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
2 years, 2 months
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
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2 years, 2 months
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
2 years, 2 months
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
2 years, 2 months
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
2 years, 2 months
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
2 years, 2 months
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
2 years, 2 months
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
2 years, 2 months
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
2 years, 3 months
finding resolution of a hotspot
by tazkera haque
Hi people,
I have a hotspot in one of my sliceplots [see attached image] and I want to
find the resolution/cell size of the hotspot, in other words, the ['x'],
['y']. ['z'] co-ordinates and ['dx'] of the cells those contain that
maximum temperature. I have written a code like this:
*import yt*
*ds = yt.load("~/super3d_hdf5_plt_cnt_0018")*
*dd = ds.all_data()*
*v, c = ds.find_max("temperature")*
*print dd['dx']*
*print dd['dy']*
*print dd['dz']*
*print dd['x']*
*print dd['y']*
*print dd['z']*
and I have an output like this:
*yt : [INFO ] 2016-09-15 22:49:18,265 Parameters: current_time
= 28.501984704*
*yt : [INFO ] 2016-09-15 22:49:18,265 Parameters: domain_dimensions
= [128 128 128]*
*yt : [INFO ] 2016-09-15 22:49:18,293 Parameters: domain_left_edge
= [ -2.80000000e+10 -2.80000000e+10 -2.80000000e+10]*
*yt : [INFO ] 2016-09-15 22:49:18,294 Parameters: domain_right_edge
= [ 2.80000000e+10 2.80000000e+10 2.80000000e+10]*
*yt : [INFO ] 2016-09-15 22:49:18,294 Parameters:
cosmological_simulation = 0.0*
*yt : [INFO ] 2016-09-15 22:49:25,099 Max Value is 4.81587e+09 at
-184570312.5000000000000000 116210937.5000000000000000
6835937.5000000000000000*
*[ 4.37500000e+08 4.37500000e+08 4.37500000e+08 ..., 4.37500000e+08*
* 4.37500000e+08 4.37500000e+08] code_length*
*[ 4.37500000e+08 4.37500000e+08 4.37500000e+08 ..., 4.37500000e+08*
* 4.37500000e+08 4.37500000e+08] code_length*
*[ 4.37500000e+08 4.37500000e+08 4.37500000e+08 ..., 4.37500000e+08*
* 4.37500000e+08 4.37500000e+08] code_length*
*[ -2.77812500e+10 -2.77812500e+10 -2.77812500e+10 ..., 2.77812500e+10*
* 2.77812500e+10 2.77812500e+10] code_length*
*[ -2.77812500e+10 -2.77812500e+10 -2.77812500e+10 ..., 2.77812500e+10*
* 2.77812500e+10 2.77812500e+10] code_length*
*[ -2.77812500e+10 -2.73437500e+10 -2.69062500e+10 ..., 2.69062500e+10*
* 2.73437500e+10 2.77812500e+10] code_length*
but I believe my code is wrong in this context, because my highest
resolution is 136 km and this is an AMR code , so I should see ['dx'] very
close to the order of 136 km. please help me get the code. thanks
Tazkera
2 years, 3 months
