Mailman 3 December 2012 - yt-users

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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Surface density profile
by Jun-Hwan Choi 28 Dec '12

28 Dec '12

Hi yt user, I try to compute the surface density profile of the gas disk from my enzo simulation. I perform this by using profile model after define disk object. In order to check the output, I compute the surface density by making the annulus object after making two disk object and using boolean object. The resulting surface density profiles are quite different. I think that it may result from the interpolation of intersecting grid cell with the object. Is there any explanation that the interpolation? And, does anyone can suggest which is the more accurate approach? FYI, I will past my yt script here ====================================== from yt.mods import * import numpy as na import matplotlib.pyplot as plt import pylab as pl import math as math from itertools import cycle lines = ["-","--"] linecycler = cycle(lines) colors = ('b', 'g', 'r', 'c', 'm', 'y', 'k') colorcycler = cycle(colors) def _RadiuspcXY(field, data): center = data.get_field_parameter("center") DW = data.pf.domain_right_edge - data.pf.domain_left_edge radius = na.zeros(data["x"].shape, dtype='float64') for i, ax in enumerate('xy'): r = na.abs(data[ax] - center[i]) radius += na.minimum(r, na.abs(DW[i]-r))**2.0 na.sqrt(radius, radius) return radius def _ConvertRadius(data): return data.convert("pc") add_field("RadiuspcXY", function=_RadiuspcXY, validators=[ValidateParameter("center")], convert_function = _ConvertRadius, units=r"\rm{pc}", display_name="RadiusXY") Msun_in_cgs = 2e33 rmin = 2e-4 rmax = 20 rdisk = rmax hdisk = 1 Nbin = 75 dr = (na.log(rmax)-na.log(rmin))/Nbin index = 153 pf = load("DD0153/DD0153") center = pf.h.find_max("Density")[1] radius = [] Sigma = [] for i in range(0,Nbin): rlow = na.exp(na.log(rmin)+dr*i) rhigh = na.exp(na.log(rmin)+dr*(i+1)) rcenter = 0.5*(rlow+rhigh) disk1 = pf.h.disk(center, [0,0,1], rhigh/pf.units['pc'], hdisk/pf.units['pc'] ) disk2 = pf.h.disk(center, [0,0,1], rlow/pf.units['pc'], hdisk/pf.units['pc'] ) disk3 = pf.h.boolean([disk1, "NOT", disk2]) Area = math.pi*(rhigh**2 - rlow**2) radius.append(rcenter) Sigma.append(disk3["CellMassMsun"].sum()/Area) plt.loglog(radius, Sigma, label='Profile1', linestyle=next(linecycler),color=next(colorcycler)) # Profile disk = pf.h.disk(center, [0,0,1], rdisk/pf.units['pc'], hdisk/pf.units['pc'] ) profile = BinnedProfile1D(disk, Nbin, "RadiuspcXY", rmin, rdisk, log_space=True, lazy_reader=True, end_collect=False) profile.add_fields('Density',weight='CellMassMsun') n_bins = profile['RadiuspcXY'].size Sigma2 = na.zeros(n_bins) Sigma2 = profile['Density']*((pf.units['cm']/pf.units['pc'])**3/Msun_in_cgs)*hdisk plt.loglog(profile['RadiuspcXY'], Sigma2, label='Profile2', linestyle=next(linecycler),color=next(colorcycler)) plt.xlabel(r'$R_{xy}$ [pc]') plt.ylabel(r'$\Sigma$') plt.legend(loc=1) plt.savefig("SurfaceDensity_comp") ======================================================== Thank you in advance, Junhwan P.S.: I think there is a way to post my script in web, but I forget where. -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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development environment issue
by Sam Leitner 24 Dec '12

24 Dec '12

Hi yt-users, I'm having a little trouble with my script environment (for yt-3.0). After installing and then "activating" a new repository (python setup.py develop) I altered mods.py to include a new frontend. When I then run e.g., plot from the command line, yt.mods imports properly and my _is_valid script runs fine. However, when I run "load" from a script my new StaticOutput class isn't found. I guess this is because I have not activated my yt environment properly(?), can anyone tell me what is going wrong? Thanks! Sam PS In case it is helpful: I get an error on load in convenience.py because the my new StaticOutput class (artio) is not defined. Here's the output if I print the c in c._is_valid . <class 'yt.frontends.enzo.data_structures.EnzoStaticOutput'> <class 'yt.frontends.chombo.data_structures.ChomboStaticOutput'> <class 'yt.data_objects.static_output.StaticOutput'> <class 'yt.frontends.athena.data_structures.AthenaStaticOutput'> <class 'yt.frontends.tiger.data_structures.TigerStaticOutput'> <class 'yt.frontends.nyx.data_structures.NyxStaticOutput'> <class 'yt.frontends.orion.data_structures.OrionStaticOutput'> <class 'yt.frontends.flash.data_structures.FLASHStaticOutput'> <class 'yt.frontends.enzo.data_structures.EnzoStaticOutputInMemory'> <class 'yt.frontends.ramses.data_structures.RAMSESStaticOutput'> <class 'yt.frontends.gdf.data_structures.GDFStaticOutput'> <class 'yt.frontends.castro.data_structures.CastroStaticOutput'> yt : [ERROR ] 2012-12-23 14:16:08,197 Couldn't figure out output type for tests/artdat/sizmbhloz-cl04SNpWRPlc30nPF-rs9_a0.9254.art Traceback (most recent call last): File "plot.py", line 3, in <module> pf = load("tests/artdat/sizmbhloz-cl04SNpWRPlc30nPF-rs9_a0.9254.art") File "/Users/sleitner/repos/yt-3.0-clone/yt/convenience.py", line 85, in load raise YTOutputNotIdentified(args, kwargs)

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Athena phase plot problem
by Stephanie Tonnesen 22 Dec '12

22 Dec '12

Hi yt-users, I am trying to make phase_objects of Athena data. I am able to make phase_objects if I use the "expected" set of variables (will show below), but kill my kernel or am kicked out of python if I try and use an "unknown field" read in from a set of vtk files. from yt.mods import * pf = load("id0/rps.0080.vtk") yt : [INFO ] 2012-12-13 23:27:08,678 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case. yt : [INFO ] 2012-12-13 23:27:08,974 Parameters: current_time = 40.00096 yt : [INFO ] 2012-12-13 23:27:08,974 Parameters: domain_dimensions = [1048 1048 655] yt : [INFO ] 2012-12-13 23:27:08,975 Parameters: domain_left_edge = [-3.2 -3.2 -2. ] yt : [INFO ] 2012-12-13 23:27:08,976 Parameters: domain_right_edge = [ 3.2 3.2 2. ] yt : [INFO ] 2012-12-13 23:27:08,977 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2012-12-13 23:27:13,214 Adding unknown field specific_scalar[0] to list of fields pf.h.field_list ['density', 'pressure', 'velocity_z', 'velocity_x', 'velocity_y', 'specific_scalar[0]'] alld = pf.h.all_data() tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25", "grid['z'] > 0.01"]) ##These commands works: radmean = tracerp25.quantities["WeightedAverageQuantity"]("Radius","Ones") pc = PlotCollectionInteractive(pf) pc.add_phase_object(alld,["z","velocity_z","CellMass"],weight=None) #The calls below fail. There is no error message. If I am in iPython, #the kernel dies. If I am running on a computer, it freezes and #eventually I just get the message #Killed pc.add_phase_object(alld,["z","specific_scalar[0]","CellMass"],weight=None) pc.add_phase_object(tracerp25,["z","velocity_z","CellMass"],weight=None) #If I read in a single vtk file ("id122/rps-id122.0080.vtk") the above #commands work Any help would be much appreciated! Thanks, Stephanie

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Definition of the Radius field
by Nathan Goldbaum 22 Dec '12

22 Dec '12

Hi all, I encountered a bit of odd code deep in the field definition code and I need some help to understand why it is the way it is. The field I'm curious about is the Radius field (defined on line 796 of universal_fields.py): def _Radius(field, data): center = data.get_field_parameter("center") DW = data.pf.domain_right_edge - data.pf.domain_left_edge radius = np.zeros(data["x"].shape, dtype='float64') for i, ax in enumerate('xyz'): r = np.abs(data[ax] - center[i]) radius += np.minimum(r, np.abs(DW[i]-r))**2.0 np.sqrt(radius, radius) return radius In particular, I don't understand this line: radius += np.minimum(r, np.abs(DW[i]-r))**2.0 Is this supposed to correct for some effect in periodic simulations? The reason I bring this up is because it caused some very weird behavior in a 1D FLASH simulation. In this simulation, the domain went from x = -.01 pc to x = +500 pc. Since the middle of the domain wasn't lined up with the 'center' of the simulation at x = 0, the offending line in the radius calculation led to an incorrect calculation of the radius beyond x = 250 pc. In that case, I was able to fix it by changing the offending line to radius += r**2.0 Before I issue a patch, I want to see why it's defined the way it is currently and see if we can come up with a workaround. Cheers, Nathan

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Ramses plot issues
by Sam Leitner 19 Dec '12

19 Dec '12

Hi yt-users, I'm compiling from the tip of yt-3.0 where plot seems to be broken for Ramses... yt plot tests/output_00001/info_00001.txttests/output_00001/amr_00001.out00001 yt : [WARNING ] 2012-12-18 10:27:10,365 No current mechanism of distinguishing cosmological simulations in RAMSES! yt : [INFO ] 2012-12-18 10:27:10,366 Parameters: current_time = 0.0 yt : [INFO ] 2012-12-18 10:27:10,366 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2012-12-18 10:27:10,366 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-12-18 10:27:10,366 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-12-18 10:27:10,366 Parameters: cosmological_simulation = 1 yt : [INFO ] 2012-12-18 10:27:10,367 Parameters: current_redshift = 0.0 yt : [INFO ] 2012-12-18 10:27:10,367 Parameters: omega_lambda = 0.0 yt : [INFO ] 2012-12-18 10:27:10,367 Parameters: omega_matter = 1.0 yt : [INFO ] 2012-12-18 10:27:10,367 Parameters: hubble_constant = 1.0 yt : [INFO ] 2012-12-18 10:27:10,367 Adding plot for axis 0 yt : [INFO ] 2012-12-18 10:27:11,597 xlim = 0.000000 1.000000 yt : [INFO ] 2012-12-18 10:27:11,597 ylim = 0.000000 1.000000 yt : [INFO ] 2012-12-18 10:27:11,597 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800 python2.7(2499,0x7fff710f6180) malloc: *** error for object 0x102f20608: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6 and for projection: yt plot -m tests/output_00001/info_00001.txt tests/output_00001/amr_00001.out00001 yt : [WARNING ] 2012-12-18 10:48:46,412 No current mechanism of distinguishing cosmological simulations in RAMSES! yt : [INFO ] 2012-12-18 10:48:46,412 Parameters: current_time = 0.0 yt : [INFO ] 2012-12-18 10:48:46,412 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: cosmological_simulation = 1 yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: current_redshift = 0.0 yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: omega_lambda = 0.0 yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: omega_matter = 1.0 yt : [INFO ] 2012-12-18 10:48:46,413 Parameters: hubble_constant = 1.0 Traceback (most recent call last): File "/Users/sleitner/repos/yt-3.0-run/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==3.0dev', 'console_scripts', 'yt')() File "/Users/sleitner/repos/yt-3.0-artio/yt/utilities/command_line.py", line 1578, in run_main args.func(args) File "/Users/sleitner/repos/yt-3.0-artio/yt/utilities/command_line.py", line 97, in run self(args) File "/Users/sleitner/repos/yt-3.0-artio/yt/utilities/command_line.py", line 1250, in __call__ v, center = pf.h.find_max("Density") AttributeError: 'RAMSESGeometryHandler' object has no attribute 'find_max' Thanks for your help! Sam Leitner

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No module named rockstar_interface
by Latif 13 Dec '12

13 Dec '12

Hi all, I am trying to run Rockstar halo finder using the sample script. It gives me the following error. Any ideas what is going wrong here. ImportError:No module named rockstar_interface Thanks in advance! Cheers Latif

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TimeSeriesData.piter() exiting early
by Nathan Goldbaum 06 Dec '12

06 Dec '12

Hi all, I'm processing some simulations that i have stored on Pleiades at NASA Ames. This machine using SGI's version of MPI so it's possible that this issue is isolated to this MPI. When I ts.piter() on this machine, it will sometimes die early, before all of the parameter files have been processed, with the following error: MPI: MPI_COMM_WORLD rank 7 has terminated without calling MPI_Finalize() MPI: aborting job This particular script saves a bunch of plots to disk. Taking a look at the list of plots that have been saved, it seems that it got about halfway through before dying. The first ~third of the plots are all on disk, most of the middle ~third are saved although there are some missing plots, and the last ~third haven't been saved at all. Any ideas what's going wrong here? Is there something simple I can do to fix it? This isn't game-ending since I can always process my data in serial but it is a bit annoying. Cheers, Nathan

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Star Projections
by Munier Azzam Salem 05 Dec '12

05 Dec '12

Hi yt gurus, I've been making projections of star_density from enzo output files and they seem to be working out fine. However, wherever particles do not exist the background remains white instead of following my chosen colormap. Is there a way to paint these areas to follow the colormap? thanks! Munier I've attached an image of what gets plotted, and the relevant bits of my script are: *from yt.mods import ** * * *fName = "DD0006/test_sim_0006"* *var = "star_density"* *axis = 0* * * *pf = load(fName)* *pf.h* * * *pc = PlotCollection(pf)* *p = pc.add_projection(var,axis)* *#p.modify["particles"](1.0)* * * *radius = .02;* * * *pc.set_xlim(.5-radius,.5+radius)* *pc.set_ylim(.5-radius,.5+radius)* * * *pc.save(fName)* -- Munier A. Salem // 845.489.6450

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