Mailman 3 February 2016 - yt-users

Quick question
by Kailash Faris 06 Feb '16

06 Feb '16

I havent been on yt in about a month and I receive this error message when I use the command 'yt notebook' http://paste.yt-project.org/show/6226/ Does anyone know how to fix it?

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Confusing distribution of the number of particles per octree node
by Bili Dong - Gmail 04 Feb '16

04 Feb '16

Hi all, I'm looking at the number of particles per octree node (n_p hereafter) (a.k.a. the ('deposit', 'all_count') field) and find the results confusing. To my understanding, an octree node is refined (into 8 sub-nodes) only when n_p (of that node) > n_ref, so eventually n_p.mean (the average value of n_p) should be greater than n_ref/8. But the number I get is much smaller. When n_ref = 64, I get n_p.mean approximately 2 for all my tests. I'm wondering if my understanding of the octree refining process if correct? And if so, how to explain the weird distribution of n_p? Here's the link to my tests: https://nbviewer.jupyter.org/gist/qobilidop/d8f4cb85f1b465770854 Thanks, Bili

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Re: [yt-users] yt-users Digest, Vol 96, Issue 2
by Slavin, Jonathan 04 Feb '16

04 Feb '16

Hi Nathan, Oddly when I just updated via conda ("conda update yt") I got version 3.2.2. Jon On Thu, Feb 4, 2016 at 11:15 AM, <yt-users-request(a)lists.spacepope.org> wrote: > Message: 1 > Date: Thu, 4 Feb 2016 10:14:46 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org>, " > yt-dev(a)lists.spacepope.org" > <yt-dev(a)lists.spacepope.org> > Subject: [yt-users] ANN: yt 3.2.3 release > Message-ID: > < > CAJXewOmW0BCr0Z9_kYdmeWamM90k0jJWCxJRYvkxgHRpkO1ziw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > We are proud to announce the release of yt 3.2.3! > > yt (http://yt-project.org) is an open-source, community-developed toolkit > for > > analysis and visualization of volumetric data of all types, with a > particular > > emphasis on astrophysical and nuclear engineering simulations. > > Version 3.2.3 is a regularly scheduled bugfix release including fixes for a > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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DM density profiles
by Junhwan Choi (최준환) 03 Feb '16

03 Feb '16

Hi yt user, I make a simple DM and gas density profile for my enzo simulation with following script: ====================== import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") Nbin= 100 rmax = 4000 index = 60 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] my_sphere = ds.sphere(center, rmax*units.pc) rmin = max([1.0e-4,2.0*ds.index.get_smallest_dx().in_units('pc')]) profile = yt.Profile1D(my_sphere, 'radiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field='cell_volume') profile.add_fields(('gas','density')) profile.add_fields(('gas','dark_matter_density')) profile.add_fields(('deposit','all_density')) plt.plot(np.log10(profile.x), np.log10(profile[('gas','density')]), label="('gas','density')", linestyle="-", color='g') plt.plot(np.log10(profile.x), np.log10(profile[('gas','dark_matter_density')]), label="('gas','dark_matter_density')", linestyle="-", color='r') plt.plot(np.log10(profile.x), np.log10(profile[('deposit','all_density')]), label="('deposit','all_density')", linestyle="-", color='b') plt.legend(loc=0,prop={'size':9}) plt.savefig('DMTest') ====================== The only particle in the simulation is the dark matter so that profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] should be same. However, as shown in the attached figure, they are very different. I would like to ask a few questions regarding to this plot. 1) Why do profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] show significant difference? 2) What limit the minimum r in profile[('deposit','all_density')]? 3) If I would like to make total density profile, what do I do? I think that profile[('deposit','all_density')] is more liable result. Can I add data[('gas','density')] and data[('deposit','all_density')], two different field types, in the derived field? Thank you in advance, Junhwan Choi _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Can I specify the particle type when loading data?
by Bili Dong - Gmail 03 Feb '16

03 Feb '16

Hi yt users, I'm working with a particle dataset and I'm wondering if it is possible to only load a certain type of particle fields from the snapshot as my dataset? For example, there might be 'PartType0' and 'PartType1' in the snapshot, but I only want to load 'PartType0'. The reason I want to do this is that, to my understanding, the octree of the particle dataset is constructed adaptively according to the number of particles, including all types of particles in the dataset. But I want the octree constructed only according to the type of particles I'm interested in. Is it possible? Thanks, Bili

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faster method for getting frbs?
by Slavin, Jonathan 03 Feb '16

03 Feb '16

Hi all, I've been using yt to handle FLASH AMR data stored in HDF5 files. I want to cycle through a series of images generated, plotting each as I go using matplotlib. To do this I have (somewhat simplified): for f in files: ds = yt.load(f) slc = ds.slice(2,0) # its 2D r-z data frb = slc.to_frb(width=(Rmax,'pc'), height=(Zmax, 'pc'), resolution=(NX,NY)) image = np.array(frb['temp']) imshow(img) etc. This works the way I want it to, but is very slow. Is there a way to speed it up? Thanks, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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