yt-users July 2019

yt-users@python.org

16 participants
13 discussions

by david collins

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

1 year, 6 months

Ytini installation for Houdini on Windows

by uran san

Hi guys, I am very new to Ytini's mailing list, mailing lists as well as Houdini. So please bear with me while I pick up the etiquette around this medium. With that out of the way here's my first question: After having succeeded installing Ytini for Houdini on a Mac OS X 10.14 I would now like to achieve the same with my Houdini install on a Windows 10 OS. I have tried to somewhat reproduce all steps described here http://www.ytini.com/getstarted.html#collapseTwoOut (Houdini 17.5 Tested on Mac OS X) on my Windows machine but wasn't surprised to learn that of course Houdini could not find the ytini module when I tried to import it in the python shell. Is there somebody, that could point me . in the right direction of how to install Ytini for Houdini on a Windows 10 OS environment? Not afraid of reading so even hints a re more than welcome. Many Thanks in advance Ur4n

1 year, 10 months

HOP vs Rockstar virial radii

by Nick Gnedin

Folks, I ran both HOP and Rockstar halo finders on the same ART simulations, and the mass functions match very well (attached hmf_m.pdf file). However, when I compare virial radii (attached hmf_r.pdf file), they don't match. Even if I try rescaling the Rockstar virial radius by 1.5, the match is much worse than for mass functions. How are the 'virial_radius' fields defined for both halo finders? This is a z=7 simulations, so all mass definitions are the same, Mvir = M200m = M200c. I also attach the script to plot virial radii if you want to check it, although it is trivial. Many thanks (as usual), Nick

2 years, 2 months

Question about YT Units Conversion

by Sean Larkin

Hello All, I am currently attempting to compare a catalog with Mvir and Rvir units of Mpc/h and Kpc/h comoving to a catalog with Mpc and Kpc proper. I am currently using yt version 3.5.1, which I just checked for updates. When doing this conversion of units within yt, there appears to be a problem where an amount of h*h is not handeled properly. I have included a screenshot of a jupyter session that outlines the problem as well as a .py and jupyter script so it can be tested. The problem arises when I try to calculate delta_vir, which is the density of a galaxy/ critical density. The correct value for both catalogs I am comparing is around 170. When I use yt to calculate the critical density at z = 2, it get the correct value, which I convert to Mpc*h*h//kpc/kpc/kpc to match with my /h catalog. Then, when I divide the densities, even thought their units are identical, their division is different than if just the float values are divided, by an exact factor of h*h. I wonder if there is something wrong with how I am initializing my values with the ytquantity, or if there is something wrong going on in the code. [image: Screen Shot 2019-07-31 at 2.36.01 PM.png]

2 years, 2 months

Lacking `particle_type` in yt 3.4.1 under Python 3.7

by Yi's Toy Repositories

I recently installed Anaconda3 with Python 3.7, as well as the latest yt 3.4.1. But when I ran my code, calculating the center of mass and angular momentum, an error saying: count_values() got an unexpected keyword argument 'particle_type' came up. Is there anything I can do to fix it except installing an Anaconda with Python 3.6?

2 years, 2 months

Increasing number of CPU cores can not speed up the works

by Tseng, Po-Hsun

Dear yt developers, I found that increasing number of CPU cores in a single node that have 16 cores and 16 additional hyper-threadings can dramatically deteriorate speed-up. figure [3] shows this result. You may reproduce figure [3] by the following steps: Running shell script [1] can automatically invoke yt script [2] and record elapsed time on files, called core_* [4]. [1] shell script: http://paste.yt-project.org/show/150/ [2] yt script: http://paste.yt-project.org/show/151/ [3] # of cores vs. elapsed time http://i.imgur.com/mFk6lKu.png [4] all scripts, data and log files: http://use.yt/upload/d8efa692 Thanks for your help. Rocky Tseng

2 years, 3 months

Python 2 support removed from yt-4 branch

by Matthew Turk

Hi all, With the merger today of https://github.com/yt-project/yt/pull/2163 , Python 2 support has been removed from the yt-4 branch. Those of you using the master branch or any release will not be affected, but if you're on yt-4, keep this in mind. Best, Matt

2 years, 3 months

cut_region() not working as intended

by Andrew Wu

Hi yt, When making projection plots of total gas density and cold gas density, averaged over the projection length (i.e. with a uniform weighting), and using cut_region() to filter out hot gas to make the cold gas plots, it appears that some areas in the cold gas plot have a higher density than the corresponding areas in the total gas plot, which shouldn't happen. If you look at the top-middle of the two plots (link below) and compare the densities, the cold gas appears to have a higher density there. The code is below: (link to plots: https://drive.google.com/drive/folders/1UJ6fmKNFQzGr8cfjov5-GwOzfS8nt2e8?us…) import yt ds = yt.load("/tigress/cen/CZ15/redshift0100") z = 0.62 # the box size is 120/0.7/(1+z) Mpc, where z is redshift boxSize = 120e3/0.7/(1+z) # virial radius in code units, r_v is virial radius in kpc codeWidth = r_v / boxSize center = [xCoord, yCoord, zCoord] left_edge = [xCoord-2.1*codeWidth, yCoord-2.1*codeWidth, zCoord-2.1*codeWidth] right_edge = [xCoord+2.1*codeWidth, yCoord+2.1*codeWidth, zCoord+2.1*codeWidth] # want a box with full width about 4 times the virial radius reg = ds.region(center, left_edge,right_edge) # total gas plot prj = yt.ProjectionPlot(ds, "x", "density", center=center, width=(4*r_v, 'kpc'), data_source=reg, method='integrate', weight_field='ones') u = 100 / 0.048 l = 0.07 / 0.048 prj.set_zlim('density', l,u) prj.set_unit('density','mbd') prj.set_cmap(field='density', cmap='CMRmap') prj.show() # cold gas plot cold_reg = reg.cut_region(["obj['temperature'] < 1e5"]) prj = yt.ProjectionPlot(ds, "x", "density", center=center, width=(4*r_v, 'kpc'), data_source=cold_reg, method='integrate', weight_field='ones') prj.set_zlim('density', l,u) prj.set_unit('density','mbd') prj.set_cmap(field='density', cmap='CMRmap') prj.show() Thanks, Andrew

2 years, 3 months

Streamline orientation

by Sushilkumar

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.**"*

2 years, 3 months

Change axis labelsize without changing ticklabel size in yt PhasePlot

by piyush.suneet＠gmail.com

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

2 years, 3 months

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yt-users July 2019