yt-users March 2018

yt-users@python.org

19 participants
23 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

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.

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3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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Registration open: LSSTC workshop "Data Visualization and exploration in the LSST Era" NCSA, June 19-21, 2018
by Matthew Turk 30 Mar '18

30 Mar '18

Hi folks, I am passing on the following message about an upcoming workshop. This workshop will feature a track about yt, including tutorials both basic and advanced, and I'm pretty excited about the breadth of topics that will be covered. -- Dear All, We are pleased to announce that our LSSTC workshop "Data Visualization and exploration in the LSST Era" will be held at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign from June 19 to June 21, 2018. The 3-day workshop is open to all interested attendees. However, preference will be given to early career scientists given the nature of the workshop format. Thanks to support from the LSST Enabling Science Group and NCSA we are glad to waive the registration fee and to provide some travel support. We welcome proposed contributions for short talks and 1 hour hands-on-tutorials on the topics listed on the website. The registration is now open and the deadline is June 1st, 2018. For more information please visit the workshop website at http://www.ncsa.illinois.edu/Conferences/LSST18/ We hope to see you there! On behalf of the SOC: Matias Carrasco Kind, University of Illinois at Urbana-Champaign Donna Cox, University of Illinois at Urbana-Champaign Leanne Guy, LSST Gilbert Holder, University of Illinois at Urbana-Champaign Xin Liu, University of Illinois at Urbana-Champaign Felipe Menanteau, University of Illinois at Urbana-Champaign William O'Mullane, LSST Laura Trouille, Adler Planetarium Matt Turk, University of Illinois at Urbana-Champaign

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hide phaseplot colorbar
by Stephanie Tonnesen 26 Mar '18

26 Mar '18

Hi yt-users! I would like to make phaseplots without the colorbar. I tried to just use the plot.hide_colorbar() command, but apparently PhasePlot has no attribute hide_colorbar() Looking at the docs, perhaps what I have to do it use PhasePlotMPL? Is there an example using this somewhere in the docs? Thanks in advance for any help/direction!! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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Down Sampling data set
by Kuo-Chuan Pan 21 Mar '18

21 Mar '18

Dear all, Is there a simple way to create a data set with lower AMR levels? something like: ds = yt.load(fname, max_level=3) I knew that there is an example to down sample for volume rendering with AMRKDTree, but I don't know how to create a downsample data set which can be analysis and plot with SlicePlot, for example. http://yt-project.org/docs/dev/cookbook/complex_plots.html#downsampling-dat… Many thanks, Kuo-Chuan

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Fwd: clump find
by Britton Smith 20 Mar '18

20 Mar '18

Returning this conversation back to the list. ---------- Forwarded message ---------- From: Le Dan <le.dan33(a)yahoo.com> Date: Tue, Mar 20, 2018 at 11:47 AM Subject: Re: [yt-users] clump find To: Britton Smith <brittonsmith(a)gmail.com> my code looks like: import matplotlib matplotlib.use('Agg') import yt import matplotlib.pyplot as plt import numpy as np nar = np.array import time import copy from yt.analysis_modules.level_sets.api import * grav_min = [] x_min = [] y_min = [] z_min = [] loc = [] loc_2 = [] leaf_indices = [] nbins = 20 bin_high = 5e6 bin_low_init=0.1 def new_grav_potential(field,data): grav_old= data['gravitational_potential'] grav_max = data.get_field_parameter('max_grav') grav_new = -grav_old+grav_max return grav_new yt.add_field('new_grav_potential',function=new_grav_potential,units = 'erg/g',validators = [yt.ValidateParameter('max_grav')]) for frame in [120]: n_cl = 0 fname = 'DD%04d/data%04d'%(frame,frame) ds = yt.load(fname) ad = ds.all_data() a = ad['gravitational_potential'].max() b = -ad['gravitational_potential']+a ad.set_field_parameter('max_grav',a) master_clump = Clump(ad,('gas','new_grav_potential')) master_clump.add_validator("min_cells", 8) c_min = ad["gas", "new_grav_potential"].min() c_max = ad["gas", "new_grav_potential"].max() step = 100 * find_clumps(master_clump, c_min, c_max, step)* # Write a text file of only the leaf nodes. write_clumps(master_clump,0, "%s_clumps.txt" % ds) leaf_clumps = get_lowest_clumps(master_clump) proj = yt.ProjectionPlot(ds,2,('gas','new_grav_potential'),center = 'c',width=(20,'kpc'),field_parameters={'grav_max':a}) proj.annotate_clumps(leaf_clumps) proj.save('clumps') The error occurs in the find_clumps function. The error I am receiving is: yt.fields.field_exceptions.NeedsParameter: (['max_grav']) Dan Le On Tuesday, March 20, 2018 1:29 PM, Britton Smith <brittonsmith(a)gmail.com> wrote: Hi Dan Le, Can you post the code you've written and the error you're seeing? Britton On Tue, Mar 20, 2018 at 9:57 AM, Le Dan via yt-users <yt-users(a)python.org> wrote: Hi all, I've created a new field and trying to get clump find to work on that field. When running my program, I received the error saying that a parameter used to define my new field could not be accessed by the function, find_clumps(master_clump, c_min, c_max, step). How would I go about getting rid of this error? Dan Le ______________________________ _________________ yt-users mailing list -- yt-users(a)python.org To unsubscribe send an email to yt-users-leave(a)python.org

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clump find
by Le Dan 20 Mar '18

20 Mar '18

Hi all, I've created a new field and trying to get clump find to work on that field. When running my program, I received the error saying that a parameter used to define my new field could not be accessed by the function, find_clumps(master_clump, c_min, c_max, step). How would I go about getting rid of this error? Dan Le

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Supernovae with Ramses and YT
by Matthieu Tricottet 20 Mar '18

20 Mar '18

Hello everyone! I'm simulating supernovae explosions with Ramses. I'm at the very very beginning of it. My first runs give nothing, but I'm unsure whether it's because I've misused Ramses or because I don't use YT properly to see results. My config file is this one: https://expirebox.com/download/59d92f446fea392dc9a6189603f1dc34.html Result files are here: https://expirebox.com/download/6bd562f210199b6b8581525c84d86eff.html When I try slices or projections, all I can see is that: https://ibb.co/jbeg9c I've loaded it with import yt ds = yt.load("my_path/output_00001/info_00001.txt") And then, tried things like yt.SlicePlot(ds, 'x', "density") or yt.ProjectionPlot(ds,'x','Density') (I've tried other axis too), but I can't get anything else that the image I've showed. Could someone help me to determine if the problem comes from my basic first simulation (Sedov supernovae phase) or from my Yt plots? I would really appreciate some help! Thank you very much

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Memory and high level covering grids
by Rachel Smullen 15 Mar '18

15 Mar '18

Hi all, I've been running into this problem for a while now, but I've reached a point where I can't avoid it any longer. I have a 6 level AMR simulation (run with Orion, but that's probably irrelevant to my problem) that has a level 0 size of (256)^3. I would like to extract a covering grid for a small subset at level 4 (for the full volume, that equates to a (4096)^3 grid). The chunk that I want has an equivalent size at level 4 of 2048x2048x1536. Basic setup: I'm running on a node with 16 cores and 256 GB of memory. I have tried both yt version 3.4 and 3.5 (updated this morning). I've tried level = 4 ds = yt.load(filename) cg = ds.covering_grid(level, ds.domain_left_edge, ds.domain_dimensions * ds.refine_by**level) result = cg["density"][1024:3072,1434:3482,512:2048] This results in the error File "/home/u14/rsmullen/anaconda3/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/home/u14/rsmullen/anaconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 641, in get_data if len(fill) > 0: self._fill_fields(fill) File "/home/u14/rsmullen/anaconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 690, in _fill_fields for field in fields] File "/home/u14/rsmullen/anaconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 690, in <listcomp> for field in fields] MemoryError Looking at the memory buildup during execution, it appears that yt is loading densities for the entire volume to then return my chunk to me. I have more than enough memory on the machine (the job exits at ~70GB usage), so I think this is a Python limit on array allocations. I have also tried creating a box region in the area that I want, but covering grids cannot be run on regions. Thus, I tried saving my region as a dataset, but it reloads with incorrect limits and sizes: box = ds.box([xmin,ymin,zmin], [xmax,ymax,zmax]) box.save_as_dataset(filename = 'box', fields = (('gas','density'))) ds2 = yt.load('box.h5') print( ds2.domain_left_edge, ds2.domain_dimensions, ds2.refine_by ) cg = ds2.covering_grid(level, ds2.domain_left_edge, ds2.domain_dimensions * ds2.refine_by**level) This gives [ -7.72500000e+18 -7.72500000e+18 -7.72500000e+18] code_length [2 2 2] 2 instead of [-1.93125e+18 -1.15875e+18 -2.896875e+18] [128 128 96] 2 (my expectation) So, to summarize my questions: 1. Is there an easy way for me to directly get my chunk at level 4 resolution with yt as it stands now? 2. Otherwise, is there an easy Python fix to allow the array memory allocation to be larger? 3. If none of the above, how can I save my region with the correct properties so I can reload my chunk as a smaller dataset? Thanks so much for your help! Rachel Smullen Graduate Student Steward Observatory University of Arizona

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yt-users March 2018