yt-users July 2020

yt-users@python.org

18 participants
15 discussions

Re: Building Merger Trees with treefarm (Andrew Emerick)
by Ari Maller 17 Jul '20

17 Jul '20

Hi Andrew, I can’t answer your yt question, but for your particular need, I would just identify the halo you want at higher z, get some ids for some of the star particles and then see where those star particles are at lower z. They will almost certainly all be in the same halo. You really don’t need the extra complexity of merger trees for what you want to do. Ari On July 17, 2020 at 12:01:28 PM, yt-users-request(a)python.org (yt-users-request(a)python.org<mailto:yt-users-request@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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… 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. Building Merger Trees with treefarm (Andrew Emerick) ---------------------------------------------------------------------- Date: Thu, 16 Jul 2020 21:30:12 -0700 From: Andrew Emerick <aemerick11(a)gmail.com> Subject: [yt-users] Building Merger Trees with treefarm To: Discussion of the yt analysis package <yt-users(a)python.org> Message-ID: <CAOo4WKK5Sidb=U6Q2p==LWQKBKQWKw++_cUsM1HkgjbD_tBrPw(a)mail.gmail.com> Content-Type: multipart/alternative; boundary="0000000000008a765305aa9b9d49" --0000000000008a765305aa9b9d49 Content-Type: text/plain; charset="UTF-8" Hi all, This is my first foray into doing halo finding / merger tree analysis so forgive me if I'm just missing something simple. My goal is to be able to identify a halo at lower-z that had specific properties at higher-z so I can get its lagrangian volume at lower-z to build a nested zoom. (And I'm assuming merger trees are the only / best way to identify the halo across snapshots for this). Anyway, I've been following the docs for yt_astro_analysis to build halo catalogs for a series of datasets and just tried the example in treefarm to build a merger tree, but I get an error. I'm using the last_yt3 changeset of yt, am on the master branch of treefarm, and halos were generated using rockstar-galaxies via master branch of yt_astro_analysis. And the datasets are DM-only Enzo runs. I get this error: https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject.org_… When running this (slightly modified from the example code): https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject.org_… Thanks for the help!! Best, Andrew --- Pasadena Fellow in Theoretical Astrophysics Carnegie Observatories California Institute of Technology --0000000000008a765305aa9b9d49 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Hi all,<div><br></div><div>This is my first foray into doi= ng halo finding / merger tree analysis so forgive me if I'm just missin= g something simple. My goal is to be able to identify a halo at lower-z tha= t had specific properties at higher-z so I can get its lagrangian volume at= lower-z to build a nested zoom. (And I'm assuming merger trees are the= only / best way to identify the halo across snapshots for this).</div><div= ><br></div><div>Anyway, I've been following the docs for yt_astro_analy= sis to build halo catalogs for a series of datasets and just tried the exam= ple in treefarm to build a merger tree, but I get an error. I'm using t= he last_yt3 changeset of yt, am on the master branch of treefarm, and halos= were generated using rockstar-galaxies via master branch of yt_astro_analy= sis. And the datasets are DM-only Enzo runs.</div><div><br></div><div>I get= this error:=C2=A0<a href=3D"https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject.org_… ">https://urldefense.proofpoint.com/v2/url?u=http-3A__-3D&d=DwICAg&c=pRW6ZPn_… paste.yt-project.org/show/256/</a></div><div><br></div><div>When running th= is (slightly modified from the example code):=C2=A0</div><div><br></div><di= v><a href=3D"https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject.org_… ">https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject-3D&d… .org/show/257/</a><br></div><div><br></div><div>Thanks for the help!!</div>= <div><br></div><div><br></div><div><br></div><div>Best,</div><div>Andrew</d= iv><div><div><div dir=3D"ltr" class=3D"gmail_signature" data-smartmail=3D"g= mail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div dir=3D"ltr"><di= v style=3D"font-size:small;font-family:arial">---</div><div style=3D"font-s= ize:small;font-family:arial"><div style=3D"font-family:Arial,Helvetica,sans= -serif"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div style=3D"fo= nt-family:arial">Pasadena Fellow in Theoretical Astrophysics</div><div styl= e=3D"font-family:arial">Carnegie Observatories</div><div style=3D"font-fami= ly:arial">California Institute of Technology</div></div></div></div></div><= /div></div></div></div></div></div></div></div></div> --0000000000008a765305aa9b9d49-- ------------------------------ Subject: Digest Footer _______________________________________________ yt-users mailing list -- yt-users(a)python.org To unsubscribe send an email to yt-users-leave(a)python.org https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… ------------------------------ End of yt-users Digest, Vol 149, Issue 7 ****************************************

2 1

Ortho Slice AMR issue
by Stephen Coleman 15 Jul '20

15 Jul '20

Hello, I am having an issue with a FLASH simulation and AMR, using the OrthoSlice method. I am aware of the note at https://yt-project.org/doc/reference/api/yt.data_objects.selection_data_con… but when I try to sort on the "t" field it is not found. Is that a derived field that should be constructed when yt loads the file, or is it the responsibility of the FLASH simulation to write the "t" field to file? Jupyter notebook: http://paste.yt-project.org/show/243/ Input file: http://use.yt/upload/cfef968c Thank you, -Stephen -- Stephen Coleman *Research Scientist* | RadiaSoft 720-502-3928 x 722 | coleman(a)radiasoft.net radiasoft.net | sirepo.com

3 8

Question about Projection Plot Color Coding
by sflarkin＠ucsc.edu 12 Jul '20

12 Jul '20

Hello All, I have a question about the Projection plot function in yt. I have a script that plots the smallest mass darkmatter particles of a simulation in all 3 of the 2-d coordinate projections, and overplots the halos found by a halo finder. This script works, and currently plots the colorbar based on the mass in a given 2-d bin as done in some of the basic yt plots included in the website. I am wondering if it is possible to have the color scheme of the particles be based on the squared mass or squared density of the particles in any given 2-d bin, so that the higher density regions are highlighted compared to the background lower density regions. I have included the plotting part of my script below, in case it is helpful. I hope everyone is having a great New Year! ds = yt.load(VELA_snaps[position[0]]) domain_width = float(ds.domain_width.in_units('Mpc/h')[0]) ad = ds.all_data() masses = yt.np.unique(ad[('darkmatter', 'particle_mass')]) #filter out the darkmatter0 particles def mass_filter(pfilter, data): filter = data[(pfilter.filtered_type, 'particle_mass')] == masses[0] return filter yt.add_particle_filter('darkmatter0', function=mass_filter, filtered_type='darkmatter', requires=['particle_mass']) ds.add_particle_filter('darkmatter0') scale = float(ds.scale_factor) fig = plt.figure() grid = AxesGrid(fig, (0.075,0.075,10,5), nrows_ncols = (3, 1), axes_pad = 1.0, label_mode = "L", share_all = False, cbar_location="right", cbar_mode="each", cbar_size="3%", cbar_pad="0%") zoom = 10 x0 = float(consistent.halo_data_sorted[index][0][17]) * scale / domain_width y0 = float(consistent.halo_data_sorted[index][0][18]) * scale / domain_width z0 = float(consistent.halo_data_sorted[index][0][19]) * scale / domain_width center = [x0, y0, z0] a = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_x'), ('darkmatter0', 'particle_position_y'),\ ('darkmatter0', 'particle_mass'), center=center) a.set_unit(('darkmatter0','particle_mass'), 'Msun') a.zoom(zoom) b = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_y'), ('darkmatter0', 'particle_position_z'),\ ('darkmatter0', 'particle_mass'), center=center) b.set_unit(('darkmatter0','particle_mass'), 'Msun') b.zoom(zoom) c = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_z'), ('darkmatter0', 'particle_position_x'),\ ('darkmatter0', 'particle_mass'), center=center) c.set_unit(('darkmatter0','particle_mass'), 'Msun') c.zoom(zoom) for halos in consistent.halo_data_sorted[index]: x = float(halos[17]) * scale / domain_width y = float(halos[18]) * scale / domain_width z = float(halos[19]) * scale / domain_width r = float(halos[11]) * scale / .7 center = [x, y, z] a.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) b.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) c.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) index = 0 for letter in [a,b,c]: plot = letter.plots[('darkmatter0', 'particle_mass')] plot.figure = fig plot.axes = grid[index].axes plot.cax = grid.cbar_axes[index] letter._setup_plots() index = index + 1 plt.savefig('{}/CatalogProjectionYT_VELA{}_Scale{}.png'.format(out_dir, VELA_number, str(scale)[2:5]), bbox_inches='tight') plt.close()

3 3

Using Rockstar (not overwriting outptus)
by Andrew Emerick 07 Jul '20

07 Jul '20

Hello all, I'm just getting into running halo finders (namely rockstar) using yt's astro analysis package and cannot figure out how to have it such that each successive run on of rockstar does not overwrite previous runs. I've been following the "Running Rockstar to Find Halos on Multi-Resolution-Particle Datasets" and both the HaloCatalog.create() and the RockstarHaloFinder.run() methods seem to overwrite everything in the output directory. One obvious fix here is to just have a different output directory for each dataset, but I had thought the indexes in the rockstar output files (e.g. "halos_0.0.ascii") and the list in "datasets.txt" were there to have the results from multiple datasets housed in the same directory. And I didn't see any obvious parameters I could pass either of the above functions to specify a desired output index. Is this possible? Or should I just write to separate folders for each dataset? Best, Andrew --- Pasadena Fellow in Theoretical Astrophysics Carnegie Observatories California Institute of Technology

2 3

Profile Plot Issues
by gardipee2＠wisc.edu 02 Jul '20

02 Jul '20

Hello, I am making profile plots as a function of height from the galactic disk with several variables for a FLASH simulation of a galaxy. For the low values of the height, the profile plot gives me nonsense for several variables. After loading in the data and setting some units, these are the few lines I am using: dd = ds.all_data() d = yt.ProfilePlot(dd, "z", ["magnetic_field_magnitude"], weight_field='ones') d.set_log("magnetic_field_magnitude", False) I then change some labels and save the plot, but these two lines are what's most important. For the first ~1 kpc on the height scale, the plot just has a "zig-zag" pattern for the y-axis, magnetic field magnitude from this code, running from the lower to upper bounds, which is complete nonsense for my data. It then follows a nice curve for the remainder of the plot. Does anyone have any suggestions on how to fix the "zig-zag" at the lower height values? Thanks, Jordan Gardipee

3 4

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users July 2020