yt-users September 2016

yt-users@python.org

17 participants
19 discussions

by david collins

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.

6 months, 1 week

Cut Region Failure

by Jason Galyardt

Dear all, I would like to generate a compound cut region for a FLASH simulation, but the output I'm getting is odd. I've pasted my simple script here: http://paste.yt-project.org/show/6839/ It loads a simulation file, creates a compound cut_region (1e4 K < T < 1e6 K), and applies it to a slice plot. The resulting image is banded, as you can see by the attached plots. Am I missing something, or is this a problem related to yt? FYI, I get the same behavior when I use a projection plot or only one of the conditionals (e.g. T < 1e6 K). I've tried both the stock 3.3.1 version, as well as the self-contained development version that I installed earlier this afternoon using install_script.sh. Let me know if any other info is useful. Cheers, Jason

4 years

Fwd: Hyperion v0.9.8 released - including a new easy installation method!

by Desika Narayanan

---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Fri, Sep 30, 2016 at 9:31 AM Subject: Hyperion v0.9.8 released - including a new easy installation method! To: hyperion-announce(a)googlegroups.com Dear colleagues, I am pleased to inform you that a new release of the Hyperion Monte-Carlo dust continuum radiative transfer code (v0.9.8) is now available! This version includes a number of bug fixes and improvements, and you can find a full list of changes here: http://docs.hyperion-rt.org/en/stable/changes.html In addition, it is now very easy to install Hyperion using the Anaconda Python Distribution or Miniconda, by doing: conda install -c conda-forge hyperion This installs both the Fortran and Python code, including the MPI functionality, and is by far the easiest way to install Hyperion! You can find out more about this installation method here: http://docs.hyperion-rt.org/en/stable/installation/installation.html As a reminder, the homepage for the code is located here: http://www.hyperion-rt.org from which you can also access the latest tar file and documentation. Please let me know if you have any questions about the release, if you run into any issues with the code, or if anything is unclear in the documentation. The best way to report issues is via GitHub: https://github.com/hyperion-rt/hyperion/issues Best regards, Thomas Robitaille -- You received this message because you are subscribed to the Google Groups "hyperion-announce" group. To unsubscribe from this group and stop receiving emails from it, send an email to hyperion-announce+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

4 years

Gadget blocks' configuration

by Bernhard Röttgers

Hello! I am trying to use trident <https://bitbucket.org/trident-project/trident> (yt-based code) to generate spectra out of my Gadget simulations (stored in HDF5). I could get the code running, but the spectra are scaled weirdly. I was able to track the problem down to a weirdly scaled metallicity block within yt. I am guessing that the issue is related to the fact, that my block “Metallicity” is in fact element masses for individual elements, i.e. for each particle I have an array of masses for the 12 elements He, C, Mg, O, Fe, Si, H, N, Ne, S, Ca, and the rest (I know, a crappy naming for such a block, but that’s the way it is). Is there a way to force yt to create the metallicity block correctly?. Cheers, Bernhard

4 years

Cello Frontend for yt

by Bolden, Thomas John

Greetings yt users, My name is Thomas and I am currently working with the new AMR code Enzo-P / Cello being developed by James Bordner. I would love to be able to analyze the data using yt, but Cello is not currently supported in any version of yt I have found. I would greatly appreciate any help with adding a Cello frontend to yt. I have uploaded a data output (~140 MB) from a recent version of Cello to my dropbox here: https://www.dropbox.com/s/ysjgnnw9tcbiu6h/sedov-cello.tar.gz?dl=0 . Thank you, -Thomas Bolden

4 years

CIC Parameters

by Jason Galyardt

Hello yt Users, Does anyone know whether the Cloud-In-Cell (CIC) kernel has user-controllable parameters? In particular, I'd like to be able to control the radius of the cloud for depositing particle mass onto the grid. I'm working with FLASH data, if that helps. Cheers, Jason ---- Jason Galyardt Center for Simulational Physics University of Georgia

4 years

Volume cutout

by Daniel Fenn

Hi everyone, I'm working with data on a cubic domain, and I'd like to be able to visualize the whole 3D domain with one octant cut out. What I'm looking for is similar to VisIt's clipping functionality. I don't really need a real volume render with opacity--rather, I'd like pseudocolor planes showing the boundaries of the domain, but cut out in one octant so that the interior is visible. The visible interior portion would then be defined by a set of orthogonal pseudocolor planes marking the interior boundaries of the desired quadrant. Is there a straightforward way to achieve this using yt? I'd appreciate any suggestions. Thanks, Dan

4 years, 1 month

Registration open for the Learn yt Workshop: Oct 10-12, 2016

by Nathan Goldbaum

Hi all, Registration is now open for the Learn yt Workshop at the University of Illinois Urbana-Champaign, October 10-12, 2016. This workshop will introduce attendees to the yt project (yt-project.org), a python toolkit for the analysis and visualization of volumetric data. We have create a website for the workshop with more information: http://yt-project.org/workshop2016/ In addition, if you wold like to register for the workshop, please fill out this online form: https://goo.gl/forms/c6oIzNQywU1YWgOe2 The workshop will cover basic usage of yt, including the yt data model, yt's field system, low-level data inspection, basic visualization workflows, and data analysis and reduction tasks. We will also cover more advanced usages like generating simulated observations, halo finding and halo analysis, volume rendering, advanced 3D visualizations, and advanced data analysis and reduction tasks. Finally, we will cover how to modify and extend yt, as well as the development and contribution process. In addition, there will be time set aside for exploring data you bring to the workshop, along with opportunities to work directly with yt developers to load and explore your data. The workshop will take place at the National Center for Supercomputing Applications building on the north end of the UIUC campus. The NCSA building is about a block away from the conference hotel and is next door to a parking structure that offers metered all-day parking. There are a number of food trucks nearby, a university-run cafeteria about 2 blocks away, and a university business district with many good lunch restaurants about a half a mile away. We are planning to offer funding for hotel and travel for those requesting support. If you request funding, you will be notified of available funds by September 15. Travel awards will be made in the form of arranged lodging and airfare, with reservations being made by the conference organizers. We hope to see you there. On behalf of the organizing committee, Matt Turk Nathan Goldbaum Jill Naiman John ZuHone Kandace Turner

4 years, 1 month

Lineout plot fo 3D dataset

by Scott Feister

Hi Yt users, I'm looking for something like the projection and slice plot, but as a 1D lineout rather than 2D projection or slice. In other words, is there a simple way to make a line plot of "x" vs. "density" at y = z = 0, for example? I unsuccessfully tried modifying the 1D profile examples, which talk about sub-regions (e.g. spheres) and plotting two data variables against one another (e.g. "dens" and "temp"). Has anyone else run into this issue? I am guessing I am just missing something simple. Thanks! Scott Scott Feister, Ph.D. Postdoctoral Researcher, Flash Center for Computational Science University of Chicago, Department of Astronomy and Astrophysics

4 years, 1 month

How to re-process a scene?

by Scott Feister

Hi yt users, Hi there! I'm just starting to use yt to make volume renderings of FLASH simulations. While working through examples, I hit a roadblock, and I've had some difficulty finding good documentation on the what the "Scene.save()" function actually does; specifically, why it does different things on the first and second call. The first example in the user tutorial page for 3D volume rendering ( http://yt-project.org/doc/visualizing/volume_rendering.html) looks something like this: ... *sc = yt.create_scene(ds, lens_type='perspective')* ... *source = sc[0]* *source.tfh.set_bounds((3e-31, 5e-27))* *...* *sc.save('rendering.png', sigma_clip=6.0)* And, voila, volume rendering saved to png. However, if I naively continue the script to re-render with new settings: *source.tfh.set_bounds((3e-35, 5e-27))* *sc.camera.zoom(2.0)* *sc.save('rendering2.png', sigma_clip=6.0)* I find that none of my new settings are reflected in "rendering2.png" -- it's just a duplicate of "rendering.png"! But if I start again from scratch with a new scene, the settings take hold. This leaves me (a new user) scratching my head. So here is my question: Once you've created and saved a scene once, how do you change scene settings like colormap and camera angle? Best, Scott Scott Feister, Ph.D. Postdoctoral Researcher, Flash Center for Computational Science University of Chicago, Department of Astronomy and Astrophysics

4 years, 1 month

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yt-users September 2016