Mailman 3 July 2019 - yt-users

Streamline orientation
by Sushilkumar July 8, 2019

July 8, 2019

Dear yt: I am trying to plot streamlines using SlicePlot(x axis) and annotate_streamlines (script below). The resulting image (google drive link below) gives the orientation of streamlines along y axis. I would like to have the streamlines orient along z-axis. I have tried switching the variables on "SlicePlot" and "annotate_streamlines" but the streamlines stays the same. Can you give me any suggestions? Thank you in advance ----------------------------------- Image link https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc ----------------------------------- script import yt import numpy as np import matplotlib.pylab as pl import matplotlib from yt.visualization.api import Streamlines from yt.units import km from mpl_toolkits.mplot3d import Axes3D ms = 24000000 vector_max=ms-(ms/3) ms1=ms-vector_max dims = (200,200,200) x = np.genfromtxt("/work/jbi157/MODEL3/UPDATE_B/yo_n_t005.mtx",skip_header=2,usecols=1, dtype="f8") x = x.reshape((8000000, 3), order="F") field1 = x[:,2].reshape(dims, order="F") field2 = x[:,1].reshape(dims, order="F") field3 = x[:,0].reshape(dims, order="F") data = dict(field_x = field1, field_y = field2, field_z = field3) bbox = np.array([[-100, 99], [-100, 99], [-100, 99]]) pf = yt.load_uniform_grid(data, dims, km, bbox=bbox, nprocs=1) slc = yt.SlicePlot(pf, 0, ["field_z"], width=(200,'km')) slc.set_cmap('field_z','B-W LINEAR_r') #slc.set_log('field_z', True, linthresh=0.001) slc.annotate_streamlines('field_z', 'field_y',factor=16,density=4,plot_args={'color':'blue'}) #slc.annotate_streamlines('field_y', 'field_z',factor=16,density=4) slc.annotate_line((0.36, 0), (0.36, 1), coord_system='axis',plot_args={'color':'white'}) slc.annotate_line((0.64, 0), (0.64, 1), coord_system='axis',plot_args={'color':'white'}) # larger the value of factor lesser the quiver #slc.annotate_quiver('field_y', 'field_z', factor=20, normalize=True) #slc.annotate_line_integral_convolution('field_y', 'field_z', lim=(0.30,0.70),cmap="YlGnBu",alpha=1,const_alpha=True) slc.annotate_sphere([0.5, 0.5, 0.5], radius=(9, 'km'),circle_args={'color':'black'}) #slc.annotate_text((50,50),'t=0',coord_system='plot',text_args={'color':'black'}) slc.annotate_title("t=005, psi=30") slc.hide_colorbar() slc.save('plane_x_t_0005.png') #slc.save('plane_x_t_0000.png', mpl_kwargs={'facecolor':'gray'}) On Thu, Jan 10, 2019 at 11:00 AM <yt-users-request(a)python.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman3/lists/yt-users.python.org/ > or, via email, send a message with subject or body 'help' to > yt-users-request(a)python.org > > You can reach the person managing the list at > yt-users-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > Today's Topics: > > 1. ANN: yt dev workshop, March 4-6 (Matthew Turk) > > > ---------------------------------------------------------------------- > > Date: Thu, 10 Jan 2019 09:58:14 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > Subject: [yt-users] ANN: yt dev workshop, March 4-6 > To: yt-dev(a)python.org, Discussion of the yt analysis package > <yt-users(a)python.org> > Cc: "Campbell, Mary Terese" <mtc(a)illinois.edu>, Samantha Walkow > <samwalkow(a)gmail.com>, Madicken Munk <madicken.munk(a)gmail.com> > Message-ID: > <CALO3=5GXrH3i0MmmzHkcBSjYcc=FkbHA2=KGab= > GfNoRaK7ujg(a)mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi everyone! > > We are delighted to invite you to a yt development workshop at the > University of Illinois Urbana-Champaign, March 4-6 of 2019. Please > feel encouraged to pass this information on to others that may find it > interesting! > > Information on logistics and registration may be found at the workshop > website: > > http://yt-project.org/workshops/spring2019/ > > This workshop will be focused on extending existing functionality, > building collaborations with other software projects, and ingestion of > new types and classes of data into yt. > > The workshop will take place at the National Center for Supercomputing > Applications building on the north end of the UIUC campus. The NCSA > building is about a block away from the conference hotel and is next > door to a parking structure that offers metered all-day parking. There > are a number of food trucks nearby, a university-run cafeteria about 2 > blocks away, and a university business district with many good lunch > restaurants about a half a mile away. > > We are planning to offer funding for hotel and travel for those > requesting support. If you request funding, you will be notified of > available funds by February 16. Travel awards will be made in the > form of arranged lodging and airfare, with reservations being made by > the conference organizers. > > Best regards, > The Organizing Committee > > MT Campbell > Nathan Goldbaum > Madicken Munk > Matt Turk > Samantha Walkow > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org > > > ------------------------------ > > End of yt-users Digest, Vol 131, Issue 8 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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Change axis labelsize without changing ticklabel size in yt PhasePlot
by piyush.suneet＠gmail.com July 5, 2019

July 5, 2019

Hi All, I could not find a solution for my issue in the archived threads so I am posting it here. I use FLASH to run my MHD simulation and then use the output hdf5 plotfile to create and save a yt PhasePlot of number density and adiabatic index 'gamma' (user-defined fields) color-coded by the cell mass: plot=yt.PhasePlot(my_sphere,"numdens","gamma",["cell_mass"]) plot.set_ylabel('$\gamma_{\mathrm{net}}$') plot.set_xlabel('$n\,\,(\mathrm{cm^{-3}})$') plot.set_ylim(1.3,1.7) plot.set_log("gamma",False) plot.set_font_size(20) plot.set_minorticks('all','on') plot.set_unit("cell_mass",'Msun') plot.save("phaseplot_numgamma.pdf") The axes labels are smaller than what I would like them to be. If I increase the font-size to a higher value (say, plot.set_font_size(30)), the axes labels are of the appropriate font size, but the x-axis tick labels also increase in size and overlap with the figure boundary. This might be because my tick labels have exponents (10^(11), 10^(12), etc.). Is there a way to only change the axes label size and not the tick label size while using yt? Thanks in Advance, Piyush Sharda

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Expressing projection plots in units of mean baryonic density
by Andrew Wu July 4, 2019

July 4, 2019

Hi all, New user of yt here. I've been using yt to make some projection plots and I was wondering if there is a way to express the units of the colorbar relative to the mean baryonic density rather than in cgs, i.e. in the form 0.048*rho_crit(at z=0) * (1+z)^3 at redshift z, where rho_crit is a critical density I can calculate and the redshift z can vary depending on which file I'm making projections of. So the colorbar may range from 0.1 (times the baryonic density) to, say, 100 (times the baryonic density). What would be the best way to do this? I'm working with yt version 3.5.1 and Python 3.7.3. Any help is greatly appreciated. Thanks, Andrew

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set resolution for frb
by Yuan Li July 1, 2019

July 1, 2019

Hello, I am trying to get an array out of an off axis projection with a chosen resolution. This is what I have: plot = yt.OffAxisProjectionPlot(ds, [1, 1, 1], 'density') plot.set_buff_size(1600) image = plot.frb[“gas”, “density”] According to Nathan's email to Stephanie last year, "image will be a 1600x1600 2D ndarray containing an image of the density field." However, it is not working for me. image is still 800x800. I do see this message: yt : [INFO ] 2019-07-01 15:51:04,868 Making a fixed resolution buffer of (('gas', 'density')) 1600 by 1600 so it seems that yt is making a FRB with the desired resolution, but how do I get the array? Thanks! Yuan

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ANN: Grackle 3.1.1 released!
by Britton Smith July 1, 2019

July 1, 2019

Greetings, I'm very happy to announce the release of Grackle version 3.1.1. Grackle is a library for chemistry and radiative cooling in astrophysical simulations and models. This is a bugfix release with a few minor enhancements as well. Look for bugfix releases to happen more frequently in the future. The Grackle repository has moved to git and GitHub and can now be found at: https://github.com/grackle-project/grackle *Minor enhancements:** Add function for clearing locally declared grackle data struct [PR <https://github.com/grackle-project/grackle/pull/36>]. * Added API for Grackle functionality using local data structures [PR <https://bitbucket.org/grackle/grackle/pull-requests/79/expose-all-data-stru…> ]. * Added/enhanced documentation for various runtime parameters [PR <https://bitbucket.org/grackle/grackle/pull-requests/80/clarifying-radiation…>, PR <https://bitbucket.org/grackle/grackle/pull-requests/83/unit-correction-in-h…> ]. * Added make file for ORNL Summit [PR <https://github.com/grackle-project/grackle/pull/33>]. *Bugfixes:** Make sure all parameters correctly printed after initialization [PR <https://github.com/grackle-project/grackle/pull/41>]. * Correct H mass fraction for tabulated cooling mode [PR <https://github.com/grackle-project/grackle/pull/40>]. * Fix memory allocation in C example [PR <https://github.com/grackle-project/grackle/pull/38>]. * Fix scaling of H2 photo-dissociation rate by Lyman-Werner intensity [PR <https://github.com/grackle-project/grackle/pull/32>]. * Fix thread-safety issue with updating UVB rates [PR <https://github.com/grackle-project/grackle/pull/26>]. * OpenMP private variable list updated [PR <https://bitbucket.org/grackle/grackle/pull-requests/84/bugfix-update-omp-pr…> ]. * Correct H number density calculation for self-shielding [PR <https://bitbucket.org/grackle/grackle/pull-requests/77/hydrogen-number-dens…> ]. * Fix scaling of H2 and H2+ rates from UV background [PR <https://bitbucket.org/grackle/grackle/pull-requests/78/scale-h2-ionization-…> ]. Source code repository: https://github.com/grackle-project/grackle Documentation: http://grackle.readthedocs.io/ Method paper: http://adsabs.harvard.edu/abs/2017MNRAS.466.2217S Since the release of Grackle 3.1, 21 pull requests have been accepted from 8 people, including 4 new contributors (in bold): *Bili Dong* Andrew Emerick Nathan Goldbaum *Loic HausammannAndrea Incatasciato* Hsi-Yu Schive Britton Smith *Bruno Villasenor* Thanks to all of these people! As always, we welcome new contributors. -The Grackle development team

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