Mailman 3 November 2016 - yt-users

to the community
by Britton Smith 11 Nov '16

11 Nov '16

Hi everyone, In light of the recent election and some of the negative events that have happened, we want to reassure you, and at the same time make it clear to all, that we expect the yt community to continue to be a place of tolerance, kindness, and respect for everyone. We will certainly not judge or discriminate against people based on their values, beliefs, political affiliation or lack thereof, lifestyles, life experiences, race, color, religion, sex, national origin, ancestry, age, order of protection status, genetic information, marital status, disability, sexual orientation including gender identity, unfavorable discharge from the military or status as a protected veteran. We have a code of conduct, which can be reviewed at http://yt-project.org/community.html , which covers interactions on the mailing list, at in person workshops, on Slack or IRC, and commit messages. Importantly, we want to make sure you are aware that this tolerance of viewpoints does *not* extend to tolerance of harassing, rude, or intolerant statements or behavior. If any of you experience or witness something along these lines, please let members of the steering committee know. If you have something you wish to report that you would like to remain confidential, please email confidential(a)yt-project.org , and we will work to address this issue. For more information, this blog post on the Committee for the Status of Women in Astronomy has suggested actions for when you find yourself to be a bystander: http://womeninastronomy.blogspot.com/2016/11/reflection-moment-importance-o… , including links to other resources. Based on our experiences with the yt community as a group and individually, none of us anticipate this to be a concern. However, we cannot condemn strongly enough hateful language or actions, and want to take this opportunity to reassure this community that we will not tolerate it in our midst. Thank you, yt steering committee

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Sudden fluctuations in the projected density
by Maan Hani 08 Nov '16

08 Nov '16

Hi all, While performing projections of the density ?field in a cosmological zoom-in simulation, I noticed sudden fluctuations between the projected density of consecutive snapshots. I thought the fluctuations were due to interlopers entering the field of view (I was looking at the zoom-in region of the box). However, regardless what region of the cosmological box I plot (below I project the whole cosmological box), the fluctuation remains. Note that the fluctuation is not seen in the particle data. Please let me know if this issue is reproducible by others (I'm using yt 3.4-dev) and how I could go about solving it. I've linked a simple sample script and the projection output. The projections are made using Arepo data, but I am treating the data as a Gadget Dataset in yt. The data is available at: http://use.yt/upload/44604f23 and http://use.yt/upload/a5e7f213 Output: - snapshot1: http://i.imgur.com/a3w6vVn.png - snapshot2: http://i.imgur.com/Bq5xlOB.png? Sample script: ``` # importing libraries import yt from yt.frontends.gadget.data_structures import GadgetHDF5Dataset # reading snapshot data ds1 = GadgetHDF5Dataset('../data/1605-2/snapshot_052.hdf5') ds2 = GadgetHDF5Dataset('../data/1605-2/snapshot_053.hdf5') # density un-weighted projections proj1 = yt.ProjectionPlot(ds1, 'z', ('gas','density')) proj2 = yt.ProjectionPlot(ds2, 'z', ('gas','density')) proj1.set_zlim('density', 1.E-4, 1.E-2) proj2.set_zlim('density', 1.E-4, 1.E-2) proj1.save() proj2.save() ``` Thanks, Maan??

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GDF format issue
by Andrea Negri 04 Nov '16

04 Nov '16

Hi all, As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script). Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer. Cheers, Andrea

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loading cosmological CHANGA data
by Christine Simpson 04 Nov '16

04 Nov '16

Hi all, I’m trying to load a cosmological snapshot from a Changa simulation (which I believe is in the tipsy format). Yt seems to find some of the cosmological parameters but not all of them (not the hubble constant), which messes up the units. See below. There is some discussion of cosmology parameters and tipsy format in the docs, but I did not understand it. Can anyone with experience loading this format give me some pointers? Thanks Christine In [1]: pf = load('agora_1e11q_l13.000400') yt : [INFO ] 2016-11-03 15:17:47,253 Parameters: current_time = 1.61048087203e+23 s yt : [INFO ] 2016-11-03 15:17:47,253 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2016-11-03 15:17:47,254 Parameters: domain_left_edge = [-0.5 -0.5 -0.5] yt : [INFO ] 2016-11-03 15:17:47,255 Parameters: domain_right_edge = [ 0.5 0.5 0.5] yt : [INFO ] 2016-11-03 15:17:47,256 Parameters: cosmological_simulation = 1.0 yt : [INFO ] 2016-11-03 15:17:47,256 Parameters: current_redshift = -1.48991929905e-13 yt : [INFO ] 2016-11-03 15:17:47,256 Parameters: omega_lambda = 0.728 yt : [INFO ] 2016-11-03 15:17:47,256 Parameters: omega_matter = 0.272 yt : [INFO ] 2016-11-03 15:17:47,256 Parameters: hubble_constant = 1.89812815754e-06

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Issue loading data with yt
by Matthew Robert Brinson 02 Nov '16

02 Nov '16

Hi yt-users, Let’s try this again. The file I sent the first time was too large. I’m using yt version 3.3.1, and I’ve recently encountered an issue loading data correctly. I’m running SPH simulations of white dwarf mergers and want to know what the mass fractions of different elements are at different times. I have two files that contain the data: 1) a tipsy file, 2) and a text file that contains the mass fraction values of helium-4. The tipsy file loads just fine and I’m able to access the information from the helium file once the tipsy file is loaded. For some reason though, when I have more than 262144 particles in my simulation, yt does not load the helium mass fraction values correctly anymore. I’ve initialized all particles to have a 4% helium mass fraction, and all of the particles up to and including the particle indexed by 262143 have this value, but after that the particles all have 0% according to yt. I’ve checked the helium files directly and all values are at 4%. I’m confused as to why yt would stop loading values correctly after a certain point. I’ve included two tipsy files as well as their corresponding helium mass fraction files. I have also written a script called visualization_test_script.py that makes scatter plots of the white dwarfs showing particles that have correct and incorrect values of helium. I can send more tipsy files if necessary, but they are too large to send any more here. Thanks, Matt

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Sudden fluctuations in the projected density
by Maan Hani 01 Nov '16

01 Nov '16

Hi all, While performing projections of the density ?field in a cosmological zoom-in simulation, I noticed sudden fluctuations between the projected density of consecutive snapshots. I thought the fluctuations were due to interlopers entering the field of view (I was looking at the zoom-in region of the box). However, regardless what region of the cosmological box I plot (below I project the whole cosmological box), the fluctuation remains. Note that the fluctuation is not seen in the particle data. Please let me know if this issue is reproducible by others (I'm using yt 3.4-dev) and how I could go about solving it. I've attached a simple sample script and the projection output. The projections are made using Arepo data, but I am treating the data as a Gadget Dataset in yt. The data is available at: http://use.yt/upload/44604f23 and http://use.yt/upload/a5e7f213 Output: - snapshot1: http://i.imgur.com/a3w6vVn.png - snapshot2: http://i.imgur.com/Bq5xlOB.png? Sample script: ``` # importing libraries import yt from yt.frontends.gadget.data_structures import GadgetHDF5Dataset # reading snapshot data ds1 = GadgetHDF5Dataset('../data/1605-2/snapshot_052.hdf5') ds2 = GadgetHDF5Dataset('../data/1605-2/snapshot_053.hdf5') # density un-weighted projections proj1 = yt.ProjectionPlot(ds1, 'z', ('gas','density')) proj2 = yt.ProjectionPlot(ds2, 'z', ('gas','density')) proj1.set_zlim('density', 1.E-4, 1.E-2) proj2.set_zlim('density', 1.E-4, 1.E-2) proj1.save() proj2.save() ``` Thanks, Maan?

1 0

Custom units.
by Kuo-Chuan Pan 01 Nov '16

01 Nov '16

Dear all, I have a custom new derived field based on density (g/cm^3) and entropy (kB/baryon but it is recognised as dimensionless). Currently, this new derived field is set to dimensionless (it should be kB/baryon). Could anyone teach me how to set this new derived filed to its correct unit (which should be kB/baryon)? Or is it possible to simply override the field label in my volume rendering plot before using save_annotated()? Many thanks, Kuo-Chuan

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ANN: Grackle 3.0 released + method paper
by Britton Smith 01 Nov '16

01 Nov '16

Hello! We are excited to announce the release of Grackle 3.0! The Grackle is a library for chemistry and radiative cooling in astrophysical simulations and models. We are also happy to announce the Grackle method paper, submitted to MNRAS and available on arXiv today as 1610.09591, viewable here: https://arxiv.org/abs/1610.09591. All comments welcome. If you use Grackle in your work, please cite this paper from now on. Grackle 3.0 uses a totally new API that is not backward compatible with Grackle 2.x versions. However, the new API is much more flexible and should allow future development to occur without again breaking backward compatibility. Grackle 3.0 comes with a number of new features: * Support for radiation transfer fields: photo-heating plus HI, HeI, and HeII photo-ionization, and H2 photo-dissociation fields. * Support for field arrays of volumetric and specific heating rates. * Approximate atomic self-shielding of UV backgrounds. * Added Case B recombination cooling rates and updated Case A recombination rates. Minor enhancements: * Updated testing framework. * Documentation improvements. Bugfixes: * Fixed unit normalization for k4 Case B recombination rate. * Fixed scaling of low-density H2 cooling rate and use newer H2 LTE rate in all appropriate places. Grackle can be obtained at: https://bitbucket.org/grackle/grackle The documentation can be found here: http://grackle.readthedocs.io/ Since Grackle 2.0, the Grackle has received contributions from 9 individuals: Greg Bryan Andrew Emerick Simon Glover Nathan Goldbaum Cameron Hummels Edward Leong John Regan Hsi-Yu Schive Britton Smith We thank these people for their contributions. Development of Grackle happens in the open on Bitbucket: https://bitbucket.org/grackle/grackle. We welcome new contributors. -The Grackle development team

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