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
PhasePlot give inconsistent results with different core count and fieldc
by Geoffrey So
The following script gives me different results in the 2d phase plot when I
use multiple cores and switch the fieldc parameter. The results are
consistent if I only use a single core. Some of the plots produced seems
like it is missing data points or under-sampled, so I'm guessing maybe not
all the data from all the cores were collected at the end.
From
G.S.
#-----------------------------------------------------------------------------------
from yt.mods import *
i=2
file = "RD%04i" % i
fn = file+"/"+file
pf=load(fn)
dd=pf.h.all_data()
fieldx='Density'
fieldy='Temperature'
fieldc='CellVolumeCode'
#fieldc='CellVolume'
#fieldc='CellMassMsun'
#fieldc='CellMass'
#fieldc='Ones'
pplot = PhasePlot(dd, fieldx, fieldy, [fieldc],weight_field=None)
pplot.save('example/'+file)
#---------------------------------------------------------------------------------------
4 years, 9 months
volume rendering
by Renyue Cen
Hi folks,
Some time ago John Wise kindly gave me a yt script that uses AMRKDTree to speed up "camera" 3-d
rendering, it worked very well and fast (takes like a few minutes to do a rendering of a galaxy with 2048x2048 pixel).
It looks like
volume = AMRKDTree(pf, le=le, re=re, fields=["Density"], no_ghost=False)
then used in
cam = pf.h.camera(c, L, W, (N,N), tf, volume=volume, no_ghost=False, north_vector=Ldm,steady_north=True)
It appears that yt has evolved and the "volume ..." statement no longer works.
Is there a solution to that in the newer version?
Alternatively, is there another speedy way to do 3-d rendering?
Thanks very much,
Renyue
4 years, 9 months
updated examples for 3.0 volume rendering
by Michael Zingale
Is there any updated examples for using the yt 3.0 volume rendering?
For instance, looking at this:
http://yt-project.org/docs/dev/cookbook/simple_plots.html#simple-volume-r...
The field name is no longer simply "Density", but now, for my data, I need
to use a tuple like:
field = ('boxlib', 'magvel')
And then when I look at the extrema, I no longer take the [0] index, as
that just gives the min, but instead if I look at:
dd.quantities["Extrema"](field)
I get:
(124.858613718 dimensionless, 18061918.0546 dimensionless)
(not sure why they are dimensionless, but that's a different problem).
Finally, if I try to make a transfer function, like:
tf = ColorTransferFunction((mi, ma))
I get:
NameError: name 'ColorTransferFunction' is not defined
I just synced up with the development version today.
Mike
--
Michael Zingale
Associate Professor
Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
11794-3800
*phone*: 631-632-8225
*e-mail*: Michael.Zingale(a)stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
4 years, 10 months
Combining a large number of disjoint shells
by Thomas Hansen
Hi everybody,
I'm a bit of a yt-newb, and I was wondering what the best way to handle a
problem I'm working on it.
Basically, I have a (large) list of locations (centers of galaxies), and I
want to make a profile plot using the data from all of the shells a
distance r > 10kpc, r < 100 kpsc from each of these centers. I tried using
a loop with the expression
x = pf.h.boolean([x, "AND", newShell])
to just build the data up over many iterations before finally using
create_profile after the end of the loop, but this approach ran out of
memory. Is there a better way to get the sum of a large data set?
Thanks in advance for any help,
Thomas
4 years, 10 months
Website font rendering issue
by Nathan Goldbaum
Hi all,
If over the past month or so you've noticed some font rendering issues on
yt-project.org when using the Google Chrome web browser, that should be
fixed now.
Unfortunately it was due to an as yet unpatched bug in the browser. We
have implemented a workaround that should fix it.
Sorry for any trouble this has caused.
Cheers,
Nathan Goldbaum
4 years, 10 months
pyx install error
by Junhwan Choi (최준환)
Hi yt users,
I try to install pyx onto my existing yt package (including yt,
python, numpy ....).
Buit I get following error message:
======
Downloading/unpacking pyx
Could not find any downloads that satisfy the requirement pyx
Some externally hosted files were ignored (use --allow-external pyx to allow).
Cleaning up...
No distributions at all found for pyx
Storing debug log for failure in /home52/jhchoi/.pip/pip.log
====
The pip.log file says
------------------------------------------------------------
/home/jhchoi/common/bin/pip run on Wed Mar 26 10:05:31 2014
Downloading/unpacking pyx
Getting page https://pypi.python.org/simple/pyx/
URLs to search for versions for pyx:
* https://pypi.python.org/simple/pyx/
Analyzing links from page https://pypi.python.org/simple/PyX/
Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.12.1/PyX-0.12.1.tar.g...
(from https://pypi.python.org/simple/PyX/) because it is externally
hosted.
Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.13/PyX-0.13.tar.gz#md...
(from https://pypi.python.org/simple/PyX/) because it is externally
hosted.
Could not find any downloads that satisfy the requirement pyx
Some externally hosted files were ignored (use --allow-external pyx to allow).
Cleaning up...
Removing temporary dir /tmp/pip_build_jhchoi...
No distributions at all found for pyx
Exception information:
Traceback (most recent call last):
File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/basecommand.py",
line 122, in main
status = self.run(options, args)
File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/commands/install.py",
line 278, in run
requirement_set.prepare_files(finder,
force_root_egg_info=self.bundle, bundle=self.bundle)
File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py",
line 1177, in prepare_files
url = finder.find_requirement(req_to_install, upgrade=self.upgrade)
File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/index.py",
line 277, in find_requirement
raise DistributionNotFound('No distributions at all found for %s' % req)
DistributionNotFound: No distributions at all found for pyx
What does this error mean? And could anyone inform me how to resolve
this problem?
Thank you in advance,
Junhwan Choi
4 years, 10 months
Code Units to CGS for PLUTO.
by Varadarajan Parthasarathy
Hi There,
There is a PlutoGrid.convert(datatype) for converting the data
sets like 'prs', 'rho' etc to CGS from code units. Have any one used it ?
In case can you let me know of how you loaded the dataset ?
Cheers,
Varadarajan
4 years, 10 months
