halo finding on a volume subset
by Irina Dvorkin
Dear yt users,
Is there a way to run the halo finder on part of the simulation volume?
For example, I have a box 256 Mpc on a side but I only want to find
halos inside a smaller box, say 20 Mpc on a side.
Thanks for your help,
Irina
8 years, 5 months
SphereCallback
by Brian Crosby
Hello everyone, could someone tell me how to plot a sphere in a color other than black? I've got this much working:
p.modify['sphere']((x,y,z), radius, )
to plot a sphere at x, y, z of radius radius, but I cannot seem to succeed in changing the color.
Thanks,
Brian
8 years, 6 months
Moving to Mercurial: SVN now deprecated
by Matthew Turk
Hi everyone,
The subversion repository for yt has been frozen, and no further
updates will be made to it. We're migrating exclusively to mercurial,
which is a different mechanism for source control. (There's a bit
more info at this blog post:
http://blog.enzotools.org/yt-has-moved-to-mercurial ) I'm pretty
excited about this -- it should open up yt as a whole to become more
user-friendly in adding contributions. I've added appropriate
suggestions to the repository:
http://yt.enzotools.org/browser/doc/how_to_develop_yt.txt
as well as a list of active branches in the repository:
http://yt.enzotools.org/wiki/ExistingBranches
The installation scripts have been updated, and I've also changed the
landing page and wiki to point to the new installation script. If you
would like to move to the hg repository, I recommend either swapping
out your existing installation or simply re-installing from scratch.
The installation instructions have info on how to get either the
stable branch or the unstable branch.
http://yt.enzotools.org/wiki/InstallationInstructions
NOTE: As per Jeff's email from a couple weeks ago, the unstable
branch (named 'yt') has moved away from the old naming convention
('lagos', 'raven', 'fido', etc) and to more descriptive names. Here's
his message, for reference:
http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2010-August/0...
.
For more information on Mercurial, and what all this means, here are
some handy links:
http://hginit.com
http://mercurial.selenic.com/
http://hgbook.red-bean.com/read/
Please feel free to dig around and submit patches! I'm pretty hopeful
that this turnover will make development and contribution of patches
much more straightforward and easy.
Let me know if you run into any problems. Best wishes,
Matt
8 years, 6 months
yt 2.0 on Kraken
by Stephen Skory
Hi all,
I have just installed and built yt-2.0 on Kraken. The Cray CNL kernel has been
upgraded on Kraken which means that the old static-Python build requirements are
no longer necessary. This means that it is easier to install yt on Kraken, which
would seem to make the common install unneeded. However, one of the requirements
for running with shared-Python is that various shared libs need to be copied to
lustre because the compute nodes cannot see the home disks. This install of yt
is in a non-volatile part of lustre, so you don't have to worry about things
being deleted from underneath you as a result of automated purges.
To use it is simple, your environment needs to be set like this (depending on
your $SHELL):
export PYBASE=/lustre/scratch/proj/yt_common/2.0
export PATH=$PYBASE/2.0/bin:$PATH
export PYTHONPATH=$PYBASE/lib/python2.6/site-packages
export LD_LIBRARY_PATH=$PYBASE/lib:$LD_LIBRARY_PATH
when you want to run a batch job, you need to also set this (you should probably
make the dot-dir by hand, first):
export MPLCONFIGDIR=$TG_CLUSTER_SCRATCH/.matplotlib/
Let me know if you have problems!
_______________________________________________________
sskory(a)physics.ucsd.edu o__ Stephen Skory
http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
________________________________(_)_\(_)_______________
8 years, 6 months
how to call HaloMassFcn
by gso＠physics.ucsd.edu
I'm getting this error on an old script I used to create the halo mass
function on Triton
I had on top
from yt.analysis_modules.halo_finding.api import HaloMassFcn
and got:
Traceback (most recent call last):
File "parallelHF.py", line 52, in <module>
hmf = HaloMassFcn(pf, halo_file=filename[3]+"ParallelHopAnalysis.out",
NameError: name 'HaloMassFcn' is not defined
I was wondering if this is because yt was updated to 2.0 on triton?
in the email there's an example of what to use for HaloFinder
from yt.analysis_modules.halo_finding.api import HaloFinder
so for HaloMassFcn do I do
from yt.analysis_modules.halo_????.api import HaloMassFcn
can someone fill in what ???? is, or how I can find that information? Or
is the 2.0 manual out that I'm not aware of that has this information
already?
From
G.S.
8 years, 6 months
Re: [yt-users] projection a rectangular region
by Christine Simpson
Thanks Matt.
This kind of worked. The region I want to project is smaller than the
entire simulation domain on the face of the projection. When I made the
projection, it left the projected region the same size relative to the
entire simulation domain and filled in the parts of the domain not
projected with white space. Is there a way I can trim the white space,
or rather have add_projection size the projection to fit the plotting
space?
I've attached an image to show you what I mean.
Thanks so much!
Christine
8 years, 6 months
BinnedProfile1D
by Jean-Claude Passy
Hi all,
I need to get radial profiles of my sims - like density as a function or
radius. I know how to plot them using the method pc.add_profile_sphere
but I now need to print out the values in a txt file. For this reason, I
tried to use the class BinnedProfile1D. Below is my script:
##################################
file = 'DD0000/CommonEnvelope0021'
pf = load(file)
r_min = pf.h.get_smallest_dx()
r_max = 0.4
sphere = pf.h.sphere([0.5, 0.5, 0.5], r_max)
prof1d = L.BinnedProfile1D(sphere, 32, "Radius", r_min,
r_max,log_space=False, lazy_reader=True)
prof1d.add_fields("Density")
prof1d.write_out('test.txt','%0.6e','left')
##################################
It run well but returned a density profile equal to 0:
##############################
[17:25:54] litai05:$ more test.txt
# Radius Density
7.812500e-03 0.000000e+00
2.006836e-02 0.000000e+00
3.232422e-02 0.000000e+00
4.458008e-02 0.000000e+00
5.683594e-02 0.000000e+00
6.909180e-02 0.000000e+00
8.134766e-02 0.000000e+00
9.360352e-02 0.000000e+00
1.058594e-01 0.000000e+00
1.181152e-01 0.000000e+00
1.303711e-01 0.000000e+00
1.426270e-01 0.000000e+00
1.548828e-01 0.000000e+00
1.671387e-01 0.000000e+00
1.793945e-01 0.000000e+00
1.916504e-01 0.000000e+00
2.039063e-01 0.000000e+00
2.161621e-01 0.000000e+00
2.284180e-01 0.000000e+00
2.406738e-01 0.000000e+00
2.529297e-01 0.000000e+00
2.651855e-01 0.000000e+00
2.774414e-01 0.000000e+00
2.896973e-01 0.000000e+00
3.019531e-01 0.000000e+00
3.142090e-01 0.000000e+00
3.264648e-01 0.000000e+00
3.387207e-01 0.000000e+00
3.509766e-01 0.000000e+00
3.632324e-01 0.000000e+00
3.754883e-01 0.000000e+00
3.877441e-01 0.000000e+00
##############################
Could someone tell me what I am doing wrong ?
Thanks,
JC
8 years, 6 months
yt doesn't see some libraries
by Irina Dvorkin
Dear yt users,
I have the following problem with my yt installation: when I start
ipython or iyt I get the following message:
WARNING: Readline services not available on this platform.
WARNING: The auto-indent feature requires the readline library
and so many useful features (like tab-completion) don't work.
I have another Python installation on my machine, and there it all
works and does not have this warning.
I can bear with the annoying editing, but now I wanted to use the
sqlite3 library, and it is the same - it works from the other Python
installation, but not from the one within yt.
How do I tell the yt installation where to look for these libraries?
Thanks for your help,
Irina
8 years, 6 months
