Mailman 3 July 2015 - yt-users

Error in Executing yt Commands
by Madison Fitzgerald July 30, 2015

July 30, 2015

Hi everyone, I’ve run into an error whenever I try to execute any yt command (see yt_run_error.txt, attached because I can’t use “yt pastebin”). I’ve tried following the steps on the help page, including re-installing yt, and I still get this same error. I just installed the latest stable yt version (I can’t execute the command to give you specific numbers) on Mac OS X 10.10.4. Does anyone know where I should start to fix this? Thank you, Madison 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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How to load multi-file particle snapshot?
by Bili Dong July 30, 2015

July 30, 2015

Hi yt users, Say I have a Gadget dataset, but instead of snapshot_200.hdf5, I have snapshot_200.0.hdf5, snapshot_200.1.hdf5, … What’s the proper way to load them as a single snapshot? Regards, Bili

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installation issues
by Shankar Agarwal July 29, 2015

July 29, 2015

Hi yt'ers, I am getting this error when I try to wget the install_script.sh. I even tried the `--no-check-certificate' option, without success. I have tried on my macbook and my office machine/supercomputer. No luck. Let me know if anyone has a clue. Best, Shankar wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh ------------------------------------------------------------------------------------------------------------ --2015-07-17 20:36:49-- http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh Resolving hg.yt-project.org... 131.103.20.167, 131.103.20.168 Connecting to hg.yt-project.org|131.103.20.167|:80... connected. HTTP request sent, awaiting response... 302 FOUND Location: https://bitbucket.org [following] --2015-07-17 20:36:52-- https://bitbucket.org/ Resolving bitbucket.org... 131.103.20.167, 131.103.20.168 Connecting to bitbucket.org|131.103.20.167|:443... connected. ERROR: cannot verify bitbucket.org's certificate, issued by `/C=US/O=DigiCert Inc/OU=www.digicert.com/CN=DigiCert SHA2 Extended Validation Server CA': Unable to locally verify the issuer's authority. To connect to bitbucket.org insecurely, use `--no-check-certificate'. Unable to establish SSL connection. ------------------------------------------------------------------------------------------------------------

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FRB with different weights
by David Collins July 29, 2015

July 29, 2015

Hi, Everybody-- When I get a field out of an frb, is it possible to specify the weight field separately for different fields? EG if I do >>> proj = ds.proj('density',0) >>> frb = proj.to_frb(1,2) >>> frb['vx', weight_field='cell_mass'] or something like that? So I make an un-weighted projection, the get a weighted average for a different field. The reason I'm asking is we're making phase plots of projected quantities, using the export_frb functionality. We'd like to have one axis a weighted quantity, and the other unweighted. Thanks! d. -- -- Sent from a computer.

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Not Implemented error on enzo3.0 1d sets
by David Collins July 27, 2015

July 27, 2015

Hi, Everybody! I have a dumb question. I'm trying to plot a 1d Zeldovich Pancake with enzo-3.0, and I keep getting "Not Implemented" errors when trying to access data. If I change Version in the parameter file from 2.2 to 2.4, it works fine. Is this a known bug, or am I doing something dumb? I'm on yt changeset 60bd0bc6b0a9, a totally fresh install as per the announcement. I'm on the tip of enzo-3.0. Below is what I do: Thanks a ton! d. >>> ds=yt.load('DD0000/DD0000') >>> ds.all_data()['density'] Parsing Hierarchy 100% ||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/data_objects/data_containers.py", line 246, in __getitem__ f = self._determine_fields([key])[0] File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/data_objects/data_containers.py", line 518, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/data_objects/static_output.py", line 505, in _get_field_info self.index File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/data_objects/static_output.py", line 321, in index self, dataset_type=self.dataset_type) File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/frontends/enzo/data_structures.py", line 217, in __init__ GridIndex.__init__(self, ds, dataset_type) File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/geometry/geometry_handler.py", line 57, in __init__ self._setup_geometry() File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/geometry/grid_geometry_handler.py", line 59, in _setup_geometry self._parse_index() File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/frontends/enzo/data_structures.py", line 324, in _parse_index self._fill_arrays(ei, si, LE, RE, npart, nap) File "/Users/dcollins/local-2015-07-27-yt3.2/src/yt-hg/yt/frontends/enzo/data_structures.py", line 648, in _fill_arrays raise NotImplementedError NotImplementedError -- -- Sent from a computer.

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max_level in ProjectionPlot
by David Collins July 27, 2015

July 27, 2015

Hi, Everybody-- Does the max_level argument work in ProjectionPlot? I have a 64^3 sim with several levels, and I don't see any difference in plots at various levels. d. -- -- Sent from a computer.

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pip binaries for yt 3.2 are available
by John ZuHone July 27, 2015

July 27, 2015

Hi all, For those of you interested in installing yt via pip on Mac OS X and Windows, the binary wheels are now available. On these platforms, “pip install yt” will give you the binary install. I have personally tested them using the following Python stacks and versions: Windows x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/ <https://www.enthought.com/products/canopy/>) (2.7) WinPython (http://winpython.sourceforge.net/ <http://winpython.sourceforge.net/>) (2.7, 3.4) Mac OS X x86_64: Enthought Canopy Python (https://www.enthought.com/products/canopy/ <https://www.enthought.com/products/canopy/>) (2.7) Homebrew Python (http://brew.sh/ <http://brew.sh/>) (2.7, 3.4) Python.org <http://python.org/> Python (2.7, 3.4) Mac OS X’s system Python (2.7) MacPorts Python (https://www.macports.org/ <https://www.macports.org/>) (2.7, 3.4) Mail the list back if you find it works on other distributions or you have any problems. Happy coding! Best, John ZuHone

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Controlling grid deposition method
by Brian O'Shea July 26, 2015

July 26, 2015

Hi folks, I'm making a movie of dark matter density from an Enzo simulation, and am doing so using the arbitrary_grid mechanism. However, when I'm making the movies, I get some annoying flickering in the color map at early times. As an example, look at the first 3 Gyr or so of this movie (warning: 122 mb): http://galactica.pa.msu.edu/~bwoshea/data/cosmo_zoom_movies/dm_dens_x_algae… I am pretty sure that the flickering is due to an unfortunate interplay between whatever grid deposition is being used by the arbitrary_grid functionality and a moving image center. I'd like to test this theory by forcing the particles to be deposited in a different way - say, by nearest-grid-point instead of cloud-in-cell. Is it possible to do this? I can't find anything in the documentation that makes it clear how to do this with the arbitrary_grid mechanism, but on the other hand there are other places in yt (the particle plotting tools, for example) where one can specify ngp vs. cic. Any suggestions would be greatly appreciated! Thanks, Brian p.s. If anybody's interested, the (hacktacular and ugly) script I'm using to generate movie frames can be found here: http://paste.yt-project.org/show/5746/

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ANN: yt-3.2 released
by Britton Smith July 24, 2015

July 24, 2015

We are proud to announce the release of yt 3.2! yt (http://yt-project.org) is an open source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical simulations and nuclear engineering simulations. Major enhancements - Particle-Only Plots - a series of new plotting functions for visualizing particle data. See here <http://yt-project.org/docs/dev/visualizing/plots.html#particle-plots> for more information. - Late-stage beta support for Python 3 - unit tests and answer tests pass for all the major frontends under python 3.4, and yt should now be mostly if not fully usable. Because many of the yt developers are still on Python 2 at this point, this should be considered a “late stage beta” as there may be remaining issues yet to be identified or worked out. - Now supporting Gadget Friend-of-Friends/Subfind catalogs - see here <http://yt-project.org/docs/dev/examining/loading_data.html#halo-catalog-data> to learn how to load halo catalogs as regular yt datasets. - Custom colormaps can now be easily defined and added - see here <http://yt-project.org/docs/dev/visualizing/colormaps/index.html> to learn how! - Now supporting Fargo3D data - Performance improvements throughout the code base for memory and speed Minor enhancements - Various updates to the following frontends: ART, Athena, Castro, Chombo, Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF, Tipsy - Numerous documentation updates - Generic hexahedral mesh pixelizer - Adding annotate_ray() callback for plots - AbsorptionSpectrum returned to full functionality and now using faster SciPy Voigt profile - Add a color_field argument to annotate_streamline - Smoothing lengths auto-calculated for Tipsy Datasets - Adding SimulationTimeSeries support for Gadget and OWLS. - Generalizing derived quantity outputs to all be YTArrays or lists of YTArrays as appropriate - Star analysis returned to full functionality - FITS image writing refactor - Adding gradient fields on the fly - Adding support for Gadget Nx4 metallicity fields - Updating value of solar metal mass fraction to be consistent with Cloudy. - Gadget raw binary snapshot handling & non-cosmological simulation units - Adding support for LightRay class to work with Gadget+Tipsy - Add support for subclasses of frontends - Dependencies updated - Serialization for projections using minimal representation - Adding Grid visitors in Cython - Improved semantics for derived field units - Add a yaw() method for the PerspectiveCamera + switch back to LHS - Adding annotate_clear() function to remove previous callbacks from a plot - Added documentation for hexahedral mesh on website - Speed up nearest neighbor evaluation - Add a convenience method to create deposited particle fields - UI and docs updates for 3D streamlines - Ensure particle fields are tested in the field unit tests - Allow a suffix to be specified to save() - Add profiling using airspeed velocity - Various plotting enhancements and bugfixes - Use hglib to update - Various minor updates to halo_analysis toolkit - Docker-based tests for install_script.sh - Adding support for single and non-cosmological datasets to LightRay - Adding the Pascal unit - Add weight_field to PPVCube - FITS reader: allow HDU in auxiliary - Fixing electromagnetic units - Specific Angular Momentum [xyz] computed relative to a normal vector Bugfixes - Adding ability to create union fields from alias fields - Small fix to allow enzo AP datasets to load in parallel when no APs present - Use proper cell dimension in gradient function. - Minor memory optimization for smoothed particle fields - Fix thermal_energy for Enzo HydroMethod==6 - Make sure annotate_particles handles unitful widths properly - Improvements for add_particle_filter and particle_filter - Specify registry in off_axis_projection's image finalization - Apply fix for particle momentum units to the boxlib frontend - Avoid traceback in "yt version" when python-hglib is not installed - Expose no_ghost from export_sketchfab down to _extract_isocontours_from_grid - Fix broken magnetic_unit attribute - Fixing an off-by-one error in the set x/y lim methods for profile plots - Providing better error messages to PlotWindow callbacks - Updating annotate_timestamp to avoid auto-override - Updating callbacks to consistently define coordinate system - Fixing species fields for OWLS and tipsy - Fix extrapolation for vertex-centered data - Fix periodicity check in FRBs - Rewrote project_to_plane() in PerspectiveCamera for draw_domain() - Fix intermittent failure in test_add_deposited_particle_field - Improve minorticks for a symlog plot with one-sided data - Fix smoothed covering grid cell computation - Absorption spectrum generator now 3.0 compliant - Fix off-by-one-or-more in particle smallest dx - Fix dimensionality mismatch error in covering grid - Fix curvature term in cosmology calculator - Fix geographic axes and pixelization - Ensure axes aspect ratios respect the user-selected plot aspect ratio - Avoid clobbering field_map when calling profile.add_fields - Fixing the arbitrary grid deposit code - Fix spherical plotting centering - Make the behavior of to_frb consistent with the docstring - Ensure projected units are initialized when there are no chunks. - Removing "field already exists" warnings from the Owls and Gadget frontends - Various photon simulator bugs - Fixed use of LaTeX math mode - Fix upload_image - Enforce plot width in CSS when displayed in a notebook - Fix cStringIO.StringIO -> cStringIO in png_writer - Add some input sanitizing and error checking to covering_grid initializer - Fix for geographic plotting - Use the correct filename template for single-file OWLS datasets. - Fix Enzo IO performance for 32 bit datasets - Adding a number density field for Enzo MultiSpecies=0 datasets. - Fix RAMSES block ordering - Fix ART star particle masses to correctly reflect current and initial mass - Updating ragged array tests for NumPy 1.9.1 - Force returning lists for HDF5FileHandler Coming Soon! The next major release of yt will be version 3.3, which is slated to include an overhaul of the volume rendering system and support for analyzing and visualizing unstructured mesh data. Standard Installation Methods As with previous releases, you can install yt from source using one of the following methods. 1) From the install script (http://yt-project.org/#getyt ): Note, many of the dependencies have been updated since version 3.1. If you previously installed yt from the install script, it is advised that you re-install yt from scratch. # Installation $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh $ bash install_script.sh # Update $ yt update 2) From pip (source or binary wheel, see below for more details): # Installation $ pip install yt # Update $ pip install -U yt 3) From the Anaconda Python Distribution ( https://store.continuum.io/cshop/anaconda/): # Installation $ conda install yt # Update $ conda update yt Note that it might take a day or two for the conda package to be updated. If you are on the “stable” branch, updating will bring you from yt 3.1 to 3.2, incorporating all changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the changes since your last update should be incorporated. Installing Binary Packages via pip New to this release is the ability to install binary packages (“wheels”) using pip on Windows and Mac OS X (64-bit only for both). This has the advantage of not needing to install yt from source using a proper compiler setup, which has caused occasional problems on both of these platforms and prevented us from installing yt easily on other Python distributions. We have so far been able to install and run the binary distribution via pip on the following platforms and Python stacks: Note that it might take a day or two for the pip wheels to be updated. Windows x86_64: - Enthought Canopy Python (https://www.enthought.com/products/canopy/) - WinPython (http://winpython.sourceforge.net/) Mac OS X x86_64: - Enthought Canopy Python (https://www.enthought.com/products/canopy/) - Homebrew Python (http://brew.sh/) - Python.org Python - Mac OS X’s system Python - MacPorts Python (https://www.macports.org/) This is somewhat experimental, so other distributions may work (or not), please submit bug reports or successes to the mailing list or to the Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). All distributions are recommended to be Python v. 2.7, although with yt 3.2 there is late-stage beta support for Python 3.4. The requirements for installing yt via this method are the same as from source: - NumPy - h5py - HDF5 - SymPy - Matplotlib - IPython (not required, but strongly recommended) To install a new version of yt on one of these platforms, simply do $ pip install yt and you should get the binary distribution automatically. Also, if your python installation is system-wide (e.g., the Mac system Python) you might need to run pip with administrator privileges. For more information, including more installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt-3.2 at http://yt-project.org/docs/3.2. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel. All the best, The yt development team

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Mapping of particle field to the grid
by Yi-Hao Chen July 24, 2015

July 24, 2015

Dear yt-users, I am working on FLASH datasets with particles. I have some self-defined fields (specifically Lorentz factors) that are stored in the particle data and would like to map them onto the mesh grid. I've been trying the "add_deposited_particle_field" that is in the dev version. Currently I use the "cic" method, in which a particle will populate the nearby 8 cells (in 3D). However, since my particles are sparser than the mesh cells, many of the cells do not have particles nearby and thus are empty. I would like to find a way to interpolate for those empty cells, i.e. to smooth the particle field. Are there any suggestions or directions I should look into? It would also be very helpful if I can get the list of N nearest neighbor particles for each cell. I've looked into the nearest neighbor function http://yt-project.org/docs/dev/analyzing/fields.html#computing-the-nth-near… But it seems that it is implemented only for octree-based data objects (and can only perform in a particle-to-particle fashion?), while FLASH data are loaded into yt as "patch-based" data object. http://yt-project.org/doc/developing/creating_frontend.html#data-localizati… Is there any function that can get the nearest particle neighbors of each cell? Thank you, Yi-Hao -- Yi-Hao Chen Graduate Student Department of Astronomy University of Wisconsin-Madison

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