Mailman 3 August 2013 - yt-users

segmentation fault while extract_obj
by Lucky Puspitarini Aug. 20, 2013

Aug. 20, 2013

Hello all, My name is Luki. I'm new in yt. I have a problem in extracting object from yt. I want to have the surface object in .obj or .ply file so then i can transform it to .u3d for 3d pdf I have a data cube that i build this way. from yt.mods import * from numpy import * myfile=loadtxt("3ddata_300_lowerres.txt") dens=myfile[:,3] densitycube=dens.reshape(61,61,61) mydata=dict(Density=densitycube) bbox=np.array([[-300,300],[-300,300],[-300,300]]) pf=load_uniform_grid(mydata,densitycube.shape,3.08e18,bbox=bbox) Then, I would like to have a surface of certain value in my data and extract it to .obj files sp = pf.h.sphere("center", (250, "pc")) trans = 1.0 distf = 3.08e18 surf = pf.h.surface(sp, "Density", 0.0006) surf.export_obj("myism.obj", transparency=trans, dist_fac = distf) But i have a problem with segmentation fault. Segmentation fault: 11 I'll also try export_ply but i have the same problem :( sp = pf.h.sphere("center", (250, "pc")) surf = pf.h.surface(sp, "Density", 0.0006) bounds = [(sp.center[i] - 125.0/pf['pc'],sp.center[i] + 125.0/pf['pc']) for i in range(3)] surf.export_ply("myism.ply",bounds=bounds) Can you help me? Thankyou in advance Best regards, luki

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How to address yt issues
by Nathan Goldbaum Aug. 20, 2013

Aug. 20, 2013

Hi all, This past week I prepared some slides on how to deal with and report issues that may come up in daily use of yt. The slides are available here: http://ngoldbaum.net/for_agora/get_help.pdf The slides were based on a talk Cameron gave at the first yt workshop at the FLASH center in January 2012 but I went ahead and updated them to reflect current best practices. If you have a minute, please take a look. Cheers, Nathan PS: The slides for the yt-3.0 demo I gave are also available: http://ngoldbaum.net/for_agora/Agora_ytdemo.slides.html

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Trouble plotting 1D scatter data from 3D Athena vtk data.
by Timothy Waters Aug. 20, 2013

Aug. 20, 2013

Hi, Here is the data and simple script to make a scatter or profile plot of my simulation output, https://www.dropbox.com/sh/ibpda938ltsxl0j/2AA2FYDUH8#/ This is a spherically symmetric (cartesian [-0.5,0.5]^3, 32cells^3) hydro simulation with initial conditions density = 1.0 if radius <= 1/3; density falls off as 1/r^2 if r > 1/3; velocity is everywhere 0 The output with these ICs is WP12.0000.vtk. When I run my script the first time using iyt I get the first image with the expected ICs. Running it again gives the second image and I don't know why. I'm hoping those other points don't actually exist in my data. Maybe I am just missing something simple? The evolved data, WP12.0030.vtk, is provided as well. Running this data 'cleans the slate' so that I can then go back to see the problem with my initial conditions again. Of course, the problem shows up in this data too. Thanks in advance! Tim

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Cylindrical and Polar Slicing (FLASH)
by Morgan MacLeod Aug. 20, 2013

Aug. 20, 2013

Dear yt gurus, I've enjoyed using yt for a number of FLASH problems in cartesian geometry. Right now I'm just starting on a setup in FLASH 2D polar (eventually also in 3D cylindrical) geometries. These are ordered 2D polar: r, theta 3D cylindrical: r, theta, z I was intrigued when I noticed this image on the yt-blog ( http://blog.yt-project.org/post/WhatsUpWith30.html) -- which is almost exactly what I would like to do. [image: http://blog.yt-project.org/attachments/cylindrical_pixelizer.png] I have updated to yt-3.0, and tried the simplest "Sliceplot" of the data: fn = "const_rho_g_atm_hdf5_plt_cnt_0013" pf = load(fn) fig = SlicePlot(pf, 2,'dens').save("myfig.png") This reads loads the 2D polar plot file correctly, but renders the result in a cartesian sense. Does anyone have advice/recipes for how to proceed with Slices rendered "cylindrically"? I understand that this feature set is not yet fully developed but I was curious if there was a solution (or parts of a solution) floating around out there. Thanks so much, Morgan MacLeod ------------------------------------------------- Graduate Student Astronomy & Astrophysics UC Santa Cruz

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao Aug. 19, 2013

Aug. 19, 2013

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao Aug. 16, 2013

Aug. 16, 2013

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Re: [yt-users] Cylindrical and Polar Slicing (FLASH)
by Mark Subbarao Aug. 15, 2013

Aug. 15, 2013

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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Field Cuts in Off-Axis Projections
by Munier Azzam Salem Aug. 14, 2013

Aug. 14, 2013

Hey guys, I've been trying to make slices of density only looking at cooler gas (i.e. with a cut in Temperature). I've found a nice way to do this for simple projections. But my strategy breaks for Off-Axis projections. Specifically, this works fine: * * *field_parameters={'field_cuts':["grid['Temperature'] < 1e6 "]})* *cold_proj = ProjectionPlot(pf,0,'Density',field_parameters=field_parameters)* * * but this does not: *cold_proj = OffAxisProjectionPlot(pf,axis,'Density',north_vector=north,* * field_parameters= field_parameters)* sensibly enough, since field_parameters is not a keyword argument for off axis projections. Is there a decent workaround for this? Or would this be simple to add into yt's functionality? I've looked briefly into the source<http://yt-project.org/doc/_modules/yt/visualization/plot_window.html#OffAxi…>and it doesn't seem obvious how to slip this in. thanks! Munier -- Munier A. Salem // 845.489.6450

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convering_grid question
by barbara ramirez Aug. 14, 2013

Aug. 14, 2013

Hello Everyone! So, I have a question about how does covering grid actually works. I have a Flash simulation output of a 28*28 Mpc box containing a cluster. I am trying to simulate the spectra from a region of size (0.08 Mpc x, 0.08 Mpc y, 28 Mpc z) around the centre, (I will assume z is my line of sight) so I use this line to define the region: #The shape of my region cube = pf.h.covering_grid(level_max, left_edge=newlep, right_edge=newrep,dims=[6, 6, 128]) where level = 5 (max level of refinement for my Flash data), "newlep" is centre coordinates (Mpc) minus 0.08 Mpc and newrep is centre coordinates plus 0.08 Mpc, and then into percentage units. I put them into an array of dimensions [6,6,128] because I want 36 spectra (one for each pixel of the ccd) so I will fix an (x,y) position and write an XSPEC file for all z elements. (I need basically temperature and density of all the elements). My question is: how does covering grid makes a single field value (temperature, for example) inside the (x,y,z) position? because I am arbitrarily saying to divide the region into 6 pixel, but the data file might have many simulation pixels inside , so how are the field values calculated? is it just an average? or are just certain points taken into consideration? Thanks for any hints/tips/help! Barbara Ramirez University of Innsbruck, Austria

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Re: [yt-users] problem with covering_grid for Nyx data sets (Wolfram Schmidt), yt-users Digest, Vol 66, Issue 17
by Wolfram Schmidt Aug. 14, 2013

Aug. 14, 2013

Hi Nathan, thanks a lot for your suggestions! I updated yt to the current development version, which didn't fix the problem. So I tried what you suggested: On 08/06/2013 07:52 PM, yt-users-request(a)lists.spacepope.org wrote: > and then try your script again. If the issue isn't fixed by updating, I > would then try applying the following diff to the nyx frontend: > > diff -r f936432ed45d yt/frontends/nyx/data_structures.py > --- a/yt/frontends/nyx/data_structures.py Tue Jul 30 10:08:24 2013 > -0700 > +++ b/yt/frontends/nyx/data_structures.py Tue Aug 06 08:10:25 2013 > -0700 > @@ -611,7 +611,7 @@ > # aliases we need > self.parameters["TopGridRank"] = > len(self.parameters["TopGridDimensions"] > self.dimensionality = self.parameters["TopGridRank"] > - self.domain_dimensions = self.parameters["TopGridDimensions"] > + self.domain_dimensions = > np.array(self.parameters["TopGridDimensions"]) > self.refine_by = self.parameters.get("RefineBy", 2) # 2 is silent > defaul > > # Nyx is always cosmological. > I replaced the definition of self.domain_dimensions with the np.array thing. Now, the script actually reads in the data, but then another problem is encountered when an FFT is applied to the data: Searching grids for values 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:03:04 yt : [ERROR ] 2013-08-07 11:56:48,958 Covering problem: 16777216 cells are uncovered Traceback (most recent call last): File "/usr/users/wschmid2/scripts/spect_sb.py", line 72, in <module> velx_hat = na.fft.fftn( cg['xmom']/cg['density'] )/cg['xmom'].size File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 332, in __getitem__ self.get_data(key) File "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py", line 3776, in get_data raise KeyError(n_bad) KeyError: 16777216 The line with the fft actually used to work and it still works just fine if I use an old yt version (which, fortunately, I was able to dig out). Do you understand what is the problem here? Cheers, Wolfram

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