Mailman 3 November 2013 - yt-users

No "NumberOfParticles" attribute for "YTRegion"
by Devin Silvia 17 Nov '13

17 Nov '13

Hi all, I've been trying to get yt-3.0 and the rockstar halofinder to work and I'm at the point where I *think* that my yt-3.0 install and rockstar are happily talking to each other, but when it goes to actually run the halofinder on my dataset, I get this issue: http://paste.yt-project.org/show/4060/ It seems like something isn't being done right in terms of accessing the particle information in the dataset, but I can't digest enough of the yt source to understand why this is the case. If anyone has any thoughts as to what is going wrong, I'd appreciate it. For what it's worth, this is the simple script I am using: http://paste.yt-project.org/show/4062/ Thanks! Devin -- Devin W. Silvia Research Associate Department of Physics and Astronomy Michigan State University www.devinsilvia.com

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add_field or grids.get_data different in yt-3.0 for FLASH data?
by James Guillochon 17 Nov '13

17 Nov '13

Hi, I have a histogram routine I wrote to process FLASH data. The routine works in yt 2.x, but gives me an error when call get_data from a grids object. Here's the snippet that fails: for cnt, g in enumerate(pf.h.grids): > if g.Level > pf.h.max_level - args.undersample: continue > if len(g.Children) != 0 and g.Level != pf.h.max_level - > args.undersample: continue > evals = list() > vvals = list() > #vvals = g.get_data(args.var).ravel() > for e, ev in enumerate(args.vars): > vvals.append(g.get_data(ev).ravel()) ...and here's the error: vvals.append(g.get_data(ev).ravel()) > AttributeError: 'NoneType' object has no attribute 'ravel' I initialized the fields using a loop in the following way: myvars = [] > for e, ev in enumerate(list(set(args.vars) | set(args.excludevars))): > myvars += [var(ev)] > add_field(ev, function=myvars[e].mesh, take_log=args.log) I understand that how fields behave has changed somewhat in 3.0. Any idea what could be causing the issue? The whole routine is here: http://goo.gl/R7FmsK Thanks all! -- James Guillochon Einstein Fellow at the Harvard-Smithsonian CfA jguillochon(a)cfa.harvard.edu

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Gadget: Isolated galaxy visualization
by Keita Todoroki 16 Nov '13

16 Nov '13

Hi, I managed to visualize gadget's isolated galaxy sims, and I'm wondering if I can improve the resolution of the image, especially the background, somehow. The image and the script can be found below: http://www.physics.unlv.edu/~keitee/isolated_low-res.png http://www.physics.unlv.edu/~keitee/gadget_agora.py Also, the disk moves a bit as time progresses (as you can see on the right-most column), and I'm wondering if yt can adjust that shift as well. -Keita

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Parallel python/yt
by Wienkers, Aaron F. 15 Nov '13

15 Nov '13

Hi YT Users, I've been trying to parallelize some of my analysis scripts using multiprocessing pools, but after a few repetitions yt produces the error, "Couldn't figure out output type for ./file_.hdf5" even though it works fine up to that point. It doesn't seem to have anything to do with my hdf5 file since it works fine serially. Just curious if anyone has run into a similar problem in the past. Thanks, Aaron

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gadget visualization
by Desika Narayanan 15 Nov '13

15 Nov '13

Hey Team YT, I have a quick question about basic visualization with yt and gadget, with reference to the following simple script: http://paste.yt-project.org/show/4058/ If I try to SlicePlot the snapshot, I get a series of errors which are copied below. Is it not possible to perform these sorts of plotting routines on the raw gadget data? (as an addendum, if I project to an octree grid using yt, I am able to make slice and projection plots). Thanks, Desika Traceback (most recent call last): File "gadget_slice.py", line 14, in <module> slc = SlicePlot(pf,'z',('PartType0', 'Density')) File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 2148, in SlicePlot return AxisAlignedSlicePlot(pf, normal, fields, *args, **kwargs) File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1322, in __init__ fontsize=fontsize) File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 809, in __init__ PWViewer.__init__(self, *args, **kwargs) File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 620, in __init__ if setup: self._setup_plots() File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 915, in _setup_plots image = self._frb[f] File "/Users/desika/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py", line 128, in __getitem__ self._period, int(self.periodic), _MPL.error: data is of incorrect type (wanted 1D float)

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annotate_grids in yt-3.0
by Butler,Michael J 15 Nov '13

15 Nov '13

Hello, I am trying to visualize the AMR grid for Enzo+RAMSES data in ProjectionPlots with the latest version of yt-3.0 but get the following error: AttributeError: 'YTQuadTreeProj' object has no attribute 'grid_left_edge' Is there a way to specify the edges of the grid manually? Thanks, Mike

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ZeroDivisionError: Gadget isolated galaxy sim
by Keita Todoroki 14 Nov '13

14 Nov '13

Hi, I am trying to read in a gadget snap from isolated galaxy sims, but I get ZeroDivisionError. As you can see below, the parameters for the domain edge seems to be not reading correctly, while it perfectly works fine for a snap from cosmological sims. In [2]: ds = GadgetStaticOutput('/Users/SilverStar/Desktop/iso_low.dat', unit_base = {"kpc": 1.0}) yt : [INFO ] 2013-11-14 14:22:03,592 Omega Lambda is 0.0, so we are turning off Cosmology. yt : [INFO ] 2013-11-14 14:22:03,593 Parameters: current_time = 0.0 yt : [INFO ] 2013-11-14 14:22:03,593 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2013-11-14 14:22:03,594 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-11-14 14:22:03,595 Parameters: domain_right_edge = [ 0. 0. 0.] yt : [INFO ] 2013-11-14 14:22:03,596 Parameters: cosmological_simulation = 0 If the domain edge is simply reading the BoxSize, the output above is understandable because isolated galaxy sims do not require to set the BoxSize (in fact we set it to 0) unlike cosmo sims. Could this be the reason for the error? -Keita

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Making a Multiplot using Ramses data
by k.grisdale＠surrey.ac.uk 13 Nov '13

13 Nov '13

Hi everyone I am trying to make a multi plot using data from Ramses. I have outputs from Ramses at 6 different times and I want to make projections at each time and place than in a multi plot to show evolution of the system. However when the code that I have written gives the results below. [cid:F88B06FF-D341-4589-9FD2-C8BEF5BE7CE8@surrey.ac.uk] Can anyone offer any suggestions as to wear my code is going wrong? Thanks Kearn The code I’m using ( the for dax lines have been commented out because every time they are included I get the error at the bottom) from yt.mods import * # set up our namespace import matplotlib.colorbar as cb from matplotlib.colors import LogNorm p1 = load("output_00001/info_00001.txt") p2 = load("output_00002/info_00002.txt") p3 = load("output_00003/info_00003.txt") p4 = load("output_00004/info_00004.txt") p5 = load("output_00005/info_00005.txt") p6 = load("output_00006/info_00006.txt") cen = [0,0,0] orient = 'vertical' fig, axes, colorbars = get_multi_plot(3, 2, colorbar=orient, bw = 4) proj1 = p1.h.proj(2, "Density", center=cen) proj2 = p2.h.proj(2, "Density", center=cen) proj3 = p3.h.proj(2, "Density", center=cen) proj4 = p4.h.proj(2, "Density", center=cen) proj5 = p5.h.proj(2, "Density", center=cen) proj6 = p6.h.proj(2, "Density", center=cen) proj1_frb = proj1.to_frb((0.7,"cm"),512) proj2_frb = proj2.to_frb((0.7,"cm"),512) proj3_frb = proj3.to_frb((0.7,"cm"),512) proj4_frb = proj4.to_frb((0.7,"cm"),512) proj5_frb = proj5.to_frb((0.7,"cm"),512) proj6_frb = proj6.to_frb((0.7,"cm"),512) dens_axes = [axes[0][0], axes[1][0]] #for dax in zip(dens_axes) : # dax.xaxis.set_visible(False) # dax.yaxis.set_visible(False) plots = [dens_axes[0].imshow(proj1_frb["Density"],origin ='lower'), dens_axes[0].imshow(proj2_frb["Density"],origin ='lower'), dens_axes[0].imshow(proj3_frb["Density"],origin ='lower'), dens_axes[0].imshow(proj4_frb["Density"],origin ='lower'), dens_axes[0].imshow(proj5_frb["Density"],origin ='lower'), dens_axes[0].imshow(proj6_frb["Density"],origin ='lower')] plots[0].set_clim((0.0,0.34)) plots[0].set_cmap("YlOrRd") plots[1].set_clim((0.0,0.345)) plots[1].set_cmap("YlOrRd") plots[2].set_clim((0.0,0.34)) plots[2].set_cmap("YlOrRd") plots[3].set_clim((0.0,0.34)) plots[3].set_cmap("YlOrRd") plots[4].set_clim((0.0,0.34)) plots[4].set_cmap("YlOrRd") plots[5].set_clim((0.0,0.34)) plots[5].set_cmap("YlOrRd") fig.savefig("test”) error: Traceback (most recent call last): File "plotterm2.py", line 34, in <module> dax.xaxis.set_visible(False) AttributeError: 'tuple' object has no attribute 'xaxis'

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Comparing different timesteps
by Stephanie Tonnesen 09 Nov '13

09 Nov '13

Hi yt-users! I am trying to compare how my magnetic field varies in a couple runs that start with different initial magnetic field configurations. Right now I would like to take a look at two things: a SlicePlot and a phase_object. I would like the "z" of the SlicePlot to be the B-field of the "current" time / B-field of the initial output. I would like the phase_plot to be the B-field of the "current" time / B-field of the initial output vs a fluid tracer field. So for a single output: >pc.add_phase_object(alld,["specific_scalar[0]","BMagnitude","CellMassSolar"], weight=None,x_bins=50,y_bins=50,x_log=False,y_log=False) But I want two phase_objects from different times divided by eachother. I looked at Time Series, but that doesn't seem to be what I want. I am not sure if I have explained myself clearly, and can try again if it doesn't make sense. If it does, can I do this? Thanks, Stephanie

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plot collection labels etc
by Semyeong Oh 09 Nov '13

09 Nov '13

Hi, I have a couple of questions on PlotCollection First, the labels on plot collection appear funny like this Here’s the code: pc = PlotCollectionInteractive(pf) pc.add_projection('H_NumberDensity', 2, data_source=reg, center=center) pc.set_width(width, 'unitary’) There seem to be a couple of mailing list discussions, but is it something that wasn’t fixed for PlotCollectionInteractive? Also, if I am making multiple plots using the same data_source, it seems that I have to do set_width every time I add a new plot. I’m wondering 1. if there is some way to set global width of a PlotCollection? 2. when is the fixed resolution buffer actually made? Is it when I save/show the plots? Thanks for your help. Semyeong

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