yt-users June 2013

yt-users@python.org

15 participants
15 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

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

8 14

Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

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 8

yt volume render/AMRKDtree help
by Renyue Cen 25 Aug '13

25 Aug '13

Hi, I did some simple volume rendering with the following script: volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"], no_ghost=False, tree_type="domain", le=c-0.5*WW, re=c+0.5*WW) cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False, north_vector=L, steady_north=True) cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j)) I got rather strange results in that the pictures look symmetric, which I am pretty sure can not be true. I attach the obtained plot. Note that I am using KD tree and using 32 cores. Your help at your earliest convenience is appreciated. Best, Renyue

6 25

Blank images for simple volume rendering
by Noel Scudder 28 Jun '13

28 Jun '13

Hello, I'm new to yt, and am having some trouble volume rendering my Castro simulation data (3D). The simulation is of two stars orbiting the center of the domain, the domain being defined by defined by [0.0, 0.0, 0.0], [1.e10, 1.e10, 1.e10], in cgs. When I run the following script, I get an image that is either all black or all white, depending on which field I use. Does anyone see anything wrong with my script?: from yt.mods import * pf = load("plt_derr_perr_grav_00020") field = "density" dd = pf.h.all_data() mi, ma = dd.quantities["Extrema"](field)[0] tf = ColorTransferFunction((mi, ma)) c = [5.0e9, 5.0e9, 5.0e9] L = [1., 1., 1.] W = pf.domain_right_edge - pf.domain_left_edge Nvec = 512 cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = tf, fields=[field], pf=pf) tf.add_layers(4, colormap="hsv") cam.snapshot("v1.png") Any advice would be greatly appreciated. Best, Noel Scudder

2 2

Not able to activate yt installation
by Morgan Presley 21 Jun '13

21 Jun '13

I tried to install yt using the commands: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh It seemed to install fine, but when I tried to run the activate script, I got the following error: $ source /Users/mpresley/yt-x86_64/bin/activate (yt-x86_64)anantes-651-1-49-78:~ mpresley$ yt usage: yt [-h] [--config CONFIG] [--paste] [--paste-detailed] [--detailed] [--rpdb] [--parallel] {help,bootstrap_dev,bugreport,hop,hub_register,hub_submit,instinfo,load,mapserver,pastebin,pastebin_grab,upload_notebook,plot,render,rpdb,notebook,serve,reason,stats,update,upload_image} ... yt: error: too few arguments I tried just deleting the files and re-doing the installation, but I encountered the same error. I am installing on iOS 10.7.5 and have attached the install log. Thanks for any help.

3 3

integrated quantities in cylindrical
by Roman Yurchak 19 Jun '13

19 Jun '13

Hello, I'm interested in getting some integrated quantities from a cylindrical 2d FLASH simulation. Just to be sure, I started by comparing the total simulation mass computed by yt ( with pf.h.all_data().quantities['TotalQuantity'] etc.) and the one provided in FLASH logs, and the results are rather different [see attachment]: * _Values_: difference of up 8% between the two methods * _Time evolution_: total mass is decreasing in time according to FLASH (which is ok with open boundary conditions) but it is increasing with the yt's integration. * _Sensitivity to resolution_: there are jumps in total density given by yt for the time steps where the maximum refinement level is manually decreased. Would anyone know what might be the reason for this behaviour? Just in case, I tried to do a second order integration instead of simply summing the values in all the cells, but if didn't make an error, the correction was negligible. I can provide data and the yt script I'm using by PM if some could look into this. Thank you, Regards, -- Roman Yurchak

3 5

Pickle vs. _type_name
by David Collins 17 Jun '13

17 Jun '13

Hi, all-- I'm trying to pickle a dataset I made with cut_region. This fails on the call to __reduce__ since the cut_region doesn't have a _type_name attribute. Is there an easy way to give _type_names to cut regions in general, or should I clone the __reduce__ method for InLineExtractedRegionBase? I generate the object like this: >> region = pf.h.region(Center,Left,Right) >> cut_region = region.cut_region(['grid[some_field] == some_value'}) >> file = open(args) >> cPickle.dump(cut_region,file) which gives the following error: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/nics/b/home/collins/yt2.0/fPickle.py", line 15, in dump output = cPickle.dump(object,file,*args,**kwargs) File "/nics/b/home/collins/local_2013_03_12/src/yt-dave/yt/data_objects/data_containers.py", line 407, in __reduce__ [getattr(self, n) for n in self._con_args] + AttributeError: 'InLineExtractedRegionBase' object has no attribute '_type_name' Thanks! d.

4 4

MBH accretion rate
by José Utreras 11 Jun '13

11 Jun '13

Hi everyone I'm working with Enzo and I have a black hole particle in my simulation. I can get the mass of this particle from every output, but I didn't find how can I get the accretion rate? Is there a way in YT to do that?

1 0

Fwd: YT fails at start
by John Regan 06 Jun '13

06 Jun '13

Hi, I just installed YT and it's failing at the very start. Python 2.7.4 (default, Jun 4 2013, 11:02:31) [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line 60, in <module> from yt.data_objects.api import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 31, in <module> from grid_patch import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 35, in <module> from yt.data_objects.data_containers import YTFieldData File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 45, in <module> from yt.data_objects.derived_quantities import GridChildMaskWrapper File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 36, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 39, in <module> from yt.utilities.lib import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", line 35, in <module> from .png_writer import * ImportError: libpng16.so.16: cannot open shared object file: No such file or directory >>> Adding the path to the libpng16.so.16 library gets me to here (it also seems strange that the .so file was not already in the LD_LIBRARY_PATH - is there a hint in there somewhere?): Python 2.7.4 (default, Jun 4 2013, 11:02:31) [GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/mods.py", line 129, in <module> from yt.visualization.api import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/nfs/scratch/jr347/2013/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py", line 32, in <module> from matplotlib.image import FigureImage File "/home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/image.py", line 22, in <module> import matplotlib._png as _png ImportError: /home/cosmos/users/jr347/2013/YT/yt-x86_64/lib/python2.7/site-packages/matplotlib/_png.so: undefined symbol: png_set_longjmp_fn Anybody come across this kind of error before. The code is built on a shared memory machine, using gcc. icc is actually the default compiler but the YT script seems to pick up gcc by default and it builds (it doesn't build at all with icc). Install script attached in case it's helpful. Let me know if you need anymore info. Thanks in advance! John

3 9

Announcing: yt 2.5.3
by Matthew Turk 06 Jun '13

06 Jun '13

Hi all, We're proud to release yt version 2.5.3. This is a scheduled point release that includes all bug fixes identified and fixed since the release of 2.5.2 on May 1. Additions, changes and bug fixes include: * yt can now export to RADMC3D * Athena frontend now supports Static Mesh Refinement and units ( http://hub.yt-project.org/nb/7l1zua ) * PlotWindows now have a set_font function and a new default font setting * Colorbars less likely to extend off the edge of a PlotWindow * Clumps overplotted on PlotWindows are now correctly contoured * Allsky projections and HEALpix camera now correctly use four channels (RGBA) * Many fixes to light ray and profiles for integrated cosmological analysis * Improvements to OpenMP compilation * Typo in value for km_per_pc (not used elsewhere in the code base) has been fixed * Enable parallel IPython notebook sessions ( http://hub.yt-project.org/nb/qgn19h ) * Change (~1e-6) to particle_density deposition, enabling it to be used by FLASH and other frontends * Addition of is_root function for convenience in parallel analysis sessions * Additions to Orion particle reader * Fix long-standing bug for plotting arrays with range of zero * Fixing TotalMass for case when particles not present * Fixing the density threshold or HOP and pHOP to match the merger tree * Reason can now plot with latest plot window * Adding option to have interpolation based on non-uniform bins in interpolator code * Issues with VelocityMagnitude and aliases with velo have been corrected in the FLASH frontend * Halo radii are calculated correctly for domains that do not start at 0,0,0. * Halo mass function now works for non-Enzo frontends. * Bug fixes for directory creation, typos in docstrings If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI). This release includes a total of over 150 changesets, contributed over the course of nearly 40 pull requests by over a dozen individuals. The next scheduled release will be on July 1, and will be version 2.6. We are hoping to include a unification of the Boxlib frontends, compatibility with Python 3 (and embedding inside Blender) and other usual improvements to the yt codebase. Documentation for this release can be found at: http://yt-project.org/docs/dev/ Thanks very much, Matt, on behalf of the yt development team

3 6

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users June 2013