yt-users March 2011

yt-users@python.org

20 participants
41 discussions

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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Clear memory?
by Elizabeth Tasker 01 Sep '11

01 Sep '11

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 17 Jul '11

17 Jul '11

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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A treecode for the clump finder
by Stephen Skory 28 Mar '11

28 Mar '11

Hi All, I have just pushed to the development branch of yt a modification to the clump finder(*) which should make the identification of gravitationally bound clumps run much more quickly. Previously, the gravitational potential energy of clumps was calculated using the full double sum that iterates over all unique pairs of cells in the clump. This is, of course, accurate, but it is quite slow because it is an O(N^2) operation. A generally much faster and very accurate (but not perfectly accurate) method of calculating gravitational potentials is the treecode method of Barnes & Hut [1] which reduces the operation down to O(N log N). Using the Octree that Matt added to yt some time ago (and had never used) I implemented a treecode on top of it. There may be some further optimizations to the code, but especially for clumps larger than 100,000 cells, the treecode is substantially faster, up to several times for very large clumps. For intermediate clumps of a few tens of thousands of cells, the treecode is actually a bit slower, but no worse than 50%. This is due to likely both the extra cost of setting up the treecode hierarchy, and perhaps some optimizations I have yet to catch. At any rate, for now the time gains from the very large clumps should offset the time losses for smaller clumps. Unfortunately, the treecode will not help unigrid datasets because the levels of the octree mirror the levels in the dataset, and a treecode needs more than one level to work. But it is my impression that people do not do clump finding on unigrid datasets. Please correct me if my impression is wrong! Also, the octree is x2 refinement-specific. In the course of this work I noticed that periodic clumps would not be processed correctly, so I have added some machinery that should fix that using either the N^2 or treecode method. The treecode is now on by default in the development branch. Let me know if you have any questions, or problems with the code. Thanks! [1] http://adsabs.harvard.edu/abs/1986Natur.324..446B (*) To be precise, the modifications are to the "IsBound" derived quantity, but that is most often called from within the clump finder. As a point of fact, I have actually not touched the clump finder at all. Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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Second y axis
by Elizabeth Harper-Clark 28 Mar '11

28 Mar '11

Hi guys, I would like to plot a graph of mass in stars against time. In addition to the normal y axis (total stellar mass in solar masses) I would like a second y axis on the right side which translates this stellar mass into a fraction of the original gas mass. Thus the line is the same it is just the two y axes are scaled versions of each other. Does that make sense? Can anyone suggest a way to do this? 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

2 1

Derived fields?
by Elizabeth Tasker 25 Mar '11

25 Mar '11

Hi, I'm sure I've seen this before, but possibly in the old version of the yt online docs .... is there a list of fields, derived and raw, that you can call via data["FieldIWant"]? I'd really like it to be linked from the "Analyzing Data" page here: http://yt.enzotools.org/doc/analyzing/index.html Perhaps right before "Derived Quantities" since I keep hopefully looking there automatically .....? (That's assuming that the list has gone awol and isn't somewhere equally obvious). Hoping doc comments are ultimately helpful and not just annoying, Elizabeth

2 1

ranges
by Elizabeth Tasker 25 Mar '11

25 Mar '11

Hi, How do I set a y-range on add_profile_sphere? As a suggestion, perhaps we could add this to one of the examples in the cookbook? Also, in the cookbook, these links no longer work: "The latest version of this recipe can be downloaded here: http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_slice.py ." Elizabeth

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Taking the magnitude of a vector field
by John ZuHone 24 Mar '11

24 Mar '11

Hi all, I'd like to create a new yt field from a yt vector field where I take its magnitude. Any thoughts on a good NumPy-ish way to do this? Best, John ZuHone

2 1

Run time error after new install
by Elizabeth Tasker 24 Mar '11

24 Mar '11

Hi, I've had to reinstall yt due to an unconnected python problem but now I have a runtime error: /home/taskere/yt/yt-2/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py in _get_agg_font(self, prop) 219 font = self._fontd.get(fname) 220 if font is None: --> 221 font = FT2Font(str(fname)) 222 self._fontd[fname] = font 223 self._fontd[key] = font RuntimeError: Could not open facefile /home/taskere/yt/yt-2/lib/python2.6/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannotpen_Resource I ... forget whether this happened before :\ Elizabeth

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multiplot with multiple datasets
by Jean-Claude Passy 24 Mar '11

24 Mar '11

Hi all, I would like to create a multi plot equivalent to the procedure described in the Cookbook (Multi plot 3x2) *BUT* with different datasets (1 slice for 1 dataset). The first issue I am encountering is that the module raven is not detected: ############################################################# Traceback (most recent call last): File "/rpod2/jcpassy/Enzo/python/MultiPlot.py", line 20, in <module> fig, axes, colorbars = raven.get_multi_plot( 2, 4, colorbar=orient, bw = 4) NameError: name 'raven' is not defined ############################################################# Then, is there a specific description somewhere of how to do a multi plot with different datasets ? Thanks a lot for your help, JC

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yt-users March 2011