Mailman 3 April 2016 - yt-dev

Issue #1210: Frontend Documentation (yt_analysis/yt)
by Axel Huebl April 13, 2016

April 13, 2016

New issue 1210: Frontend Documentation https://bitbucket.org/yt_analysis/yt/issues/1210/frontend-documentation Axel Huebl: Hi fabulous folks at yt! :) @ngoldbaum [catched](https://github.com/openPMD/openPMD-yt/issues/7) my at our GitHub frontend project for [openPMD](https://github.com/openPMD/openPMD-standard) files. What we are trying to read into yt is a simple 2D and 3D, domain-decomposited particle-mesh domain. Our mesh is regularly spaced and cartesian and our particles are stored in … [View More]as array of struct in long, contiguous 1D arrays. Additionally, we have an index table called `particlePatches` that can be used to read chunks of particles from the 1D particle arrays (guaranteeing that in its specific spatial extend no other chunks of particles are also present). We write all our data efficiently via MPI-I/O in one parallel HDF5 file (and ADIOS `.bp` files, but let us stick with HDF5 for now). ### Ask your question, man! Long story short, domain-decomposited data structures are e.g., implemented in the `FITS` frontend. The following quesitons arise: - What is the general concept to read data into yt? Does all data need to be in the same domain (e.g., have the same spatial extent)? - If I have several domains, a discrete, spaced field domain and a position-wise continuous particle domain (with finite "density" shape on the particles) - how are they represented to the front-end? - How would one implement to load a [staggered grid](https://en.wikipedia.org/wiki/Finite-difference_time-domain_method) of fields? - What classes and methods actually need to be implemented? What are their interfaces (input parameters and return types)? What private members need to be populated? - How to describe a [disjoint](https://en.wikipedia.org/wiki/Disjoint_sets) domain decomposition in both domains (mesh & particles) so one can read those in parallel? - is `yt.load` supposed to read a single file or is it expected to handle full time series (if I give it a prefix that can match several files that might make one up)? ### Our Current Status We (think) we found a way to read mesh (field) values from our files in a generic way for now https://github.com/openPMD/openPMD-yt/pull/6 Nevertheless, describing the parallelization we used (simple 3D domain decomposition) and getting particles in seems to be a bit tricky. This issue is about @ngoldbaum idea to tell specific questions so one can improve the documentation (also in-code documentation) of the frontends in yt. Any help is very much appreciated :) ### Resources - our file format in fancy slides: http://openPMD.org - our file format in many words: https://github.com/openPMD/openPMD-standard - our half-way frontend: https://github.com/openPMD/openPMD-yt - a short-term intern of us contacting the mailing list: http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2015-September/00… - some example files: https://github.com/openPMD/openPMD-example-datasets (I will add an example with parallel/tiled `particlePatches` these days) [View Less]

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smoothed particle fields
by Britton Smith April 11, 2016

April 11, 2016

Hi everyone, Please forgive my ignorance on this question. Is it possible to create a smoothed field that has the same shape as a particle field? Specifically, I would like to create a density field that is as close to how SPH codes calculate densities for each particle. I believe this would involve evaluating smoothing kernels at particle positions instead of octree cell centers as we do with deposited fields. If this is not possible, does anyone have any thoughts on how this might be implemented? Thanks, Britton

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SciPy financial aid
by Nathan Goldbaum April 11, 2016

April 11, 2016

Hi all, I wanted to highlight the opportunity to apply for financial aid to attend the SciPy conference: http://scipy2016.scipy.org/ehome/146062/388110/?&& If you are thinking about attending but are worried about financial issues, this is a very viable option. I was given aid to attend in 2014, and the process was very painless. Nathan

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Re: [yt-dev] smoothed particle fields
by Matthew Turk April 11, 2016

April 11, 2016

Hi Britton, Yup, this is possible. Take a look at how the nearest neighbor field is implemented in particle_fields.py for an example. Matt On Apr 11, 2016 8:13 AM, "Britton Smith" <brittonsmith(a)gmail.com> wrote: Hi everyone, Please forgive my ignorance on this question. Is it possible to create a smoothed field that has the same shape as a particle field? Specifically, I would like to create a density field that is as close to how SPH codes calculate densities for each particle. … [View More]

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NumFOCUS blog post
by Matthew Turk April 10, 2016

April 10, 2016

Hey folks, We're on the NumFOCUS blog! http://www.numfocus.org/blog/numfocus-announces-new-fiscally-sponsored-proj… -Matt

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Issue #1209: Covering grids do not fill data outside domain boundaries for a periodic simulation (yt_analysis/yt)
by Nathan Goldbaum April 7, 2016

April 7, 2016

New issue 1209: Covering grids do not fill data outside domain boundaries for a periodic simulation https://bitbucket.org/yt_analysis/yt/issues/1209/covering-grids-do-not-fill… Nathan Goldbaum: The following test script (adapted from a script provided to me by Marco Surace): http://paste.yt-project.org/show/6396/ Produces the following image: ![test.png](https://bitbucket.org/repo/BXbAb/images/1362080846-test.png) Since this simulation uses periodic boundary conditions, I would expect … [View More]

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Issue #1208: `upload_image` command line argument no longer works (yt_analysis/yt)
by Cameron Hummels April 6, 2016

April 6, 2016

New issue 1208: `upload_image` command line argument no longer works https://bitbucket.org/yt_analysis/yt/issues/1208/upload_image-command-line-… Cameron Hummels: When you want to upload an image automatically to the web, you used to be able to use: ``` #!python $ yt upload_image image.png ``` But this now returns the error: ``` #!python ERROR HTTP Error 404: Not Found ``` It appears the imgur.com API version has changed, and they no longer accept API version 1, which is how it was … [View More]

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Pull request review hangout: Wednesday April 6 1:00 PM CDT
by Nathan Goldbaum April 6, 2016

April 6, 2016

Hi all, Here's the link for this week's pull request review hangout. If you'd like to come, indicate that you are attending so you get a reminder on Wednesday. https://plus.google.com/b/107728486871834552760/events/csf9srcjo18cilbhoko9… Hope you're all having a good weekend, Nathan

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Issue #1207: size of annotate_axes can be very small in a VR (yt_analysis/yt)
by Michael Zingale April 6, 2016

April 6, 2016

New issue 1207: size of annotate_axes can be very small in a VR https://bitbucket.org/yt_analysis/yt/issues/1207/size-of-annotate_axes-can-… Michael Zingale: if you draw the axis triad on a domain with annonate_axes(), it sometimes comes out really small. See the image below (the triad is the few pixels in the upper right). ![subchandra_test.png](https://bitbucket.org/repo/BXbAb/images/3287899079-subchandra_test.png)

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Issue #1206: OWLS dataset instantiation is quite slow (yt_analysis/yt)
by Matthew Turk April 5, 2016

April 5, 2016

New issue 1206: OWLS dataset instantiation is quite slow https://bitbucket.org/yt_analysis/yt/issues/1206/owls-dataset-instantiation… Matthew Turk: The setting up of fields for ion states is somehow quite slow for OWLS datasets. I'm not entirely sure why that is, but it is around 30 seconds.

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