Mailman 3 December 2013 - yt-users

Radial velocity Projections
by John Regan 19 Dec '13

19 Dec '13

Hi All, I was trying to make an OffAxis radial projection. Naively using proj = OffAxisProjectionPlot(pf, L, "RadialVelocityKMS", center='max', width=(width, 'pc'), depth=depth) fails with a message of type yt.data_objects.field_info_container.NeedsParameter: (['center']) The RadialVelocity probably isn't the field to use here and requires some manipulation to be a quantity suitable for plotting. Any suggestions on the best way forward would be much appreciated. Cheers, John

2 6

Running Rockstar Halo Finder to create a merger tree
by Hilary Egan 18 Dec '13

18 Dec '13

Hi all, I'm quite confused on a number of points related to running the rockstar halo finder, so I hope its alright that I put all these questions into this one email! 1. I can't seem to run the rockstar halo finder at all without getting this error followed by a segmentation fault and crash. [Warning] Network IO Failure (PID XXXXXX): Connection reset by peer [Network] Packet receive retry count at: 1 It sort of seems like this issue ( http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-November/002…) but I couldn't really figure out what the resolution was from the thread. Im attempting to run this on kraken and it doesn't matter if I use a single compute node or multiple, I get the same error. (I hope this isn't the infiniband issue the docs warned about, I couldn't figure out if that is how kraken is connected and I got an error that the suggested flag doesn't exist so I didn't press the issue.) 2. Whenever I finally do get the halo finder to work, I need the results to be in a form that the merger tree can use. It seems as though the MergerTree needs the results in the same form as the other halo finders give, so would getting the halo list and then dumping it as usual be the appropriate strategy? Ie: rh.run() halo_list = rh.halo_list() halo_list.dump('MergerHalos') 2.5. The docs sort of give mixed messages on whether or not I could just be calling MergerTree with the argument halo_finder_function = RockstarHaloFinder. At this point I've pretty thoroughly convinced myself that I can't, but it would be nice if that was clarified. (Just a thoroughly overwhelmed new user's perspective!) 3. I'm a little confused as to whether or not I have to use a TimeSeriesData object rather than the usual single time output when instantiating the halo finder. Under "Rockstar Halo Finding" it uses TimeSeriesData, unlike the rest of the examples, but under the subheading "Output Analysis" it just uses pf. The "Output Analysis" example also doesn't call the run() method, which leads me to believe something else entirely is going on, but its not quite clear. Thanks! -Hilary

7 8

Install yt in oak ridge system with system python package
by Junhwan Choi (최준환) 17 Dec '13

17 Dec '13

Hi yt user, Here, I have a naive question on installing yt. I try to install yt in the oak ridge super computer system particularly lens. People at the help desk suggest to use system python package in case I launch the analysis tool through the queueing system. What python package do I need to ask them? Can I simply turn on the default python in the system and install yt on my home directory? Or I need to request particular python package with numpy, matplotlib, scipy and so on. In addition, I would like to also use mpi4py since I will use large simulation data. Thank you, Junhwan

2 3

How yt deals with AMR grids and data objects
by k.grisdale＠surrey.ac.uk 16 Dec '13

16 Dec '13

Dear yt-users I am attempting to make a tool that will sample the properties of a RAMSES galactic disk simulation. The tools needs to be able to work on different scales going from very large (10kpc) to the very small (2x the size of the smallest cell ~140pc). So far I have achieved this using data objects and calling required property/Quantities that I need. On large scales this works very well, however on small scales I have run into the issue that only part of cells are within in my data object. While this is to be expected it is presenting so interesting results. From what I can tell if the centre of the cell is in my data object yt treats the cell as if the whole cell is within my data object but if the centre is missed it treats it as if the whole cell is absent from the data object, I’m looking for a median between these extremes. My question is is there a way to get yt to only take into account the proportion of the cell in side my data object? Also if the cell only has small corner in my data object is there away to get yt to fetch the properties of that cell (say the density and cell volume) and then multiply these values by the proportion of the cell that is in my object? Thank you in advance for you help Kearn

4 7

sample_colormap
by Mateusz Ruszkowski 11 Dec '13

11 Dec '13

Hi, I am trying to do a very simple test of the sample_colormap function: from yt.mods import * tf = ColorTransferFunction( (-30.0, -25.0) ) tf.sample_colormap(-27.0, 0.01, 'algae') and I am getting this error message triggered by the last line above: Traceback (most recent call last): File "layer_test.py", line 9, in <module> tf.sample_colormap(-27.0, 0.01, 'algae') File "/home/mateuszr/yt/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/transfer_functions.py", line 632, in sample_colormap self.add_gaussian(v, w, [r, g, b, alpha]) File "/home/mateuszr/yt/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/transfer_functions.py", line 404, in add_gaussian tf.add_gaussian(location, width, v) File "/home/mateuszr/yt/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/transfer_functions.py", line 81, in add_gaussian vals = height * np.exp(-(self.x - location)**2.0/width) TypeError: only integer arrays with one element can be converted to an index Am I doing something very silly here or is it a bug? Thanks, Mateusz

2 1

Reason gui after yt update --all
by CCAC South 10 Dec '13

10 Dec '13

Hello all, I recently update YT but now when I run Reason I cannot view slices or plots on any datasets. I get the following error message: Traceback (most recent call last): File "/home/ctay6066/yt-x86_64/src/yt-hg/yt/gui/reason/basic_repl.py", line 81, in execute exec code in self.locals File "", line 1, in File "/home/ctay6066/yt-x86_64/src/yt-hg/yt/gui/reason/widget_store.py", line 70, in create_slice setup = False, plot_type='SlicePlot') TypeError: __init__() got an unexpected keyword argument 'plot_type' Here is some additional info that may be helpful: The current version of the code is: --- be524f912750 --- This installation CAN be automatically updated. yt dependencies were last updated on Mon Dec 9 21:59:01 EST 2013 http://paste.yt-project.org/show/35x3VUOpItAuLpZgtcBl Please let me know if you need additional information.

2 1

Data objects in yt
by k.grisdale＠surrey.ac.uk 10 Dec '13

10 Dec '13

Hi yt users I am using yt to create data objects to sample properties in a RAMSES simulation at different locations. I want to create a cuboid data object with x and y width of 0.2 and a z width of 0.4. I have been using the following commands to create the object: >>> left = [0.4,0.4,0.3] >>> cen = [0.5,0.5,0.5] >>> right = [0.6,0.6,0.7] >>> box = pf.h.region(cen, left, right) My Question is will this create a data object of the shape that I want or will it create something else? Is there a way to see the shape of the data object? Thanks in advance for the help Kearn

3 2

camera rotation
by Mateusz Ruszkowski 07 Dec '13

07 Dec '13

Hi all, I am trying to understand how the camera rotation works in yt. I verified that the following set of commands C = (0.0,-50*kpc,zPos) L = (0.0,-1.0,0.0) W = 100*kpc N = (0.0,0.0,1.0) cam = pf.h.camera(C, L, W, 512, tf, N) cam.snapshot("single_snapshot.png") produces a nice image of a flat gas distribution located in the (x,y) plane anchored at zPos. I would like to move the camera around the z-axis while pointing it at (0,0,zPos) and take 10 snapshots. This should result in a sequence of 10 identical images of the same pancake-flat distribution of the gas. I tried this: for i, snap in enumerate(cam.rotation(2*np.pi, 10,N)): print "Taking snapshot % 3i" % (i+1) snap.write_png("rot_%04i.png" % i) My assumption was that "N" in the above command defines the vector around which to move the camera. This procedure did generate 10 images but they were all different rather than identical. My question is how do I move the camera around the z-axis while pointing it at (0,0,zPos), or in other words, how do I define the point where "N" is anchored. Thanks, Mateusz

3 4

How to efficiently control the memory in yt with large simulation?
by Junhwan Choi (최준환) 06 Dec '13

06 Dec '13

Hi all, I try to make some visualizations (density/temperature project) for large simulation with yt. The simulation is 4096^3 unigrid Ramses simulation. I try to implement the basics density and temperature projection plot with following script and I got memory problem and yt run is crashed. ===== from yt.mods import * ds = load("../output_00048/info_00048.txt", fields = ["Density","x-velocity", "y-velocity","z-velocity","Pressure","Metallicity","Rad"]) center = [0., 0., 0.] pw = ProjectionPlot(ds, "x", ("gas", "Density"), weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "y", ("gas", "Density"), weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "z", ("gas", "Density") , weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "x", "Temperature", weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "y", "Temperature", weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "z", "Temperature" , weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") ==== Is there any way to reduce the memory usage when I make visualization? If I use slice instead of projection, can I save the memory? I saw there is parallelization for yt. Does parallelization distribute the data at the beginning of the read? (But, I prefer to do so w/o parallelization at this moment.) Thank you in advance, Junhwan

4 7

Fw: yt command not found
by Michael Roberts 06 Dec '13

06 Dec '13

Hi ht-users, Just wondering, my terminal is returning yt command not found when executing the yt notebook command… Small problems but do you have any tips? /Michael

3 2