yt volume render/AMRKDtree help
by Renyue Cen
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
5 years, 6 months
Blank images for simple volume rendering
by Noel Scudder
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
5 years, 8 months
Not able to activate yt installation
by Morgan Presley
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.
5 years, 9 months
integrated quantities in cylindrical
by Roman Yurchak
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
5 years, 9 months
Pickle vs. _type_name
by David Collins
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.
5 years, 9 months
MBH accretion rate
by José Utreras
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?
5 years, 9 months
Fwd: YT fails at start
by John Regan
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
5 years, 9 months
Announcing: yt 2.5.3
by Matthew Turk
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
5 years, 9 months
Installation Failure
by Joseph Godino
Hello,
I am trying to install yt with enzo on a computer running Springdale
Linux 6.4 using the shell script install_script.sh. However, I keep
getting the following error -
********************************************
FAILURE REPORT:
********************************************
running install_egg_info
Writing /home/jgodino/Software/enzo/yt-x86_64/lib/python2.7/site-packages/mercurial-2.5.4-py2.7.egg-info
using https://bitbucket.org/yt_analysis/yt-supplemental/
sending capabilities command
abort: Python SSL support not found
using https://bitbucket.org/yt_analysis/yt/
sending capabilities command
abort: Python SSL support not found
abort: repository /home/jgodino/Software/enzo/yt-x86_64/src/yt-hg/ not
found!
/home/jgodino/Software/enzo/yt-x86_64/bin/python2.7: can't open file
'/home/jgodino/Software/enzo/yt-x86_64/src/yt-hg//distribute_setup.py':
[Errno 2] No such file or directory
Any suggestions on how to solve this.
Regards,
Joe
5 years, 9 months
Rendering non-cubical volumes
by Chris Beaumont
Hi,
I'm new to yt and this list, so I apologize if this question has been
answered before.
I'm trying to render a non-cubical volume (observational data: see an early
attempt at https://vimeo.com/67421373). If I supply a scalar "resolution"
to Camera.__init__, the output is a square, even though the input data is
~2x wider than it is tall. If I supply a tuple of values, I can manually
stretch the image but, as you can tell from the movie, I want to spin
around the volume. I don't think that messing with resolution will help me
in this case, since the projected aspect ratio of the plot changes at each
rotation step.
I did find an old thread similar to this (
http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2012-July/002...),
but the recipe there seem specific to axis-aligned slices, and not generic
rotations.
Is there a natural way to force yt to render pixels with the "right" aspect
ratio?
Thanks,
Chris
--
************************************
Chris Beaumont
Graduate Student
Institute for Astronomy
University of Hawaii at Manoa
2680 Woodlawn Drive
Honolulu, HI 96822
www.ifa.hawaii.edu/~beaumont
************************************
5 years, 9 months
