Mailman 3 May 2011 - yt-users

ThermalEnergy units
by Elizabeth Tasker 16 May '11

16 May '11

Hi, Really quick query --- When I do a slice of the ThermalEnergy, the units come out as ergs/cm3. Shouldn't it be ergs/g ? Thanks, Elizabeth

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Covering Fraction / Solid angle
by Elizabeth Harper-Clark 16 May '11

16 May '11

Hi Guys, Is there a way to quantify values in yt by solid angle around a point? For example I have a simulation of star clusters forming within a turbulent GMC. When a bubble is present I want to calculate the covering fraction of the shell. One way to do this would be using where the radiation pressure is absorbed and calculate the fraction of solid angle (around the oldest cluster) radiation pressure is absorbed above a minimum value out to a given radius. See attached for projections of this simulation at a time with a bubble shell! (bottom left shows radiation pressure absorption). Has anyone written any code/script to calculate solid angle before? Many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Astrophysics, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca AIM: edphc1 MSN: edphc1(a)hotmail.com Skype: eharperclark Office phone: 416-978-5759

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yt Logo Winner!
by Sam Skillman 16 May '11

16 May '11

Hello avid yt logo contest followers! In a battle the likes of which we've never seen before (mostly because it was the first time), only one logo could survive. And the winner is.......Logo 5 by Carolyn Peruta! Logo 5 started off with an early lead, continued to lead in the middle, and finished strong! Congratulations, Carolyn, and enjoy your new mug and the pride that comes along with it! The winning logo can be seen here: http://i.imgur.com/0AAv5.png . Thanks for playing, everyone! Sam

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Halo Profiler
by Carolyn Peruta 13 May '11

13 May '11

I have a script which calls HaloProfiler and throws the following error: Traceback (most recent call last): File "sim_halo_profiler.py", line 28, in <module> fancy_padding=True, rearrange=True)) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 22 8, in __init__ self.pf = load(self.dataset) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/convenience.py", line 85, in load if c._is_valid(*args, **kwargs): candidates.append(n) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/frontends/tiger/data_structures.py", line 202, in _is_valid return os.path.exists(args[0] + "rhob") TypeError: unsupported operand type(s) for +: 'EnzoStaticOutput' and 'str' I did a quick test with iyt and it turns out it produces this error with the most simple form, hp=HaloProfiler(pf). Any ideas? Best, Carolyn On May 13, 2011, at 3:19 PM, Britton Smith wrote: > Hi Carolyn, > > I don't think it's a version difference. The halo profiler is supposed to take just the path to the dataset. It should do the load call in the halo profiler. I'm not sure why that would be happening. Either way, if it's working, that's all that matter. > > Also, nice job with the logos. I think yours had the best aesthetics of them all. I voted for 7. > > Britton > > On Fri, May 13, 2011 at 12:27 PM, Carolyn Peruta <perutaca(a)msu.edu> wrote: > Thanks again for sending such great looking volume renderings! > > I started halo analysis today and I couldn't get your sim_halo_profiler script to work unless I added: pf=load(output['filename']) and changed all the calls of output['filename'] to pf. I kept getting an error, 'str' object has no attribute 'h'. Could this be due to some change in yt versions between your use of this script and mine? > > -C > > On Mar 22, 2011, at 4:23 PM, Britton Smith wrote: > > > Hi Carolyn, > > > > I'm attaching some analysis code you might find useful. > > > > yt-advanced-plotting.tar contains some scripts for making projections and nice images from those projections. The subdirectory in there called advanced_examples contains the scripts needed to make the image in the test_frames directory in there. Specifically, those scripts can make the image which has particles overlaid that are colored by age and sized by mass. I think that will be perfect for what you're working on. > > > > I've also attached a script for running the halo profiler to make radial profiles of all the halos in your simulation. Something you might find useful in there is that I've added profile fields for stellar_density, StarAgeYrs, and StarMetallicity. These may be very interesting to look at as a function of radius within your target halo. > > > > Let me know if you have any questions about this stuff. Also, if you have any other ideas for analysis that you're not sure how to implement, let me know and we can discuss ways to implement them. > > > > Keep rocking. > > > > Britton > > <yt-advanced-plotting.tar><sim_halo_profiler.py> > >

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iterating through data in AMRCoveringGrid
by Elizabeth Tasker 13 May '11

13 May '11

Hi, I want to write a script in yt that reads in data from a simulation output, extracts a 3-dimensional grid from it of a set size at a fixed resolution and then iterate through the data points calculating various properties. I think I can do this using covering_grid using the example in the cookbook: cube = pf.h.covering_grid(4, left_edge=[16.4299, 10.8963, 16.0], right_edge=[18.4299, 12.8963, 16.02], dims=[258,258,4], fields=["PotentialField"]) But I'm now not sure how to get to the data! I'd like to write a loop in the form: k = 0, 3 j=0, 257 i = 0, 257 something = data(i,j,k)*etc I feel this should be obvious but I can't figure out the AMRCoveringGrid object! Thanks, Elizabeth

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Memory Error in parallelHF
by Carolyn Peruta 13 May '11

13 May '11

I'm getting a memory error running parallelHF on Ranger. Is this a bug or is there some sort of way to request more memory in my job script? Here is the full traceback: Traceback (most recent call last): File "sim_halo_profiler.py", line 17, in <module> rearrange=True, safety=1.5, fancy_padding=True) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1921, in __init__ threshold=threshold, dm_only=dm_only, rearrange=rearrange, premerge=premerge) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1368, in __init__ HaloList.__init__(self, data_source, dm_only) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 992, in _ _init__ self._run_finder() File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1389, in _run_finder self.threshold, rearrange=self.rearrange, premerge=self.premerge) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf ace.py", line 68, in __init__ yt : [INFO ] 2011-05-13 11:42:17,599 Building kd tree for 9519616 particles... self._chain_hop() File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf ace.py", line 1428, in _chain_hop self._chain_hop() File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf ace.py", line 1428, in _chain_hop self._init_kd_tree() File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf ace.py", line 347, in _init_kd_tree fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64')) self._init_kd_tree() File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf ace.py", line 347, in _init_kd_tree MemoryError fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64')) File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/numpy/core/numeric.py", line 408, in asfortranarray return array(a, dtype, copy=False, order='F', ndmin=1) MemoryError

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Control of thread/program not returning to ipython after creating a plot
by Jean-Claude Passy 13 May '11

13 May '11

Hi all, I am analyzing some MESA data using iyt instead of a regular ipython. Everything works well except that when I make a plot with yt, control is not returning to the prompt. I have tried to start yt with different thread options (-gthread, -qthread, -q4thread and -wthread) but none of them worked. My version of yt is built with python 2.7.1. The weird thing is that it works smoothly with a regular version of ipython built from python 2.6.4. I would really appreciate if someone could help me to fix this. I would like to keep using yt and not have to change all my settings. Thanks a lot, JC

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yt Logo Voting
by samskillman＠gmail.com 11 May '11

11 May '11

If you have trouble viewing or submitting this form, you can fill it out online: https://spreadsheets.google.com/spreadsheet/viewform?formkey=dGxwcGxfMU1pQl… yt Logo Voting Go here to see the entries: http://imgur.com/a/hZmq6. Voting is open until 11:59:59pm EST on Friday, May 13th. Cast your vote for your favorite logo * The entries are all on the above link. Choose your favorite! Logo 1 - Note that background is transparent Logo 2 Logo 3 Logo 4 Logo 5 Logo 6 Logo 7 Powered by Google Docs Report Abuse - Terms of Service - Additional Terms

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Profiles, root grid
by david collins 10 May '11

10 May '11

Hi there-- I'd like to add a profile object using only the root grid. I typically do something like this: pc.add_profile_object(region,fields, weight=weight) Is there a way to restrict this to only root grid tiles? I've tried using a covering grid, but that's throwing some key error (that I'm looking into presently, I'll have more info if/as I sort it out) Thanks, d. -- Sent from my computer.

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yt Logo Contest, and possibly a free mug!
by Sam Skillman 10 May '11

10 May '11

Hi all, yt is in need of an awesome new logo, which is why we are announcing the first ever new logo contest! So here's the deal: We'll accept entries for the next two weeks. Let's arbitrarily say Tuesday, May 10th, at 11:59:59 pm EST. If there is more than one entry, we will put it up for a community vote at that time. Oh, and the most important part -- the winner will get a coffee mug with their new logo front and center!!! Please email yt(a)enzotools.org with your image attached. Good luck, and happy logo-ing! Sam

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