Mailman 3 May 2015 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 15, 2022

Aug. 15, 2022

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

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 April 11, 2020

April 11, 2020

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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Profile plot of a 2d projection FRB object
by Ben Thompson June 3, 2015

June 3, 2015

Hello everyone. I was wondering if anyone has had experience with producing a profile plot from a 2d projection object (FRB object). Essentially, what I am trying to do is plot the stellar surface density of a galaxy as a function of radius. This is achieved by doing the following from a disk YT object called cylinder (in which the origional simulation object is called shot) center = cylinder.get_field_parameter("center") normal = cylinder.get_field_parameter("normal") image_width = (100,"kpc") three_image_width = YTArray((image_width[0], image_width[0], image_width[0]),image_width[1]) left = center - image_width right = center + image_width region = shot.region(center, left, right) proj = yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc") the error arrises here prof = yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None ) where I get the error /gpfs/home/........./profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional) 1304 else: 1305 raise NotImplementedError -> 1306 bin_fields = data_source._determine_fields(bin_fields) 1307 fields = data_source._determine_fields(fields) 1308 if units is not None: AttributeError: 'FixedResolutionBuffer' object has no attribute '_determine_fields' Any ideas how to get around this error? Also some other things to add as a postscript. Since how the projection works, if I provide weights=None as a keyword argument within the ProjectionPlot object, I get a surface density (g/cm^2). But also a "cylindrical_r" in cm^2 as well. I *think* the way to get around this is to do another projection where weights="ones", get the radius values out of that profile.. and then in matplotlib, useing the surface density array from the former profile, and the radius bin array from the latter... Produce a plot of the surface density as a function of radius from those two arrays (I might check by hand afterwards to see if this does the trick). This seems kinda convoluted so I am wondering if there is an easier way than this. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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local install of yt on Blue Waters
by Kenza Arraki June 1, 2015

June 1, 2015

Hi all, I am trying to locally install yt on Blue Waters. I did a module of swap to PrgEnv-gnu and then bash install_script.sh. Has anyone run into this error before? http://paste.yt-project.org/show/5576/ Thanks, Kenza

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Rendering Volume of FLASH file
by Kilian Gärtner May 30, 2015

May 30, 2015

Hi, I want to render a Volume Plot based on data from a FLASH file, which uses HDF5 file format. I tried the tutorial at http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume… with my file, but I always get this error: yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) This is the complete log: yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: current_time = 1.10472907814e+17 yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: domain_dimensions = [16 16 16] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge = [ -2.20000000e+25 -2.20000000e+25 -2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge = [ 2.20000000e+25 2.20000000e+25 2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2015-05-29 20:51:32,513 Loading field plugins. yt : [INFO ] 2015-05-29 20:51:32,513 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded astro (15 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded cosmology (22 new fields) yt : [WARNING ] 2015-05-29 20:51:32,515 Field ('gas', 'number_density') already exists. To override use force_override=True. yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid (63 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid_vector (95 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded geometric (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded local (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded magnetic_field (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded my_plugins (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded species (121 new fields) yt : [INFO ] 2015-05-29 20:51:42,595 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. Ray casting100% ||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 C:\Anaconda\lib\site-packages\yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) C:\Anaconda\lib\site-packages\yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) The image itself is created, but only black, also the rendering process is instantly finished. I've tried it with the "Enzo_64/DD0043/data0043" file as used for the tutorial, this works with errors. Then I've tried using a given FLASH dataset, the "GalaxyClusterMerger" - same result as my dataset, also the error. I'm using Win 8.1 64-bit Anaconda distribution and yt-project 3.1. Also tried the same thing on Ubuntu 14 with freshly installed yt-project, same error. Is there a solution to create a volume render with FLASH files? Thank you for your attention! Kilian

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is there a limit on image size?
by Dave Semeraro May 29, 2015

May 29, 2015

Helly yt-crowd. I am doing some volume rendering in yt and getting some errors when I try to grow the image size. I am trying to write a png image that is 1024 x 1024. I get the following errors: image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) The largest image I can generate is about 800x 800. It is a nice image too I tell ya. Just wish I could do a bigger one to submit for publication. Attached is the script I am using. Any help would be great. Thanks, Dave Semeraro _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Temperature with Enzo
by David Collins May 28, 2015

May 28, 2015

Hi, Everybody-- I have a dumb question about temperature in enzo. Where is it? I thought I rememberd that being a stock derived field, but I don't see it in the enzo frontends. I can go ahead and make a PR for that if there's not something obvious I'm missing. Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Storing multiple calculations using yt.parallel_objects
by Joshua Wall May 27, 2015

May 27, 2015

Dear users, This there a simple way to store multiple values at each step using parallel_objects? I'm doing: ######################################################## yt.enable_parallelism() num_procs = 4 plot = glob.glob(./plot*) my_storage = {} for sto, p in yt.parallel_objects(plots, num_procs, my_storage): sto.result_id = 'energy' + p sto.resutl = dd["total_energy"] sto.result_id = 'Px' + p sto.result = dd["total_mom_x"] ###################################################### which is just overwriting my energy with the momentum. I also tried to just set to different dictionaries without passing it to yt.parallel_objects as storage, but of course each proc as only a local copy then. Cordially, Josh _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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code units
by David Collins May 26, 2015

May 26, 2015

Hi, Everyone-- I'm trying to get code units from enzo for a cosmology run, but in_units('code_density') seems to do nothing. 'code_mass/code_length**3' seems to work. Is this a bug, or a feature? >>> ad['density'].in_units('code_mass/code_length**3') YTArray([ 0.9970247 , 0.99774731, 0.99854185, ..., 0.99993769, 0.99914176, 0.99841755]) code_mass/code_length**3 >>> ad['density'].in_units('code_density') YTArray([ 1.87321000e-29, 1.87456764e-29, 1.87606042e-29, ..., 1.87868293e-29, 1.87718755e-29, 1.87582689e-29]) code_density Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] How to use yt.load_hexahedral_mesh?
by Matthew Turk May 25, 2015

May 25, 2015

Hi Jonah, That's right -- the volume rendering won't work, but slices will. The VR should be working relatively soon, though. -Matt On Sun, May 24, 2015 at 8:47 PM, Jonah Miller <jonah.maxwell.miller(a)gmail.com> wrote: > Oh, I should add that I don't think 3D visualization is possible with > hexahedral meshes at the moment. The pixelizer doesn't support them yet... > At least that's my understanding. If you really need a 3D visualization, you > might want to try transforming your data into a regularly spaced grid (using > another tool) and then loading uniformly spaced data as in this example: > http://yt-project.org/docs/dev/examining/spherical_data.html > > Best, > Jonah > > > On 15-05-24 09:41 PM, Jonah Miller wrote: > > Hi Katharina, Andrew, > > There is a convenience function to create the coordinates and connectivity > arguments: hexahedral_connectivity. This function takes three 1D arrays, > which are the projections of your grid points onto your coordinate axes, > here called x,y, and z. The function then returns the connectivity and > coordinates arrays. > > Here's an example: > http://yt-project.org/docs/dev/examining/loading_data.html#semi-structured-… > > Best, > Jonah > > On 15-05-24 09:35 PM, Andrew Myers wrote: > > Hi Katharina, > > I don't have an example handy, but the "coordinates" and "connectivity" > arguments are arrays you construct that describe the vertices and zones of > the hexahedral mesh you want. The "coordinates" argument is supposed to be a > (N_vertices, 3) - shaped array of floats that has the x, y, and z positions > of all the vertices in the hexahedral mesh. The "connectivity" argument is a > (N_zone, 8) - shaped array of ints that gives, for each zone, the indices of > the 8 vertices that surround it. So for example, if connectivity[0][2] is > '12', then coordinates[12] would give the position coordinate of the third > vertex surrounding the first zone, if that makes sense. > > Once you've constructed those arrays from the information in your dataset > and fed them into "load_hexadral_mesh", yt shouldn't care whether the data > came from an HDF5 file or not. > > -Andrew > > On Sun, May 24, 2015 at 11:46 AM, Katharina Wollenberg > <kwollenberg89(a)gmail.com> wrote: >> >> Hello together, >> >> for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a >> single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has >> ratioed zones. For that I want to use the command >> yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, >> ...) . However, since I am new to yt, I am a little bit stuck right now… >> I am not quite sure what is meant in detail by the arguments connectivity >> and coordinates and how to formulate them in the load_hexahedral_mesh >> command. >> >> Furthermore, do I need to pay particular attention on some commands >> because of using HDF5 data? >> >> If anyone has an example for me, that’d be very helpful! >> >> Thanks a lot! >> >> Katharina Wollenberg >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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How to use yt.load_hexahedral_mesh?
by Katharina Wollenberg May 25, 2015

May 25, 2015

Hello together, for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has ratioed zones. For that I want to use the command yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, ...) . However, since I am new to yt, I am a little bit stuck right now… I am not quite sure what is meant in detail by the arguments connectivity and coordinates and how to formulate them in the load_hexahedral_mesh command. Furthermore, do I need to pay particular attention on some commands because of using HDF5 data? If anyone has an example for me, that’d be very helpful! Thanks a lot! Katharina Wollenberg _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Plot Rotation
by Jason Galyardt May 20, 2015

May 20, 2015

Hi all, Is there a convenient way to rotate a slice or projection plot (with associated axis labels and tick marks) in yt? My simulation domain is long and skinny, and yt automatically plots it with the long edge aligned horizontally; I'd like to rotate these 2D plots by 90 degrees. I've combed through the docs and the only way I can think to do it would be to create a fixed resolution buffer and then manipulate it via matplotlib functions. The camera seems only applicable for 3D (and doesn't paint the axes, so far as I can tell). Any ideas or pointers to docs? Thanks, Jason ---- Jason Galyardt jeg(a)uga.edu Department of Physics and Astronomy University of Georgia _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Enzo Tracer Particle Visualization
by Yuan Li May 19, 2015

May 19, 2015

Hi all, I am trying to make projection plots (e.g. average particle temperature) using Enzo tracer particles. Is there a way of doing this using yt? Thank you! Yuan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Profile Plot range question
by Stephanie Tonnesen May 19, 2015

May 19, 2015

Hi all, I am trying to make a profile plot of a cylindrical radial value. So I politely ask: ds = yt.load("/data/stonnes/dwarf_test_rhopress_extrarot/DD"+sys.argv[1]+"/DD44sMBherlr"+sys.argv[1]) .... my_disk = ds.disk([0.5,0.5,0.5],[0,0,1],(30,"kpc"),(0.1,"kpc")) .... profiles.append(yt.create_profile(my_disk,"cylindrical_r","density",weight_field="cell_mass")) .... plot=yt.ProfilePlot.from_profiles(profiles,labels=labels) plot.set_unit('cylindrical_r','kpc') plot.set_log('cylindrical_r',False) plot.save() And when my box is 96 kpc across, with a root 512 512 512 grid, 2 levels of refinement at 20.0 times initial density, I get what I wanted, a nice profile out to 30 kpc. BUT, when I ask the same thing starting with a lower resolution root grid: 256 256 256, my profile only goes out to 15 kpc! I changed my disk to have a 40 kpc radius and it made no difference. Can anyone tell me why this is happening? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Python Compilation Error while Installing Stable yt on OS X 10.10.3
by Madison Fitzgerald May 18, 2015

May 18, 2015

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Questions on using yt - ENZO simulation data
by Patrick King May 18, 2015

May 18, 2015

Hello yt-users, I am a graduate student working at the University of Virginia, and I would really appreciate some help! I’ve been using yt for a few weeks now to visualize some simulations I’ve run using the ENZO AMR code. I’ve been able to produce several derived fields using the documentation, but I’ve gotten to the point where I need some help with a more advanced usage of the code. Under some approximations, I’ve used yt to determine the Stokes parameters for the radiation field at each grid point. Using yt I can quite easily produce column-averaged plots using projection plot. However, to determine the values I need, I need to actually manipulate the column averaged values. The Stokes parameters give me all the information I need to do this, but these must be column averaged first - I’m essentially using yt to produce values which can be compared to observational data. Can I use projection plot to produce a numpy array that I can manipulate just like in regular python? I’ve been combing the documentation but I can’t find out how to do this. Alternatively, I would like to produce a numpy array from the derived field I calculated and then I can just integrate along columns. Thanks for your help! Patrick King PhD Candidate Department of Astronomy University of Virginia _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Projection of 2D cylindrical FLASH data
by Ken Shen May 15, 2015

May 15, 2015

Thanks for the suggestions, I'll give them a try! On Fri, May 15, 2015 at 8:18 AM, Roman Yurchak <roman.yurchak(a)crans.org> wrote: > If your observation direction is orthogonal to the revolution axis, you > could also map your 2D cylindrical data to a 2D numpy array (i.e. > re-sample on a uniform grid) and then do a forward Abel transform (the > integral transform to do this particular projection), implemented for > instance in https://github.com/luli/hedp/blob/master/hedp/math/abel.py#L19 > Although, volume rendering approaches would probably be more general and > better integrated with yt. > -- > Roman > > > On 15/05/15 03:27, Suoqing JI wrote: > > One way (imperfect but definitely doable) you might want to try is to > > map 2D cylindrical data into a 3D numpy array, which could be loaded > > by yt.load_uniform_grid and passed into the volume rendering module. > > > > See here: http://yt-project.org/doc/examining/generic_array_data.html > > > > Best wishes, > > -- > > Suoqing JI > > Ph.D Student > > Department of Physics > > University of California, Santa Barbara > > http://web.physics.ucsb.edu/~suoqing > > > >> On May 14, 2015, at 6:01 PM, Nathan Goldbaum <nathan12343(a)gmail.com > >> <mailto:nathan12343@gmail.com>> wrote: > >> > >> > >> > >> On Thu, May 14, 2015 at 5:35 PM, Ken Shen <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > >> I'm really sorry, I can't seem to explain this very clearly in > words! > >> > >> I have 2D axisymmetric data. Let's suppose that I map this to a > >> 3D Cartesian dataset. I'd like to make a 2D plot from this 3D > >> data that consists of integrating the density along rays from the > >> observer through the dataset onto a plane on the other side of the > >> data. Ideally, I'd like to do this with the observer at an > >> arbitrary position with respect to the axes. > >> > >> I haven't done it, but it seems like this is built in to yt's > >> functionality for 3D datasets. But I haven't found how to do it > >> for a 2D axisymmetric dataset. > >> > >> > >> In yt we would call this a volume rendering using rays that are > >> aligned with the cartesian axes and a projection transfer function. > >> > >> I don't think this has been implemented yet, but volume renderings of > >> data with non-cartesian geometries or with unstructured meshes is > >> something we would like to do. > >> > >> > >> > >> Sorry for all the messages! > >> Ken > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> On Thu, May 14, 2015 at 5:28 PM, Michael Zingale > >> <michael.zingale(a)stonybrook.edu > >> <mailto:michael.zingale@stonybrook.edu>> wrote: > >> > >> to be clear here, what Flash calls cylindrical is 2-d > >> axisymmetric, r-z. If I understand what you are asking, you > >> basically want to still have a 2-d plot where each cell is the > >> integral over an annular region as if that cell were rotated > >> about the symmetry axis -- is that right? > >> > >> On Thu, May 14, 2015 at 8:21 PM, Ken Shen > >> <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > >> Hi, sorry I wasn't very clear before. I'd like to make 2D > >> column density plots of my 2D cylindrical data as if my > >> data were 3D cylindrical data with no phi-dependence. > >> > >> (The ProjectionPlot fails for axis = 1 or 3. For axis = > >> 2, it essentially recreates the regular density slice plot.) > >> > >> > >> Thanks, > >> Ken > >> > >> > >> > >> > >> On Thu, May 14, 2015 at 5:00 PM, Matthew Turk > >> <matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>> > wrote: > >> > >> Hi Ken, > >> > >> (I think Suoqing's answer may work as well.) If you > >> want to project > >> along r, z, or theta, you can do a ProjectionPlot (or > >> "ds.proj") and > >> specify "r", "z", or "theta", and the result will be > >> along that axis > >> with the correct path lengths. I think that the "r" > >> direction may be > >> what you're looking for here, i.e., a soup-can label. > >> > >> -Matt > >> > >> On Thu, May 14, 2015 at 6:31 PM, Ken Shen > >> <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > Hi all, I'd like to make column density plots of my > >> 2D cylindrical FLASH > >> > data. Ideally, these would be at arbitrary angles > >> to the z-axis. I'm new > >> > to yt, so I could very well have missed it, but I > >> couldn't seem to find this > >> > in the documentation. Any hints? > >> > > >> > > >> > Thanks, > >> > Ken > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> > >> -- > >> Michael Zingale > >> Associate Professor > >> > >> Dept. of Physics & Astronomy • Stony Brook University • Stony > >> Brook, NY 11794-3800 > >> /phone/: 631-632-8225 <tel:631-632-8225> > >> /e-mail/: Michael.Zingale(a)stonybrook.edu > >> <mailto:Michael.Zingale@stonybrook.edu> > >> /web/: http://www.astro.sunysb.edu/mzingale > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Projection of 2D cylindrical FLASH data
by Ken Shen May 15, 2015

May 15, 2015

Hi all, I'd like to make column density plots of my 2D cylindrical FLASH data. Ideally, these would be at arbitrary angles to the z-axis. I'm new to yt, so I could very well have missed it, but I couldn't seem to find this in the documentation. Any hints? Thanks, Ken _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Cython Build Errors in Development Version
by Jason Galyardt May 15, 2015

May 15, 2015

Hi yt Devs, In the latest development version of yt (changeset 23506337f1e8), I'm getting 3 Cython build errors from yt/utilities/lib/pixelization_routines.c to do with the 'faces' variable: yt/utilities/lib/pixelization_routines.pyx:382:14: Assignment to non-lvalue 'faces' yt/utilities/lib/pixelization_routines.pyx:385:14: Assignment to non-lvalue 'faces' yt/utilities/lib/pixelization_routines.pyx:388:14: Assignment to non-lvalue 'faces' This occured when I did the following: python setup.py develop --user --prefix= Is anyone else seeing these errors? I'm using python 2.7.3 and Cython version 0.20.1. If you need more info on my setup, please let me know. Thanks, Jason _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Create_profile error in parallel
by John Regan May 15, 2015

May 15, 2015

Hi All, I'm seeing an error when I run YT 3.2 in parallel. Running in serial mode everything is fine. I have a bunch of fields I'm creating profiles for 'DarkMatter' is not one of them but that's where it fails. It looks like its picking up the DarkMatter radius rather than the gas radius? rp = yt.create_profile(sphere, 'radius', Fields, units = {'radius': 'kpc'}, n_bins=40) P002 yt : [ERROR ] 2015-05-14 22:09:54,308 YTFieldNotFound: Could not find field '('DarkMatter', 'radius')' in RD0001. I've attached the error file http://paste.yt-project.org/show/5547/ and the version info is: --- Version = 3.2-dev Changeset = 3e1887de7362+ (yt) tip --- Thanks! John _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Using time series data from FLASH with particle files.
by Joshua Wall May 14, 2015

May 14, 2015

Dear users, Since I'm already 0 for 1 today, I thought I'd also ask about this error I've seen. I'm trying to get the time series of momentum density in the x-dir from a simulation in FLASH where I have both the plot and particle files with: ############################################################ ts = yt.load("/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_plt_cnt_0??[!0]", particle_filename='/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]') times = [] Mom_x = [] Mom_y = [] for ds in ts: try: ds.add_field("total_px", function=_px, units="kg/s/m**2") ds.add_field("total_py", function=_py, units="kg/s/m**2") except: continue dd = ds.all_data() Mom_x.append(dd["total_px"]) Mom_y.append(dd["total_py"]) times.append(ds.current_time.in_units("Myr")) ########################################################### But this gives the error: --------------------------------------------------------------------------- IOError Traceback (most recent call last) <ipython-input-3-4be7349ef199> in <module>() 9 Mom_y = [] 10 ---> 11 for ds in ts: 12 13 /usr/local/lib/python2.7/dist-packages/yt/data_objects/time_series.pyc in __iter__(self) 158 for o in self._pre_outputs: 159 if isinstance(o, types.StringTypes): --> 160 ds = load(o, **self.kwargs) 161 self._setup_function(ds) 162 yield ds /usr/local/lib/python2.7/dist-packages/yt/convenience.pyc in load(*args, **kwargs) 78 if c._is_valid(*args, **kwargs): candidates.append(n) 79 if len(candidates) == 1: ---> 80 return output_type_registry[candidates[0]](*args, **kwargs) 81 if len(candidates) == 0: 82 if ytcfg.get("yt", "enzo_db") != '' \ /usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, particle_filename, units_override) 206 self._particle_handle = HDF5FileHandler(self.particle_filename) 207 except: --> 208 raise IOError(self.particle_filename) 209 # These should be explicitly obtained from the file, but for now that 210 # will wait until a reorganization of the source tree and better IOError: /home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0] ############################################################# Any ideas? Joshua Wall Drexel University _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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weird square feature in dark matter density slice map
by Junhwan Choi (최준환) May 14, 2015

May 14, 2015

Hi yt users, I make a simple dark matter slice map from my enzo simulation output with following script. ================== pc = yt.SlicePlot(ds, "z", ('deposit', 'io_cic'), width = (244.0, 'Mpccm/h'), center=cen_center) pc.annotate_text((0.7,0.9),'z=%4.2f' % ds.current_redshift, coord_system='figure', text_args = text_dict) pc.annotate_velocity(factor=16, scale=None, scale_units=None, normalize=False) pc.save("cen_all_0000") ================= I see the weird 5x6 square shapes on the plot. Why this square/cube shape result from and how to remove this? Thank you in advance, Junhwan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt inline (feed information to Enzo)
by Yuan Li May 14, 2015

May 14, 2015

Hi all, I am trying to calculate the mass flux through a sphere and modify a simulation parameter accordingly. I heard that it is possible to use yt to extract information from an Enzo simulation and feed it back to Enzo, but I was having a hard time finding an example. Is this where I should start: http://enzo.readthedocs.org/en/latest/user_guide/EmbeddedPython.html ? If not, please direct me to the right place. If that is what I should be looking at, I am having trouble compiling Enzo with "make python-yes". I tried to use the python 2.7 that comes with yt2.x, but got an error message related to "architecture x86_64" on my macbook (I am able to compile Enzo with python-no). I looked at the example Make.mach.orange. LOCAL_INCLUDES_PYTHON is using python2.7, but LOCAL_LIBS_PYTHON is using python2.6. I am confused: is that how it is supposed to be done? Do I have to install a python2.6 separately? Thank you! Yuan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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2015 IEEE Scientific Visualization Contest
by Matthew Turk May 12, 2015

May 12, 2015

Hi everyone, We invite you to participate in the 2015 IEEE Scientific Visualization Contest. This year's contest targets data from cosmology research that studies the formation of structure in the Universe. Participants are challenged to create a comprehensive set of analysis and visualization capabilities that enable domain experts to gain deeper insight into the formation of various structures in the Universe and better understanding of observations from next generation telescopes. Besides a number of interesting incentives, the contest winners will be presenting their work at IEEE VIS 2015 and they will get a chance to publish their results as a full, peer-reviewed IEEE CG&A article. Find out more at http://sciviscontest.ieeevis.org/2015/ Please pass this announcement along to other interested parties! _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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