Notebook server question
by Andrew Myers
Hello yt users,
I have a (perhaps naive) ssh question related to the yt notebook. I would
like to run a yt notebook server on machine A. However, machine A cannot be
directly accessed via ssh from the wider internet. Instead, I must first
ssh into machine B, and then ssh from B to A. Machine B cannot run the
notebook server itself. Does anyone know how I can configure things -
perhaps by using a more complicated ssh tunnel command - so I that access a
notebook server running on machine A through machine B?
Thanks,
Andrew
4 years, 9 months
change size of phase plot
by Stephanie Tonnesen
Hi all,
I am trying to make my phase plots smaller so they can fit more nicely into
a paper. Alternatively, I would be fine with upping the font size so when
I shrink them you can read the axes. I found advise on how to do this for
slices, but not for phase_objects.
pc = PlotCollection(pf)
tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.5", "grid['z']
< 0.192","grid['z'] > -0.192","grid['cyl_RCode'] < 1.2"])
pc.add_phase_object(tracerp25,["Density","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds
= [-4e7,8e7],x_bounds=[5e-28,5e-23],x_log=True,y_log=False)
Any help is much appreciated!
Thanks,
Stephanie
4 years, 9 months
GADGET visualization
by Andrew Weis
Hello,
I am an astronomy graduate student at Columbia University, and am trying to
use YT to create a 3D visualization of GADGET simulations. Matt Turk
suggested I send an email to this list while he is traveling. I have seen
that the source code for visualizing GADGET data is in
yt/frontends/sph/data_structures.py, but am not sure how to access/use
this? I have looked at:
http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/e209c55b6aaa...
and
http://yt-project.org/doc/visualizing/volume_rendering.html#generating-a-...
but remain unsure of where to find the relevant source code/what I do with
it after I find it. Matt explained that
yt/frontends/sph/data_structures.py is "where the data frontend is. The
broader yt codebase uses that to index and manage the data but it uses
generic interfaces on top," and encouraged me to email the list for more
information. Where is the relevant code? Also, where does the generic
vs. frontend interface distinction appear?
Best,
Andrew Weis
4 years, 10 months
Fitting an absorption spectrum
by Pengfei Chen
Hi all,
I've used the
yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit
script to fit an Lya absorption spectrum generated by yt.
But there are some abnormal peaks when I did statistics of line width b and
column density N. Two figures are attached. I've tried with different
redshifts and all of them had peaks in b-distribution at init_b (which is
40km/s here) and maxb(which is 300km/s here). For the N-distribution I got
peaks around 10^12 cm^-2 at every redshift. The parameters I used were:
HI_parameters = {'name':'HI',
'f': [.4164],
'Gamma':[6.265E8],
'wavelength':[1215.67],
'numLines':1,
'maxN': 1E22, 'minN':1E11,
'maxb': 300, 'minb':1,
'maxz': 5, 'minz':0,
'init_b':40,
'init_N':1E14}
Could someone please tell me how to solve this? All the analysis were done
with the latest development version of yt and I made no changes to the
source code.
Please tell me if you need any datasets.
Thank you!
Pengfei
4 years, 10 months
FLASH polar coordinates support
by Miguel de Val-Borro
Hello,
I have tried to plot the results of 2D FLASH simulation using the
SlicePlot function and got the attached images using the development
versions of yt-2.7 and yt-3.0. It looks like the range in the radial
coordinate and the labels are not correct. Also I would like to
transform to a Cartesian coordinate system, is this possible for FLASH
2D polar data?
Thanks,
Miguel
4 years, 10 months
Light Cone Projection
by Pengfei Chen
Hi all,
I downloaded the example script of light cone projectoin(
http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-...)
to my laptop and changed the Enzo simulation parameter file and redshifts.
But when I ran it the following error occurred:
File "light_cone_projection.py", line 19, in <module>
find_outputs=False)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py",
line 158, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py",
line 44, in __init__
find_outputs=find_outputs)
File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line
131, in simulation
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 81, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py",
line 343, in __init__
self._parse_parameter_file()
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 273, in _parse_parameter_file
param, vals = (i.strip() for i in line.split("="))
ValueError: need more than 1 value to unpack
Does the parameters "near_redshift" and "far_redshift" in LightCone need to
be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in
enzo parameter file?
Does anyone know how to solve this?
Thank you all!
Pengfei
4 years, 10 months
fixed coordinates when pan_rel is used.
by Juan Camilo Ibanez Mejia
Hi all,
is there is a way to maintain fixed the coordinates in a slice plot when moving the camera around.
Every time I use the slc.pan_rel(*args, **kwargs), the coordinates are rested with (0.0 , 0.0) in the center of the plot.
Thanks,
Juan
_____________________________
Juan Camilo Ibañez Mejia
Department of Astrophysics
American Museum of Natural History
+1-212-313-7435
jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org>
_____________________________
4 years, 10 months
seg fault in Quadtree
by Britton Smith
Hi all,
I'm trying to make projections of a rather large Enzo dataset and getting a
segfault somewhere in Quadtree.so. This dataset is ~230 GB in size with 27
levels of AMR. As far as I can tell, the only hard coded limit I could
find in QuadTree.pyx is for 80 levels, which I am clearly below. Does
anyone familiar with this part of the code have any idea if there are any
other hard-coded limits in here that I might be exceeding? If not, does
anyone have any advice for how I might debug this? I'm seeing this
behavior in both yt-2.x and yt-3.0, so it does seem to be something
intrinsic to the quadtree code.
Thanks!
Britton
4 years, 10 months
Issues Installing yt
by Alex Bogert
Hi all,
I am trying to install yt using pip in an anaconda environment I just
setup. I am running into an issue with freetype. I installed freetype from
this location:
http://download.savannah.gnu.org/releases/freetype and I created the
freetype.cfg file as shown in the example. Yet, installing with pip
produces the same error that it cannot read the FTYPE location from
freetype.cfg .
Thanks,
Alex
Install Log :
Downloading/unpacking yt
Downloading yt-2.6.1.tar.gz (2.3MB): 2.3MB downloaded
Running setup.py
(path:/global/scratch2/sd/bogert/pip_build_bogert/yt/setup.py) egg_info for
package yt
non-existing path in 'yt/utilities/spatial': 'tests'
PNG_LOCATION: PNG found via ctypes in: /usr/include, /usr/lib64
Reading FTYPE location from freetype.cfg failed.
Please place the base directory of your
FTYPE install in freetype.cfg and restart.
(ex: "echo '/usr/local/' > freetype.cfg" )
You can locate the path by looking for ft2build.h
Complete output from command python setup.py egg_info:
non-existing path in 'yt/utilities/spatial': 'tests'
PNG_LOCATION: PNG found via ctypes in: /usr/include, /usr/lib64
Reading FTYPE location from freetype.cfg failed.
Please place the base directory of your
FTYPE install in freetype.cfg and restart.
(ex: "echo '/usr/local/' > freetype.cfg" )
You can locate the path by looking for ft2build.h
4 years, 10 months
FixedResolutionBuffer problem
by Mike Butler
Hello,
I am trying to make a fixed resolution buffer of a projection of a region
in one of my simulations. Here is the relevant part of the script:
size=0.025
center=[0.48,0.545,1.003]
right0=[center[0]+size,center[1]+size,center[2]+size]
left0=[center[0]-size,center[1]-size,center[2]-size]
region=pf.h.region(center,left0,right0)
p=pf.h.proj(0,"Density",data_source=region)
test=FixedResolutionBuffer(p,[0.52,0.57,0.978,1.028],(512,512))
f=h5py.File("test.h5","w")
f.create_dataset("/density",data=test["Density"])
f.close
When I write the buffer to a h5 file, it seems to be projecting through the
whole domain, instead of only the 0.05x0.05x0.05 region I specify. Any
ideas what I am doing wrong?
Thanks,
Mike
4 years, 10 months
