Mailman 3 July 2015 - yt-users

Pressure/temperature gradient field
by Yuan Li 23 Jul '15

23 Jul '15

Dear all, I am using yt2.6. I was trying to define a field of the temperature gradient like gradPressureX, but I got an error message: ... new_field[1:-1,1:-1,1:-1] = data["Temperature"][sl_right,1:-1,1:-1]/ds ValueError: could not broadcast input array from shape (62,62,64) into shape (62,62,62) I then tried to re-define gradPressureX by copying the original definition ( http://yt-project.org/docs/2.6/reference/field_list.html#gradpressurex) and giving it a different name, and I got the same error. The original gradPressureX works fine. Is it because I did not load some specific module or something? Thank you! Yuan

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Installing matplotlib-1.4.0
by Shankar Agarwal 23 Jul '15

23 Jul '15

Hi, My yt installation quits at matplotlib. The machine is http://www.idris.fr/eng/ada/ada-presentation-eng.html Any idea how may I solve/bypass the following error: Thanks Shankar Installing distribute Installing pip Installing numpy-1.8.2 Installing matplotlib-1.4.0 ******************************************** FAILURE REPORT: ******************************************** Processing dependencies for matplotlib==1.4.0 Searching for mock Reading http://pypi.python.org/simple/mock/ Best match: mock 1.2.0 Downloading https://pypi.python.org/packages/source/m/mock/mock-1.2.0.tar.gz#md5=94ec3b… Processing mock-1.2.0.tar.gz Writing /tmp/easy_install-a12wMg/mock-1.2.0/setup.cfg Running mock-1.2.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-a12wMg/mock-1.2.0/egg-dist-tmp-1nkTUJ mock requires setuptools>=17.1. Aborting installation error: Setup script exited with 1 ********************************************

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Creating Derived Fields and Plotting Error
by Madison Fitzgerald 22 Jul '15

22 Jul '15

Hello, I am trying to create two new derived fields and then make a simple phase plot using one of these fields, but I am running into a pretty consistent error involving “convert_to_units". I get basically the same error when using the ds.sphere object and a ds.all_data object, so if there’s something I’ve messed up on, it’s not obvious to me and I would appreciate any help figuring out what’s wrong. I am running yt on a MacBook Pro with OS 10.10.4. I have the newest version of stable yt (3.1 and changeset 665e2b6cdf78), and you can find my script at this link (http://paste.yt-project.org/show/5733/ <http://paste.yt-project.org/show/5733/>) and my error output at this link (http://paste.yt-project.org/show/5734/ <http://paste.yt-project.org/show/5734/>). Thank you very much, Madison Fitzgerald Madison Fitzgerald Astrophysics | Lyman Briggs College Women’s & Gender Studies | College of Arts & Letters LGBTQ and Sexuality Studies Specialization Women in Science, President Undergraduate Teaching Assistant Undergraduate Research Assistant Department of Physics and Astronomy Honors College Michigan State University

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Re: [yt-users] Particle Fields Deposition
by Bili Dong 22 Jul '15

22 Jul '15

Hi Desika, Thanks for your help! Regards, Bili > On Jul 20, 2015, at 7:19 PM, Desika Narayanan <dnarayan(a)haverford.edu> wrote: > > > Hi Bili, > 1 . I wrote an example script that does some of the things you want in > question 1 here > > http://paste.yt-project.org/show/5727/ > > 2. When you load the octree, you can change the threshold number of > particles necessary for refinment by : > > ds = load(filename, n_ref = 32) > > Not sure about 3 or 4, but I think the answer is that the kernel is > hardcoded in. > > > -d > > On Mon, Jul 20, 2015 at 4:56 PM, Bili Dong <qobilidop(a)gmail.com> wrote: > >> Hi yt users, >> >> Recently I started using yt to analyze a Gadget-like data (one of the main >> difference being a different kernel function). I?ve got several questions >> about the fields depostion mechanism: >> >> 1. How do I get the information of the underlying mesh onto which the >> fields are deposited? >> 2. Can I specify the properties of the underlying mesh? If so, how? >> 3. Can I customize the smoothing process, like using a different smoothing >> kernel? >> 4. I?m looking into the file yt/geometry/particle_smooth.pyx to learn the >> implementation details of the smoothing process. But for me, the code is >> not easy to read. So I?m wondering if there are further documentations I >> could refer to? (The only relevant doc I find for now is this one >> <http://yt-project.org/docs/dev/analyzing/fields.html#general-particle-fields> >> ) >> >> I?m new to yt, so these questions might be dumb. Sorry for wasting your >> time if that?s the case. >> >> Thanks, >> Bili >> >> >> >> _______________________________________________ >> 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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Particle Fields Deposition
by Bili Dong 20 Jul '15

20 Jul '15

Hi yt users, Recently I started using yt to analyze a Gadget-like data (one of the main difference being a different kernel function). I’ve got several questions about the fields depostion mechanism: 1. How do I get the information of the underlying mesh onto which the fields are deposited? 2. Can I specify the properties of the underlying mesh? If so, how? 3. Can I customize the smoothing process, like using a different smoothing kernel? 4. I’m looking into the file yt/geometry/particle_smooth.pyx to learn the implementation details of the smoothing process. But for me, the code is not easy to read. So I’m wondering if there are further documentations I could refer to? (The only relevant doc I find for now is this one <http://yt-project.org/docs/dev/analyzing/fields.html#general-particle-fields>) I’m new to yt, so these questions might be dumb. Sorry for wasting your time if that’s the case. Thanks, Bili

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Problem generating python executable in yt 3.0
by Juan Camilo Ibanez Mejia 17 Jul '15

17 Jul '15

Hi all, I'm running into some problems while trying to generate a python executable in yt3.0 I was able to do it in yt2.6 but not in this newer version, this is an example of what I'm doing: >#!/home/jcibanezm/codes/yt30/yt-x86_64/bin/python > >import yt >print "Hello World" And when I run this, I get the following error: Traceback (most recent call last): File "./Test.py", line 3, in <module> from yt.config import ytcfg;ytcfg["yt","__withinreason"]="True" File "/home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/__init__.py", line 121, in <module> from yt.data_objects.api import \ File "/home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 53, in <module> from .image_array import \ File "/home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/data_objects/image_array.py", line 15, in <module> from yt.visualization.image_writer import write_bitmap, write_image File "/home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/visualization/image_writer.py", line 24, in <module> import yt.utilities.png_writer as pw File "/home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/utilities/png_writer.py", line 13, in <module> import matplotlib._png as _png ImportError: libpng16.so.16: cannot open shared object file: No such file or directory Any idea ? thanks for your help. Best, Juan -------------------------------------------------- Juan Camilo Ibáñez-Mejia PhD student in Physics. Institut für Theoretische Astrophysik, Zentrum für Astronomie Heidelberg jibanez(a)zah.uni-heidelberg.de<mailto:jibanez@zah.uni-heidelberg.de> American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> ----------------------------------------------------

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Changing length variable in Rockstar
by Paco Holguin 16 Jul '15

16 Jul '15

Hi, I have been having problems with the halo finding with Gadget (and also Arepo) data in Rockstar. I think the problem is that the conversion for length is not being set correctly. This variable is GADGET_LENGTH_CONVERSION and is currently set to 1, and I want it to be set to 1e-3 (b/c the code length is in Kpc, not Mpc). When I run the halo finder in with the HaloCatatlog, yt creates/overwrites a directory, and outputs a configuration file called "rockstar.cfg" with the parameters that it used. However, I can't just change that configuration file to add GADGET_LENGTH_CONVERSION = 1e-3, because when I run the halo finder again, it just gets overwritten and the variable used is still 1. I did try to give it as a finder argument in the Halocatalog function, as is done with "force_res", but it does not recognize the variable. Does anyone know how to get the halo finder/rockstar to take a configuration file, and not overwrite it each time? Or some other way to change the parameters used in halo finding? I appreciate the help, Paco

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units_override not working for Flash or Enzo datasets
by Alex Hill 16 Jul '15

16 Jul '15

Hi, I’m trying to use the units_override option in loaddata (because I have a data set with metadata labeling itself as cgs but is actually in kpc-Myr-Msun units), following the example in the documentation here: <http://yt-project.org/doc/analyzing/units/comoving_units_and_code_units.html> I find that, for data sets created with FLASH 2.5 and FLASH 4.2, units_override does nothing. units_override also does nothing for the sample enzo data sets enzo_tiny_cosmology and IsolatedGalaxy. It *does* work for the sample Athena data set. Any suggestions? Is units_override supported for Athena but not for Flash or Enzo? Examples here and copied below with the output: <http://paste.yt-project.org/show/5713/> units_override={"length_unit":(1.0,"cm"),"time_unit":(1.0,"s"),"mass_unit":(1.0,"g")} ds=yt.load('/Users/hil32p/src/yt/doc/source/quickstart/IsolatedGalaxy/galaxy0030/galaxy0030') print ds.length_unit print ds.mass_unit print ds.time_unit output: 3.086e+24 cm 8.11471080586e+43 g 2.32946e+18 s ds=yt.load('/Users/hil32p/src/yt/doc/source/quickstart/IsolatedGalaxy/galaxy0030/galaxy0030',units_override=units_override) print ds.length_unit print ds.mass_unit print ds.time_unit output: 3.086e+24 cm 8.11471080586e+43 g 2.32946e+18 s However, it does work for the Athena dataset used in the example: ds = yt.load('/Users/hil32p/Downloads/MHDSloshing/virgo_low_res.0054.vtk') 1.0 cm 1.0 g 1.0 s units_override={"length_unit":(1.0,"kpc"),"time_unit":(1.0,"Myr"),"mass_unit":(1.0,"Msun")} ds = yt.load('/Users/hil32p/Downloads/MHDSloshing/virgo_low_res.0054.vtk', units_override=units_override) 1.0 kpc 1.0 Msun 1.0 Myr I am running yt 3.1 with python 2.7, both installed via conda. Cheers, Alex --------- Alex Hill Senior Postdoctoral Research Associate Strawbridge Observatory Department of Astronomy, Haverford College 370 Lancaster Ave, Haverford, PA 19041 USA phone: +1 484 297 2136 email/iMessage: ashill(a)haverford.edu

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yt notebook, PuTTY, and port forwarding
by j s oishi 16 Jul '15

16 Jul '15

Hi all, I have an extremely strange problem. I'm trying to connect to the yt notebook running on a remote server on a windows laptop using PuTTY. If I try port forwarding using PuTTY, I can make [remote-machine] $ python -m SimpleHTTPServer 8888 work just fine. That is, I can see the directory at localhost:8888 on the windows laptop. However, if I try [remote-machine] $ yt notebook the windows laptop shows no route to host. I can confirm that on the server, the yt notebook log registers nothing when the page is loaded or reloaded on the laptop. Has anyone seen this very strange behaviour before? I've tried running yt notebook on port 8888, 8000, and 9999. All of those ports work fine for SimpleHTTPServer, but all of them fail for yt notebook. I also tried running the ipython notebook directly; it fails in exactly the same way. I tried connecting from a linux machine to the same server; everything worked just fine. Any suggestions you might have would be most welcome! thanks, jeff

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ANN: "Effective Computation in Physics" Released, 50% Off until Friday July 17th
by Anthony Scopatz 15 Jul '15

15 Jul '15

Hello All! We are ecstatic to announce the release of the first edition of *Effective Computation in Physics - Field Guide to Research with Python* <http://shop.oreilly.com/product/0636920033424.do>, published by O'Reilly Media. *You (or your students and colleagues) can even get a 50% discount if you grab it before July 17th using the code: WKPYDP <http://shop.oreilly.com/product/0636920033424.do?code=WKPYDP>*. This book was heavily inspired by Software Carpentry. Though it draws on many examples from the physical sciences, many of the topics and chapters are broadly applicable to all of scientific computing. We hope that you'll find it useful even if your domain is biological, chemical, or mathematical in nature! For more information, please check out: - The website: http://physics.codes/ - The summary post at Software Carpentry: http://software-carpentry.org/blog/2015/07/effective-physics-book.html - The lightning talk announcement at SciPy 2015: https://youtu.be/yCStple1-28?t=29m20s Don't hesitate to contact us via email at authors(a)physics.codes or on twitter @physics_codes <https://twitter.com/physics_codes> with any questions or concerns that you have. Accompanying Jupyter Notebooks for all of the code in the book can be found on GitHub at https://github.com/physics-codes/examples released under the CC0 license. Please remember to review the book and give feedback online once you have finished reading it. We truly appreciate it, no matter what you say. Sorry if you received this announcement multiple times. We promise this will be the only time we ever send out such an announcement. We couldn't have done it without you! Katy Huff & Anthony Scopatz

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