Is there a way to quantify values in yt by solid angle around a point?
For example I have a simulation of star clusters forming within a turbulent
GMC. When a bubble is present I want to calculate the covering fraction of
the shell. One way to do this would be using where the radiation pressure is
absorbed and calculate the fraction of solid angle (around the oldest
cluster) radiation pressure is absorbed above a minimum value out to a given
radius. See attached for projections of this simulation at a time with a
bubble shell! (bottom left shows radiation pressure absorption).
Has anyone written any code/script to calculate solid angle before?
Elizabeth Harper-Clark MA MSci
PhD Candidate, Astrophysics, UofT
Office phone: 416-978-5759
Hello avid yt logo contest followers!
In a battle the likes of which we've never seen before (mostly because it
was the first time), only one logo could survive.
And the winner is.......Logo 5 by Carolyn Peruta! Logo 5 started off with
an early lead, continued to lead in the middle, and finished strong!
Congratulations, Carolyn, and enjoy your new mug and the pride that comes
along with it!
The winning logo can be seen here: http://i.imgur.com/0AAv5.png .
Thanks for playing, everyone!
I have a script which calls HaloProfiler and throws the following error:
Traceback (most recent call last):
File "sim_halo_profiler.py", line 28, in <module>
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 22
8, in __init__
self.pf = load(self.dataset)
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/convenience.py", line 85, in load
if c._is_valid(*args, **kwargs): candidates.append(n)
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/frontends/tiger/data_structures.py", line 202, in _is_valid
return os.path.exists(args + "rhob")
TypeError: unsupported operand type(s) for +: 'EnzoStaticOutput' and 'str'
I did a quick test with iyt and it turns out it produces this error with the most simple form, hp=HaloProfiler(pf).
On May 13, 2011, at 3:19 PM, Britton Smith wrote:
> Hi Carolyn,
> I don't think it's a version difference. The halo profiler is supposed to take just the path to the dataset. It should do the load call in the halo profiler. I'm not sure why that would be happening. Either way, if it's working, that's all that matter.
> Also, nice job with the logos. I think yours had the best aesthetics of them all. I voted for 7.
> On Fri, May 13, 2011 at 12:27 PM, Carolyn Peruta <perutaca(a)msu.edu> wrote:
> Thanks again for sending such great looking volume renderings!
> I started halo analysis today and I couldn't get your sim_halo_profiler script to work unless I added: pf=load(output['filename']) and changed all the calls of output['filename'] to pf. I kept getting an error, 'str' object has no attribute 'h'. Could this be due to some change in yt versions between your use of this script and mine?
> On Mar 22, 2011, at 4:23 PM, Britton Smith wrote:
> > Hi Carolyn,
> > I'm attaching some analysis code you might find useful.
> > yt-advanced-plotting.tar contains some scripts for making projections and nice images from those projections. The subdirectory in there called advanced_examples contains the scripts needed to make the image in the test_frames directory in there. Specifically, those scripts can make the image which has particles overlaid that are colored by age and sized by mass. I think that will be perfect for what you're working on.
> > I've also attached a script for running the halo profiler to make radial profiles of all the halos in your simulation. Something you might find useful in there is that I've added profile fields for stellar_density, StarAgeYrs, and StarMetallicity. These may be very interesting to look at as a function of radius within your target halo.
> > Let me know if you have any questions about this stuff. Also, if you have any other ideas for analysis that you're not sure how to implement, let me know and we can discuss ways to implement them.
> > Keep rocking.
> > Britton
> > <yt-advanced-plotting.tar><sim_halo_profiler.py>
I want to write a script in yt that reads in data from a simulation
output, extracts a 3-dimensional grid from it of a set size at a fixed
resolution and then iterate through the data points calculating various
I think I can do this using covering_grid using the example in the cookbook:
cube = pf.h.covering_grid(4,
left_edge=[16.4299, 10.8963, 16.0],
right_edge=[18.4299, 12.8963, 16.02],
But I'm now not sure how to get to the data! I'd like to write a loop in
k = 0, 3
i = 0, 257
something = data(i,j,k)*etc
I feel this should be obvious but I can't figure out the AMRCoveringGrid
I'm getting a memory error running parallelHF on Ranger. Is this a bug or is there some sort of way to request more memory in my job script?
Here is the full traceback:
Traceback (most recent call last):
File "sim_halo_profiler.py", line 17, in <module>
rearrange=True, safety=1.5, fancy_padding=True)
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1921, in
threshold=threshold, dm_only=dm_only, rearrange=rearrange, premerge=premerge)
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1368, in
HaloList.__init__(self, data_source, dm_only)
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 992, in _
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1389, in
self.threshold, rearrange=self.rearrange, premerge=self.premerge)
ace.py", line 68, in __init__
yt : [INFO ] 2011-05-13 11:42:17,599 Building kd tree for 9519616 particles...
ace.py", line 1428, in _chain_hop
ace.py", line 1428, in _chain_hop
ace.py", line 347, in _init_kd_tree
fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64'))
ace.py", line 347, in _init_kd_tree
MemoryError fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64'))
File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/numpy/core/numeric.py", line 408, in asfortranarray
return array(a, dtype, copy=False, order='F', ndmin=1)
I am analyzing some MESA data using iyt instead of a regular ipython.
Everything works well except that when I make a plot with yt, control is
not returning to the prompt. I have tried to start yt with different
thread options (-gthread, -qthread, -q4thread and -wthread) but none of
them worked. My version of yt is built with python 2.7.1. The weird
thing is that it works smoothly with a regular version of ipython built
from python 2.6.4.
I would really appreciate if someone could help me to fix this. I would
like to keep using yt and not have to change all my settings.
Thanks a lot,
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I'd like to add a profile object using only the root grid. I
typically do something like this:
Is there a way to restrict this to only root grid tiles? I've tried
using a covering grid, but that's throwing some key error (that I'm
looking into presently, I'll have more info if/as I sort it out)
Sent from my computer.
yt is in need of an awesome new logo, which is why we are announcing the
first ever new logo contest! So here's the deal:
We'll accept entries for the next two weeks. Let's arbitrarily say Tuesday,
May 10th, at 11:59:59 pm EST. If there is more than one entry, we will put
it up for a community vote at that time.
Oh, and the most important part -- the winner will get a coffee mug with
their new logo front and center!!!
Please email yt(a)enzotools.org with your image attached. Good luck, and happy
A little over a month ago Jeff put out a "yt user survey" which had
pretty good turnout, along with some very useful and helpful
responses. I'm writing with a brief summary (please feel free to
chime in, if you have further comments you'd like to bring up here on
the list) and a bit of a 'state of stuff' as well, to summarize how
this feedback has been received and acted upon.
The breakdown of responses:
* 80% said "yt is easy to use", 20% said "yt is difficult to use" and
0% said "yt is too hard to use"
* 80% said "yt is the right level of complexity" and 20% said "yt is
more complex than [they] use", with 0% saying it's too complex
* 70% said "yt docs are kind of hard to navigate", 15% said "pretty
easy to navigate" and 15% said "not easy to navigate"
* The request for what people would like to see more of peaked in
"cookbook recipes", "complex multi-step analysis procedures" and
* Most people (80%) only ran scripts to analyze data.
* There was a 50/50 split on having run yt in parallel.
* There was a 50/50 split on whether or not a Web GUI would be useful.
* Most people were in favor of how the mailing lists are currently
run, and we had a few indicate they would like to use IRC.
This spurned a number of interesting discussions between developers,
along with some concrete responses to the feedback. I've summarized
1. We've registered an IRC channel on irc.freenode.net. You can
access this with any IRC client, such as Adium, irssi, XChat [Aqua],
and so on. We have also created a web interface to IRC:
http://yt.enzotools.org/irc.html . Typically there are three or four
people in the channel and a bot that echoes commits to the main yt
repo. So far I think it's been a success; please feel free to come
visit or ask questions there.
2. A few developers, led by Cameron Hummels, Jeff Oishi and Britton
Smith (with help from me) have written a web GUI. This will be a
focal point of the yt 2.2 release, which we anticipate happening in
the relatively near future. If you are interested in experimenting
with these BETA sequences, feel free to drop by IRC or shoot an email
to yt-dev and we can help you get started. Once the final release is
out we'll have some documentation that describes how to use it.
3. The next major build of the documentation will address the primary
complaint in the user survey: search in the docs is simply broken.
Too many results that are not germane are returned, as a result of the
inclusion of many redundant docstring pages. While the API docs are
nice, it is clear they overwhelm the search functionality and need to
be excluded. Additionally, the recipe system is going to be expanded.
Several new recipes have been added, but unfortunately we are now
reaching a scaling issue. If anyone has any suggestions how to scale
to dozens of recipes/snippets, they would be greatly appreciated!
4. Multi-step analysis routines are tricky, but Jeff Oishi and I are
going to try to include a few examples, including scripts that produce
publication plots and analysis. If anyone has any scripts they would
like to share, in particular that perform multi-step analysis, they
would be greatly appreciated.
5. We're moving all the old bugs and wiki pages to BitBucket soon, and
I'm going to add the ability to file bug reports from the command
line. This should enable much easier tracking of items and making
sure problems and issues don't get lost. We're also optimistic that
BitBucket will help to make developing easier; we've seen this so far
with the forking capabilities, and hopefully we'll continue seeing
this with the bug tracking and wiki transitions.
If anyone has any other suggestions or feedback, please consider this
an opportunity to raise your voice! If you have any ideas in
particular about future directions, or feelings on complexity or the
documentation, we'd love to hear them. If there's any way you'd like
to contribute -- either through developing, or non-technical
contributions like documentation, designing how the yt API works,
touching up the website or anything else -- please feel encouraged to
head on over to the yt-dev list or IRC and strike up a conversation.
Thanks everyone who responded to the survey!