Mailman 3 May 2015 - yt-users

Create_profile error in parallel
by John Regan 15 May '15

15 May '15

Hi All, I'm seeing an error when I run YT 3.2 in parallel. Running in serial mode everything is fine. I have a bunch of fields I'm creating profiles for 'DarkMatter' is not one of them but that's where it fails. It looks like its picking up the DarkMatter radius rather than the gas radius? rp = yt.create_profile(sphere, 'radius', Fields, units = {'radius': 'kpc'}, n_bins=40) P002 yt : [ERROR ] 2015-05-14 22:09:54,308 YTFieldNotFound: Could not find field '('DarkMatter', 'radius')' in RD0001. I've attached the error file http://paste.yt-project.org/show/5547/ and the version info is: --- Version = 3.2-dev Changeset = 3e1887de7362+ (yt) tip --- Thanks! John _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Using time series data from FLASH with particle files.
by Joshua Wall 14 May '15

14 May '15

Dear users, Since I'm already 0 for 1 today, I thought I'd also ask about this error I've seen. I'm trying to get the time series of momentum density in the x-dir from a simulation in FLASH where I have both the plot and particle files with: ############################################################ ts = yt.load("/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_plt_cnt_0??[!0]", particle_filename='/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]') times = [] Mom_x = [] Mom_y = [] for ds in ts: try: ds.add_field("total_px", function=_px, units="kg/s/m**2") ds.add_field("total_py", function=_py, units="kg/s/m**2") except: continue dd = ds.all_data() Mom_x.append(dd["total_px"]) Mom_y.append(dd["total_py"]) times.append(ds.current_time.in_units("Myr")) ########################################################### But this gives the error: --------------------------------------------------------------------------- IOError Traceback (most recent call last) <ipython-input-3-4be7349ef199> in <module>() 9 Mom_y = [] 10 ---> 11 for ds in ts: 12 13 /usr/local/lib/python2.7/dist-packages/yt/data_objects/time_series.pyc in __iter__(self) 158 for o in self._pre_outputs: 159 if isinstance(o, types.StringTypes): --> 160 ds = load(o, **self.kwargs) 161 self._setup_function(ds) 162 yield ds /usr/local/lib/python2.7/dist-packages/yt/convenience.pyc in load(*args, **kwargs) 78 if c._is_valid(*args, **kwargs): candidates.append(n) 79 if len(candidates) == 1: ---> 80 return output_type_registry[candidates[0]](*args, **kwargs) 81 if len(candidates) == 0: 82 if ytcfg.get("yt", "enzo_db") != '' \ /usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, particle_filename, units_override) 206 self._particle_handle = HDF5FileHandler(self.particle_filename) 207 except: --> 208 raise IOError(self.particle_filename) 209 # These should be explicitly obtained from the file, but for now that 210 # will wait until a reorganization of the source tree and better IOError: /home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0] ############################################################# Any ideas? Joshua Wall Drexel University _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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weird square feature in dark matter density slice map
by Junhwan Choi (최준환) 14 May '15

14 May '15

Hi yt users, I make a simple dark matter slice map from my enzo simulation output with following script. ================== pc = yt.SlicePlot(ds, "z", ('deposit', 'io_cic'), width = (244.0, 'Mpccm/h'), center=cen_center) pc.annotate_text((0.7,0.9),'z=%4.2f' % ds.current_redshift, coord_system='figure', text_args = text_dict) pc.annotate_velocity(factor=16, scale=None, scale_units=None, normalize=False) pc.save("cen_all_0000") ================= I see the weird 5x6 square shapes on the plot. Why this square/cube shape result from and how to remove this? Thank you in advance, Junhwan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt inline (feed information to Enzo)
by Yuan Li 14 May '15

14 May '15

Hi all, I am trying to calculate the mass flux through a sphere and modify a simulation parameter accordingly. I heard that it is possible to use yt to extract information from an Enzo simulation and feed it back to Enzo, but I was having a hard time finding an example. Is this where I should start: http://enzo.readthedocs.org/en/latest/user_guide/EmbeddedPython.html ? If not, please direct me to the right place. If that is what I should be looking at, I am having trouble compiling Enzo with "make python-yes". I tried to use the python 2.7 that comes with yt2.x, but got an error message related to "architecture x86_64" on my macbook (I am able to compile Enzo with python-no). I looked at the example Make.mach.orange. LOCAL_INCLUDES_PYTHON is using python2.7, but LOCAL_LIBS_PYTHON is using python2.6. I am confused: is that how it is supposed to be done? Do I have to install a python2.6 separately? Thank you! Yuan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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2015 IEEE Scientific Visualization Contest
by Matthew Turk 12 May '15

12 May '15

Hi everyone, We invite you to participate in the 2015 IEEE Scientific Visualization Contest. This year's contest targets data from cosmology research that studies the formation of structure in the Universe. Participants are challenged to create a comprehensive set of analysis and visualization capabilities that enable domain experts to gain deeper insight into the formation of various structures in the Universe and better understanding of observations from next generation telescopes. Besides a number of interesting incentives, the contest winners will be presenting their work at IEEE VIS 2015 and they will get a chance to publish their results as a full, peer-reviewed IEEE CG&A article. Find out more at http://sciviscontest.ieeevis.org/2015/ Please pass this announcement along to other interested parties! _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Disabling yt info outputs
by Joshua Wall 11 May '15

11 May '15

Dear users, I recently updated yt to the latest verison, and now when I run it in an ipython notebook I get obscene amounts of yt: INFO and yt: WARNING messages. So many that it actually hangs some analysis loops I'm running. How do I turn this output off? Sample from loading a file: yt : [INFO ] 2015-05-11 16:01:16,453 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,455 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,456 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,512 Parameters: current_time = 1.80820359458e+12 yt : [INFO ] 2015-05-11 16:01:16,514 Parameters: domain_dimensions = [8 8 8] yt : [INFO ] 2015-05-11 16:01:16,516 Parameters: domain_left_edge = [ -1.29093000e+17 -1.29093000e+17 -1.29093000e+17] yt : [INFO ] 2015-05-11 16:01:16,517 Parameters: domain_right_edge = [ 1.29093000e+17 1.29093000e+17 1.29093000e+17] yt : [INFO ] 2015-05-11 16:01:16,519 Parameters: cosmological_simulation = 0.0 Any assistance is greatly appreciated. I checked the docs, but I was unable to find a way to pass to yt the configuration option which I suspect is the problem, namely one: suppressStreamLogging. Cordially, Joshua Wall Drexel University _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Deposited Particle Data
by Jason Galyardt 11 May '15

11 May '15

Hi all, Has anyone had success accessing deposited particle data generated with FLASH? It appears in the dataset derived field list, but when I go to access it (via ds.all_data()['deposit', 'io_mass']), I get an error concerning zero-length selection. I get the same error when I try to access the 'standard' particle data (from ds.field_list), such as ds.all_data()['io', 'particle_mass']. Does this ring any bells? This very well could be user error, so please let me know if that seems to be the case. I've pasted a basic script to reproduce the error here: http://paste.yt-project.org/show/5538/ I'd rather not post the dataset publicly, but I can send you a link, if you're interested. Cheers, Jason Galyardt _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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PYTHONPATH
by mc knabbits 06 May '15

06 May '15

hi everybody, this question aint very yt specific but more on the python way of treating its PATH variable. since having installed yt I have 2 versions of python on my machine. (the yt one and my previous 2.7.3 with the main scipy packages) I wonder how its possible to have each of them having its own PYTHONPATH variable? so when yt is activated it uses its yt path and when switched off the independend python install uses another. right now even when deactivated the first entry in the PPATH is the yt link to the yt python site packages where numpy etc is stored. but these packeges would not work with the original python version I may want to use as well so that I need to re-source my bashrc or restart the terminal... hope theres a solution to this thanx, phil _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Pressure in Enzo methods
by David Collins 05 May '15

05 May '15

Hi, Everybody! I'm having a little trouble with getting pressure when using HydroMethod=6. For instance, >>> ds0.all_data()['pressure'] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__ f = self._determine_fields([key])[0] File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/data_containers.py", line 489, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/static_output.py", line 482, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'pressure')' in data0000. while this works for a run with HydroMethod = 0. Could someone give me the nickel tour of hydro method impacts setting of variables, and where I should look to make sure pressure is defined? Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Plot 2D magnetic field lines
by Stella Offner 05 May '15

05 May '15

Many thanks, Nathan! This does annotate the streamlines like I wanted for yt 3.1, and I think it would be useful for the cookbook. Once I reformat it a little, I'm happy to send my version back to you. Stella P.S. Matt, I'm sorry to say the users archive is still 'forbidden' to me. On Mon, May 4, 2015 at 3:01 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > > > On Mon, May 4, 2015 at 11:43 AM, Stella Offner <offner(a)gmail.com> wrote: > >> Hi, >> >> Is there a way to do annotate streamlines and use get_multi_plot with yt >> 3.1? The single-plot example below works for me, but it doesn't work with >> this example of get_multi_plot (i.e. annotations are not carried over): >> >> http://yt-project.org/docs/3.1/cookbook/complex_plots.html#multipanel-with-… >> > > Hi Stella, > > With a bit of fiddling, I was able to get this to work in the latest > development version of yt, although I think it should work in 3.1 as well, > see: > > http://paste.yt-project.org/show/5532/ > > This is a bit tricky, since it depends sensitively on details of how > matplotlib stores imshow plots and that way we interface with that in the > streamline callback. > > It might be worthwhile to add a new cookbook script using this example - > we'd be very grateful for any docs improvements you might want to make! > > > >> >> Sorry if this was already answered in the mailing list archive somewhere, >> the user discussion archives is still unsearchable: >> Forbidden >> >> You don't have permission to access /pipermail/yt-users-spacepope.org/ >> on this server. >> > Additionally, a 404 Not Found error was encountered while trying to use an >> ErrorDocument to handle the request. >> > > This has come up a few times before although the lack of mailing list > archives might make that hard to discover! It's an issue with our ISP. Matt > has been sending them angry e-mails for a while now.... > > > -Nathan > > >> Thanks! >> Stella >> >> On Tue, Apr 28, 2015 at 9:05 AM, David Collins <dcollins4096(a)gmail.com> >> wrote: >> >>> Hi, Dominik-- >>> >>> What was the yt command you used to make the streamlines and generate >>> the error you sent? I used the following and it was successful: >>> >>> ds = yt.load('DD0004/data0004') >>> >>> proj = yt.ProjectionPlot(ds,2,'density') >>> >>> proj.annotate_streamlines('Bx','By') >>> >>> and it made this image: >>> http://imgur.com/eZQmqTB >>> Can you try the above and let me know if it works? >>> >>> d. >>> >>> >>> On Tue, Apr 28, 2015 at 2:58 AM, Dominik Derigs <derigs(a)ph1.uni-koeln.de >>> > wrote: >>> >>>> Hi together, >>>> >>>> I want to use yt for plotting magnetic field lines in FLASH simulations >>>> from 2D simulations and slices from 3D simulations. >>>> An example of what it could look like can be seen here: >>>> http://aprg.mae.ufl.edu/wp-content/uploads/2014/07/tang_51.png >>>> >>>> I tried to use yt's streamline function, but this does not work for me: >>>> http://yt-project.org/doc/visualizing/streamlines.html >>>> >>>> The error shown is: >>>> ValueError: operands could not be broadcast together with shapes >>>> (9,9,2) (9,9,95) (9,9,2) >>>> >>>> The used FLASH file is attached. >>>> >>>> Thanks a lot >>>> >>>> Dominik >>>> >>>> -- >>>> Dominik Derigs >>>> I. Physikalisches Institut >>>> Universität zu Köln >>>> Zülpicher Straße 77 >>>> 50937 Köln >>>> GERMANY >>>> >>>> Tel. (+49|0) 221 470-8352 >>>> Fax. (+49|0) 221 470-5162 >>>> >>>> Diese Email ist vertraulich und nur für den angegebenen Empfänger >>>> bestimmt. Zugang, Freigabe, die Kopie, die Verteilung oder Weiterleitung >>>> durch jemand anderen außer dem Empfänger selbst ist verboten und kann eine >>>> kriminelle Handlung sein. Bitte löschen Sie die Email, wenn Sie sie durch >>>> einen Fehler erhalten haben und informieren Sie den Absender. >>>> >>>> This email and any files transmitted with it may contain confidential >>>> and/or privileged material and is intended only for the person or entity to >>>> which it is addressed. Any review, retransmission, dissemination or other >>>> use of, or taking of any action in reliance upon, this information by >>>> persons or entities other than the intended recipient is prohibited. If you >>>> have received this email in error, please notify the sender immediately and >>>> delete this material from all known records. >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> >>> -- >>> -- Sent from a computer. >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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