Mailman 3 February 2012 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

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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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

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.

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problem with fields that use ghost zones
by Britton Smith 29 May '12

29 May '12

Hi everyone, I'm having a problem using fields that use ghost zones. The following simple script: http://paste.yt-project.org/show/2010/ gives this error: http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/ I am working from the tip, but I get the same behavior from yt/2.3. In yt/2.2, everything is working. I am working now to narrow that range down a bit, but does anyone have an idea? Britton

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shine through images
by Elizabeth Tasker 13 Mar '12

13 Mar '12

Hi, Is there a way to create an image that, rather than being a projection, shows the maximum or minimum point of a field? Elizabeth

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Kraken yt/dev import error
by Britton Smith 29 Feb '12

29 Feb '12

Hi, The yt/dev and yt/dev-local modules on Kraken are giving errors when trying to do 'from yt.mods import *'. Just doing that give the following error: http://paste.yt-project.org/show/5A6G4lAjr7UE2y1wsLNQ I get the exact same thing with both of those two modules. Thanks! Britton

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Velocity dispersion profile
by Jun-Hwan Choi 29 Feb '12

29 Feb '12

Hi YT users, I would like to make a (spherical and/or cylindrical) profile of the velocity dispersion. In order to do so, I need to compute the mean velocity (BulkVelocity) for a given shell (or ring), and pass this value to newly defined velocity dispersion field, and then make a profile for the velocity dispersion field. Is there a particular way in yt to handle this? Junhwan P.S.: A few weeks ago I posted a similar question and Matt gave me a following hint. @derived_field(name = "deltaLocalCircularVelocity") def delta_LocalCircularVelocity(fi eld, data): fn, x, cv = data.get_field_parameter("local_circular_velocity") cv0 = na.interp(data[fn].ravel(), x, cv) cv0 = cv0.reshape(data[fn].shape) delta_cv = cv0 - data["LocalCircularVelocity"] return delta_cv You'll need to do something like this on the data object from which you are getting your data: sp.set_field_parameter("local_circular_velocity", (fn, prof[fn], prof["LocalCircularVelocity"])) However, it does not work for me and it is also complicate to understand and modify it. -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Velocity dispersion profile
by Jun-Hwan Choi 29 Feb '12

29 Feb '12

Hi YT users, I would like to make a (spherical and/or cylindrical) profile of the velocity dispersion. In order to do so, I need to compute the mean velocity (BulkVelocity) for a given shell (or ring), and pass this value to newly defined velocity dispersion field, and then make a profile for the velocity dispersion field. Is there a particular way in yt to handle this? Junhwan P.S.: A few weeks ago I posted a similar question and Matt gave me a following hint. @derived_field(name = "deltaLocalCircularVelocity") def delta_LocalCircularVelocity(field, data): fn, x, cv = data.get_field_parameter("local_circular_velocity") cv0 = na.interp(data[fn].ravel(), x, cv) cv0 = cv0.reshape(data[fn].shape) delta_cv = cv0 - data["LocalCircularVelocity"] return delta_cv You'll need to do something like this on the data object from which you are getting your data: sp.set_field_parameter("local_circular_velocity", (fn, prof[fn], prof["LocalCircularVelocity"])) However, it does not work for me and it is also complicate to understand and modify it. -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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yt error on kraken
by Yuan Li 28 Feb '12

28 Feb '12

Hi all, I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken. I tried to run it interactively and it worked, but when I submit it as a job, I get this error: P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__ File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data ....... File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either. Sorry the error message is quite messy... Yuan

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volume rendering brightness
by Geoffrey So 28 Feb '12

28 Feb '12

Hi volume rendering experts, I was playing around with a density volume render of a tiny cube on my laptop, everything went smoothly, however, I notice a change in "overall" brightness between images when I did a rotation. I'm not sure how to explain this, but it seems that from images of different angles, sometimes the average brightness is consistent, but sometimes it suddenly drops and the image would look about half as bright, and after a couple frames it would light back up. I'm guessing this is after each image is ray casted, it gets normalized to a certain value, and that value changes depending on the angle? Is there a way to pin the brightness between images so if I make a movie it won't dim and light up as I rotate? Also I was wondering if I'm the only person to notice this? (the only other post I found about volume render brightness is about AMR cell contributions) From G.S.

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Bad grid edges in particle fields
by Casey W. Stark 28 Feb '12

28 Feb '12

Hi all. This is a projection of the Dark_Matter_Density field from the initial output of a standard enzo cosmological run with just 2 cores. It looks like something is going wrong on the grid boundaries. This occurs for projections and slices, but only for gridded particle data. The gas density looks fine. It seems to occur at every grid boundary, which I tested by increasing the number of cores (so the same number of grids). I can't tell if this is an enzo or yt issue, but I figured I should ask here first in case I missed something on the yt side. Has anyone seen this before? Best, Casey P.S. What is the status of the yt image server? Should we attach or imgur images in the future?

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yt-users February 2012