Mailman 3 May 2011 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

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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Clear memory?
by Elizabeth Tasker Sept. 1, 2011

Sept. 1, 2011

Hi, Is there any way in yt to get a script to delete (or ignore) all the .yt and .harray files and clear its memory? I run into errors when I'm re-doing a plot or I've re-run the simulation and over-written the last data set I looked at with yt. I have to exit yt, delete the above files by hand and restart, which is a bit of a pain. Elizabeth

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new fields in output
by Elizabeth Tasker July 17, 2011

July 17, 2011

Hi, I've added PotentialField to the data that gets outputted. I'd like to read this into yt, but how does this work when yt won't be expecting PotentialField to be one of the data sets? Elizabeth

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Reason
by Christine Simpson June 8, 2011

June 8, 2011

Hi all, I'm not sure if this is the right list to send this to, but I think a bunch of knowledgeable people read this one, and hopefully one of you can help me. I'm trying to use Reason and I'm kind of confused about the ssh tunneling part. I start up yt serve on a remote machine (ranger) and I'm told to create a ssh tunnel by executing these commands: ~C -L55185:localhost:55185 My local machine doesn't recognize "~C" and I'm not sure what it is either. I tried creating an ssh tunnel with this: ssh tg803911(a)ranger.tacc.utexas.edu -L 55185:localhost:55185 I was then able to successfully open the gui in a browser with the url provided, but I am unable to load data (I can view the help though). In order to do the ssh tunnel properly do I need to install something on my local machine? Christine

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Trestles module
by Matthew Turk June 2, 2011

June 2, 2011

Hi all, Adam Jundt at SDSC just let me know that there's now a yt module on Trestles. If you're running there you should be able to load yt with "module load yt". We now have modules at Trestles, Nautilus, Kraken and I'm also told on Odyssey and SciNet. Having modules created for community usage is a strategy we're going to try to keep pursuing, so let me know if there are modules elsewhere; this will soon be on a central wiki or document of "maintained installations." Best, Matt

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Support for cylindrical coordinates?
by Pan, Kuo-Chuan June 1, 2011

June 1, 2011

Hi, Does yt support FLASH data with 2D cylindrical coordinates? If yes, how to enable it? If not, is it easy to implement it? I couldn't find info about it in the website. Thank you very much. Sincerely yours, Kuo-Chuan

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question about the star analysis module
by Christine Simpson May 28, 2011

May 28, 2011

Hi all, I have a question about the star analysis module. I understand how to run it and print out a file with the results, but is there a way to run it and access the results within the script? I am ignorant of how classes work in python, and I am uncertain whether there is a trivial way to access the contents of a star analysis object, or whether I need a method to access its contents. I looked at the code for the class and I didn't see a method that does this, so I'm guessing there is a simple way to do this? Christine

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YT's treecode
by Andrew Davis May 28, 2011

May 28, 2011

Hello again, First, thanks for the code fix. I am, however having some problems with the speed up -- at the moment, I'm not seeing any, unfortunately. I'm testing this with ~ 140000 cells of a zoom in AMR simulation. The number of levels in the region is 11, so it's very similar to what is posted on the YT clump-finding help page (http://yt.enzotools.org/doc/analysis_modules/clump_finding.html#treecode-op…) -- namely the first figure for L=10 dataset with slightly fewer cells. When I run: > sp = pf.h.sphere(c,0.065/pf['pc']) > pot = sp.quantities["IsBound"](truncate=False, include_thermal_energy=False, treecode=False, opening_angle=0.0) the timing is just ~230 seconds. However, just changing to opening_angle=1.0 and treecode=True, the time is roughly 900 seconds. Higher opening angles only decrease the time by a little bit (opening_angle = 8.0 takes rougly 850 seconds). The error is still very small, so it is calculating the right number at least, just slower than I think it should, as the figures on the help page suggest around a factor of two speedup is expected. Is there anything that you see that I'm doing wrong? Thanks! Andrew ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

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Treecode question
by Andrew Davis May 27, 2011

May 27, 2011

Hi folks, I just updated my yt yesterday to use the new treecode algorithm in calculating binding energies. Many many thanks to those who worked on it and tested it. However, I'm looking at the code, and I see this in the function (on line 388 of derived_quantities.py): octree = Octree(cover_ActiveDimensions, 1, True) #print 'here', cover_ActiveDimensions # Now discover what levels this data comes from, not assuming # symmetry. dxes = na.unique(data['dx']) # unique returns a sorted array, dyes = na.unique(data['dy']) # so these will all have the same --->>>> dzes = na.unique(data['dx']) # order. # We only need one dim to figure out levels, we'll use x. dx = 1./data.pf.domain_dimensions[0] I've marked the line where I would think it should be getting data['dz'] instead of 'dx'. Am I just not getting this or should this be changed? Thanks! Andrew ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

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halo profiling memory problem
by gso＠physics.ucsd.edu May 27, 2011

May 27, 2011

Hi Stephen, I'm trying to do halo profiling with parallelHP on a 1024 cube dataset 14 Mpc/h at z=5. I used to be able to do this on data of the same size on Triton with 256GB of RAM, and I'm trying it on Nautilus with the same amount of RAM. Should I be using more processors for faster results or should I cut down the number of processors as there's memory overhead as I increase the core count? From G.S.

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