[yt-users] phase plot and time series
Mateusz Ruszkowski
mateuszr at umich.edu
Sun Feb 28 18:04:40 PST 2016
Hi Britton/Nathan,
I was able to upgrade yt to the latest development version and generate the figure.
Thanks very much for your help,
Cheers,
Mateusz
> On Feb 28, 2016, at 7:14 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
> I think I see what broke: you shouldn't be doing "yt update --all", since you didn't install using the install script.
>
> Instead, you should do the following:
>
> $ conda uninstall yt
> $ cd nobackupnfs2/mruszkow/yt/
> $ hg pull https://bitbucket.org/yt_analysis/yt <https://bitbucket.org/yt_analysis/yt>
> $ hg update yt
> $ python setup.py develop
>
> This assumes that nobackupnfs2/mruszkow/yt/ is a clone of the yt mercurial repository and you have all of yt's hard dependencies installed (numpy, matplotlib, and cython).
>
> On Sun, Feb 28, 2016 at 6:04 PM, Mateusz Ruszkowski <mateuszr at umich.edu <mailto:mateuszr at umich.edu>> wrote:
>
>
>
> Hi Britton et al.,
>
> Thanks very much. This is very useful!
>
> I have a somewhat unrelated technical question. I just attempted to upgrade yt to the latest dev version and yt stopped working for me (i.e., yt script derails in the first couple of lines). Details are below. Presumably the problem stems from the fact that the upgrade did not fully complete. Could I get some help with this?
>
> Thanks,
> Mateusz
>
>
> % yt update --all
>
> yt module located at:
> /nobackupnfs2/mruszkow/yt
>
> The current version and changeset for the code is:
>
> ---
> Version = 3.3-dev
> Changeset = 96e7ac3e7175 (yt) tip development
> ---
>
> This installation CAN be automatically updated.
> Updating the repository
> Updated successfully.
> Could not determine when yt stack was last updated.
>
> We will now attempt to update the yt stack located at:
> Traceback (most recent call last):
> File "/nobackupnfs2/mruszkow/miniconda3/bin/yt", line 9, in <module>
> load_entry_point('yt==3.3.dev0', 'console_scripts', 'yt')()
> File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 1095, in run_main
> print()
> File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 89, in run
> class YTCommand(object):
> File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 1033, in __call__
> os.environ["YT_DEST"], "src", "yt-supplemental")
> File "/nobackupnfs2/mruszkow/yt/yt/utilities/command_line.py", line 321, in _update_yt_stack
> def _get_yt_stack_date():
> File "/nobackupnfs2/mruszkow/miniconda3/lib/python3.4/os.py", line 633, in __getitem__
> raise KeyError(key) from None
> KeyError: 'YT_DEST'
>
>
> % python profiles.py
> Traceback (most recent call last):
> File "profiles.py", line 2, in <module>
> import yt
> File "/nobackupnfs2/mruszkow/yt/yt/__init__.py", line 123, in <module>
> from yt.data_objects.api import \
> File "/nobackupnfs2/mruszkow/yt/yt/data_objects/api.py", line 16, in <module>
> from .grid_patch import \
> File "/nobackupnfs2/mruszkow/yt/yt/data_objects/grid_patch.py", line 19, in <module>
> from yt.data_objects.data_containers import \
> File "/nobackupnfs2/mruszkow/yt/yt/data_objects/data_containers.py", line 51, in <module>
> from yt.utilities.parallel_tools.parallel_analysis_interface import \
> File "/nobackupnfs2/mruszkow/yt/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 32, in <module>
> from yt.utilities.lib.quad_tree import \
> ImportError: No module named 'yt.utilities.lib.quad_tree'
>
>
>
> > On Feb 28, 2016, at 12:19 PM, Britton Smith <brittonsmith at gmail.com <mailto:brittonsmith at gmail.com>> wrote:
> >
> > Hi Mateusz,
> >
> > Below is a reasonably simple way that someone might do something like this. This makes use of some newer functionality that currently only exists in the development branch, so you would have to update to that to use it. This results in the following plot:
> > http://i.imgur.com/Qlgg6sV.png <http://i.imgur.com/Qlgg6sV.png>
> >
> > To do this, I first made some profiles over a time-series of datasets with the following script:
> > http://paste.yt-project.org/show/6278/ <http://paste.yt-project.org/show/6278/>
> >
> > The last line is the new functionality, which saves all of the compiled profile data in a way that it can be reloaded as a yt dataset. You can see more information about that here:
> > http://yt-project.org/docs/dev/analyzing/saving_data.html <http://yt-project.org/docs/dev/analyzing/saving_data.html>
> >
> > Now, yt is awfully close to being able to plot this itself, but not quite there yet, so I plotted this using matplotlib. The plotting script is here:
> > http://paste.yt-project.org/show/6279/ <http://paste.yt-project.org/show/6279/>
> >
> > At the top of that script, you can see how I get access to the data that was saved by the first script. All that needs to be done is to call yt.load with the file that was created and the data fields are all accessible with full unit support through ds.data. So, for example, ds.data["density"].
> >
> > I hope this is helpful.
> >
> > Britton
> >
> > On Sat, Feb 27, 2016 at 2:44 AM, Nathan Goldbaum <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
> > While I think this is a really cool idea, I don't think this is possible within yt right now. Britton Smith might know a trick to do this though...
> >
> > On Fri, Feb 26, 2016 at 3:59 PM, Mateusz Ruszkowski <mateuszr at umich.edu <mailto:mateuszr at umich.edu>> wrote:
> >
> > Hi,
> >
> > Is there a simple way in yt to generate a "phase plot" of the gas density, with time and radius on the axes, using a time series of data files?
> >
> > Thanks,
> > Mateusz
> >
> >
> >
> >
> >
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