yt-users January 2014

yt-users@python.org

32 participants
36 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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Notebook server question
by Andrew Myers 19 Apr '14

19 Apr '14

Hello yt users, I have a (perhaps naive) ssh question related to the yt notebook. I would like to run a yt notebook server on machine A. However, machine A cannot be directly accessed via ssh from the wider internet. Instead, I must first ssh into machine B, and then ssh from B to A. Machine B cannot run the notebook server itself. Does anyone know how I can configure things - perhaps by using a more complicated ssh tunnel command - so I that access a notebook server running on machine A through machine B? Thanks, Andrew

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change size of phase plot
by Stephanie Tonnesen 15 Apr '14

15 Apr '14

Hi all, I am trying to make my phase plots smaller so they can fit more nicely into a paper. Alternatively, I would be fine with upping the font size so when I shrink them you can read the axes. I found advise on how to do this for slices, but not for phase_objects. pc = PlotCollection(pf) tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.5", "grid['z'] < 0.192","grid['z'] > -0.192","grid['cyl_RCode'] < 1.2"]) pc.add_phase_object(tracerp25,["Density","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds = [-4e7,8e7],x_bounds=[5e-28,5e-23],x_log=True,y_log=False) Any help is much appreciated! Thanks, Stephanie

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Light Cone Projection
by Pengfei Chen 01 Mar '14

01 Mar '14

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

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Two Point Correlation Function in yt 3.0 with RAMSES
by David Sullivan 03 Feb '14

03 Feb '14

Hi all, I’m trying to compute the two point halo correlation function for RAMSES data using the code found at http://yt-project.org/docs/2.6/analyzing/analysis_modules/two_point_functio… (I’ve already run HOP and written to HopAnalysis.out). I get an error saying ‘add_tree’ is not defined, but yt.utilities.kdtree is imported and build properly. Is this feature working in version 3.0? Many thanks, David P.S Sorry if this gets duplicated as I accidentally tried to send this with an unregistered e-mail

2 1

chemical species abundances discrepancy
by poetaste＠gmail.com 02 Feb '14

02 Feb '14

Hi Guys, I did a simple test with enzo and I tried to plot a radial profile of the chemical species fractions with YT. The problem is that if I use the YT function which intrinsically plot the fraction for a species, let's say H2I_Fraction (as usual), and compare this with a direct evaluation of the mass fraction: data['H2I_Density']/data['Density'] I obtain some slightly different results, mostly at large radii. Anyone might explain this discrepancy!? This happens with all the species. Thank you in advance Stefano

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More PhasePlots questions
by Stephanie Tonnesen 30 Jan '14

30 Jan '14

Hi everyone! I have a few more PhasePlots questions. 1) I would like to force my axes to be a particular range. I am looking at several times in my simulation, and the length of the stripped tail increases, so different PhasePlots end up with different height above the disk x-axis ranges, which makes comparison more annoying. 2) I would like for the last tick label to be blank--to not print out on the figure (in the attachment, I would like for '100' to not be there). 3) On a slightly different note, I want the bin size to be bigger. The PhasePlots look very streaky, see attached. I will paste my current set of commands for making my PhasePlot. Thanks for any help! Stephanie plot = PhasePlot(tracerp25,"zkpc","zvelocity8",["CellMassMsun"],weight_field=None,fontsize=19)#,x_bounds=[3e-28,5e-23],y_bounds=[-0.7,1.2]) plot.set_log("zkpc",False) plot.set_log("zvelocity8",False) plot.set_zlim("CellMassMsun",1e4,1e9) plot.set_figure_size(3) ax = plot.plots['CellMassMsun'].axes ax.set_ylabel(r'z-velocity (10$^8$ cm/s)',fontsize=10) ax.set_xlabel(r'Height above disk (kpc)',fontsize=10) print r'z-velocity (10$^8$ cm/s)' for label in ax.xaxis.get_ticklabels(): #label.set_color('red') label.set_rotation(35) label.set_fontsize(11) for label in ax.yaxis.get_ticklabels(): label.set_fontsize(10) plot.save()

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Trouble with SciPy Install
by Nathan Butcher 30 Jan '14

30 Jan '14

Hello, I am trying to install yt with SciPy on Michigan State University's HPCC system and am running into errors that I cannot resolve by following the instructions in the install script. I have tried uncommenting each of the NUMPY_ARGS statements and had no success. I have attached the log file from my most recent installation attempt as the error message is long. My guess is that it has to do with the "recompile with -fPIC" message but I cannot figure out what that means. Can anybody explain what this error message means and how to resolve it. Thank you, Nathan Butcher

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Mailing list issues
by Matthew Turk 29 Jan '14

29 Jan '14

Hi all, We were having some mailing list issues earlier in the day, but I have been assured they are now fixed. So if you're seeing this, and got a bounce earlier, the clog seems to have been resolved. Sorry about that. -Matt

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yt-users January 2014