing merger tree... [ 152s] Constructing merger tree... [ 153s] [Success] Done with snapshot 9. [ 153s] [Finished] generates the outputs halos_0.0.ascii halos_1.14.bin halos_2.4.ascii halos_3.9.bin halos_5.14.ascii halos_6.3.bin halos_7.9.ascii halos_9.13.bin halos_0.0.bin halos_1.15.ascii halos_2.4.bin halos_4.0.ascii halos_5.14.bin halos_6.4.ascii halos_7.9.bin halos_9.14.ascii halos_0.10.ascii halos_1.15.bin halos_2.5.ascii halos_4.0.bin halos_5.15.ascii halos_6.4.bin halos_8.0.ascii halos_9.14.bin halos_0.10.bin halos_1.16.ascii halos_2.5.bin halos_4.10.ascii halos_5.15.bin halos_6.5.ascii halos_8.0.bin halos_9.15.ascii halos_0.11.ascii halos_1.16.bin halos_2.6.ascii halos_4.10.bin halos_5.16.ascii halos_6.5.bin halos_8.10.ascii halos_9.15.bin but they are all empty.... yet within profiling, it seems to imply that there were some particles submitted to be analised [Prof] S0,C0 0s: 10191 fofs, 123365 particles, 0s for conf. [Prof] S0,C0: 0p,0h,0w; wt:0s; rcv:0s,0s; snd:0s; wk:0s; idl:1s [Prof] S1,C0 0s: 10377 fofs, 123363 particles, 0s for conf. [Prof] S1,C0: 1814p,73h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s [Prof] S2,C0 0s: 9843 fofs, 123353 particles, 0s for conf. [Prof] S2,C0: 5115p,139h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s [Prof] S3,C0 0s: 9616 fofs, 123359 particles, 0s for conf. [Prof] S3,C0: 9637p,221h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s [Prof] S4,C0 1s: 9256 fofs, 123367 particles, 0s for conf. [Prof] S4,C0: 14849p,314h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s [Prof] S5,C0 0s: 9233 fofs, 123361 particles, 0s for conf. [Prof] S5,C0: 17771p,369h,1w; wt:0s; rcv:0s,0s; snd:1s; wk:0s; idl:0s [Prof] S6,C0 0s: 8964 fofs, 123365 particles, 0s for conf. [Prof] S6,C0: 19888p,388h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s [Prof] S7,C0 0s: 8996 fofs, 123356 particles, 0s for conf. [Prof] S7,C0: 22352p,426h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s [Prof] S8,C0 0s: 8801 fofs, 123361 particles, 0s for conf. [Prof] S8,C0: 22553p,441h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s [Prof] S9,C0 1s: 8806 fofs, 123361 particles, 0s for conf. [Prof] S9,C0: 22685p,440h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s Is there anything I should consider looking at to debug this problem? Any suggestions of what to look at? Thanks Ben

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