Anybody want to write a blog post or two for the blog? I think having
just short little ones about some new things in yt would be great.
Like, a short one talking about new things in 3.0 for instance.
I have a work-in-progress PR in the hopper regarding GDF reading and writing:
What it does is implement direct writing of covering grids to GDF
files (something I've been using in my research, to work with the
resulting files directly in yt) and clobbering existing files with the
same path if the user allows for it.
However, when fiddling around with this I determined that it was
necessary to make GDF more unit-aware. Ultimately, I determined that
changes were needed that would break the standard that we had
determined for the files (http://yt-project.org/gdf.txt).
The two main changes are:
1) Remove "field_to_cgs", and allow the fields to be in whatever units
we wish them to be in the file (which are specified as HDF5
2) Add a new top-level group containing the information for
"length","mass", and "time" units. These will be used when the file is
opened up in yt to determine the units.
Since (for now) we do automatic conversion to cgs, that is something
that is still left unimplemented, but otherwise I think this is all to
do for now.
I'm writing the email in case anyone has any suggestions or objections
to the format changes--particularly Jeff or Kacper. We'll obviously
need to document them if they are accepted.
NASA/Goddard Space Flight Center
Well, I was only here in Cambridge for two weeks and someone already asked me if we could do a local yt workshop for users. They suggested that between CfA, MIT, and the other various institutions that there is probably a critical mass for a small workshop.
I would be happy to organize and lead such a workshop, but it would be a lot easier on me if I had one or two others to help assist. This would be a small endeavor, and only local, but I was wondering if any of you might be potentially interested in coming up this way to help out. I cannot promise anything in the way of reimbursement at the outset, but I'm presuming so long as it's just one or two of you we can work something out easily. I am thinking December at the earliest, or maybe early next year.
I know we are focused right now on the broader, more important workshop coming up at UIUC (yay, I get to go home!), but I thought I'd put this out there in case anyone is interested.
New issue 907: changing units manually in FLASH datasets
I am a new yt user; working with FLASH datafiles. FLASH files work smoothly in general, but the front-end seems to lack the possibility to change the unit system in reading, on the contrary of some other dataset (e.g. Athena) where one can specify units at load time.
I need to specify a custom unit system; either at load time or later. I mean, I want yt to read the exact numbers on the file, but attach different physical units to them.
My files may be a bit special under this aspect, but it's true that the FLASH front-end assumes cgs only. Under http://yt.readthedocs.org/en/latest/examining/supported_frontends_data.html, the user is warned that this will happen, but there's no solution or workaround proposed...
I'd please like to know whether there's a way to change the units of a dataset, or to include the possibility of doing this manually in the front-end at load time.
New issue 906: Active Particle FieldNotFound
I've added an ActiveParticle to Enzo which is created at a user appointed time. Running YT on the output before the particle is created causes YT to exit with the error yt.utilities.exceptions.YTFieldNotFound: Could not find field '('RadiationParticle', 'particle_velocity_z')'. Tunning YT on the outputs after the particle is created presents to problems. The problem can be recreated easily with the following script
import yt # set up our namespace
Filename = "/homeappl/home/regan/appl_taito/ENZO/3.0/RP-fork/enzo-3.0-rp/run/CosmologySimulation/AMRCosmology_RadiationParticle/RD0000/RD0000"
ds = yt.load(Filename)
The output (RD0000) can be found here.
New issue 905: Cannot create plots from a data source
A field detection/generation issue is breaking `to_pw`:
ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
prj = ds.proj('density', 2)
plot = prj.to_pw()
This raises the following traceback on the current tip of the yt branch:
Traceback (most recent call last):
File "test.py", line 4, in <module>
plot = prj.to_pw()
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 389, in to_pw
pw = self._get_pw(fields, center, width, origin, 'Projection')
File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 810, in _get_pw
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 618, in __init__
PlotWindow.__init__(self, *args, **kwargs)
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 203, in __init__
self._set_window(bounds) # this automatically updates the data and plot
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_container.py", line 46, in newfunc
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 254, in _recreate_frb
File "/Users/goldbaum/Documents/yt-hg/yt/visualization/fixed_resolution.py", line 143, in _get_data_source_fields
if f not in exclude and f not in self.data_source.ds.particle_types:
TypeError: 'NoneType' object has no attribute '__getitem__'
New issue 904: Reading in orion sink / star particle files is busted in yt-3.0
This was reported via email by Stella Offner and Brandt Gaches. The code that reads them in needs to be updated to handle units. Also, the detection of particle fields got busted in some of the refactoring that went along with the transition from 2.X to 3.0.