Mailman 3 August 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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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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quick question
by Daniel Whalen 26 Sep '14

26 Sep '14

I am trying to use yt to visualize 3D spherical coordinate data sets created with the ZEUS-MP code. I know yt can directly read in such data, but are there any issues when the grid is ratioed in the radial coordinate (ie, logarithmically spaced zones in radius). Thanks! Dan Whalen

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Plotting 3D Data
by Owen McCrossan 28 Aug '14

28 Aug '14

Hello, I am trying to plot the density of a 3D simulation for only the first quadrant of a simulation. Since there is only one quadrant of data, I would like to eliminate the empty space and focus on only the data . I have gotten to a point where I have manipulated the graph to show only the data, but now the domain and range of the graph are wrong. Is there a way to set the x and y limits for a 3D plot? Thanks, -Owen

2 1

Plotting 1D data
by Hao Wang 22 Aug '14

22 Aug '14

Hi all, I'm trying to plot the density profile of a 1D simulation, but can't find any instruction on how to do this. I tried ray=pf.h.ortho_ray(0,[ord1,ord2]) with several different ord1 and ord2, including [0.5, 0.5]; while "ray['x']" returns an array of values, "ray[FieldName]" (where FieldName can be Density, TotalEnergy, GasEnergy, etc) returns nothing but "YTArray([],dtype=float 64) (dimensionless)". Using ortho_ray on the 2D simulation of the same problem gives correct answer. Also, the "all_data" and "sphere" object do not work for 1D (they work for 2D, too). Thanks, Hao

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How to install yt 2.6 in a computer without internet?
by Reju Sam John 21 Aug '14

21 Aug '14

Dear all, How to install yt 2.6 in a computer without internet? -- Reju Sam John

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problems with star spectrum generator?
by Eric Hallman 20 Aug '14

20 Aug '14

Hello again, I'm again running a very simple script from the cookbook, learning how to use the stellar spectrum generator. It's just a simple tests of spectrum generation with stars of all the same age and mass. It fails with a key error on the dataset, even thought it's not really using the dataset for anything but a reference time (I think). Since it's all small, I'll clip it in below. Here's the script itself: from yt.mods import * from yt.analysis_modules.star_analysis.api import * ds = load("RD0009") spec = SpectrumBuilder(ds, bcdir="/Users/hallman/work/data/sfData", model="chabrier") sm = np.ones(100) ct = np.zeros(100) spec.calculate_spectrum(star_mass=sm, star_creation_time=ct, star_metallicity_constant=0.02) spec.write_out(name="spec.out") And here is the output: Traceback (most recent call last): File "starSpec.py", line 13, in <module> spec.calculate_spectrum(star_mass=sm, star_creation_time=ct, star_metallicity_constant=0.02) File "/Users/hallman/work/yt-x86_64/src/yt-hg/yt/analysis_modules/star_analysis/sfr_spectrum.py", line 387, in calculate_spectrum dt = (self.time_now - self.star_creation_time * self._ds['Time']) / YEAR File "/Users/hallman/work/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 249, in __getitem__ return self.parameters[key] KeyError: 'Time' Even if I modify "sfr_spectrum.py" to use the key "current_time", it still fails with the same error. This is with yt-3.0, dataset created with the tip of enzo-dev as of about 20 minutes ago. It fails on older enzo datasets as well with the same error. Thanks for any help. Eric -- Eric Hallman Tech-X Corporation hallman(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 254-5833 Boulder, CO 80303 Fax: (303) 448-7756 -- _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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how to make a SlicePlot colorbar use mathtext?
by Michael Zingale 20 Aug '14

20 Aug '14

Does anyone know how to make a SlicePlot colorbar from yt use mathtext in the tick labels? I am doing the following in a loop over x, y, z planes: p = yt.SlicePlot(ds, d, var, center=(center[0], center[1], center[2]), origin="native", fontsize=10) p.set_log(var, log) plot = p.plots[var] plot.figure = fig plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i] I can get at the colorbar object via cb = plot.cb, but I can't seem to turn on mathtext. I can modify the axes to use my formatter so they look pretty, but I've tried to set a colorbar formatter with no success. Here's my image: http://bender.astro.sunysb.edu/random/test.png Notice that the offset text for the colorbar is "1.e6" instead of in latex (I still have to remove the offset text for the two rightmost y-axes later, but I know how to do that). Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 5

Difference between the fields "Mach" and "MachNumber"
by Reju Sam John 19 Aug '14

19 Aug '14

Dear all, In one of my user defined field, I have to do a multiplication with Mach number. I found that, I can use both * data["Mach"]* and *data["MachNumber"]. *What is the difference between "Mach" and "MachNumber". Thank you -- Reju Sam John

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TypeError: 'NoneType' object is not iterable
by Wing-Kit Lee 19 Aug '14

19 Aug '14

Hi, I am new to yt and enzo. I have been able to compile and run a few 'test' simulations in enzo. However, when I use 'yt plot xxx', it complains the following: 310 if active_particles: 311 ptypes = _next_token_line("PresentParticleTypes", f)--> 312 counts = [int(c) for c in _next_token_line("ParticleTypeCounts", f)] 313 for ptype in self.parameters.get("AppendActiveParticleType", []): 314 if ptype in ptypes: TypeError: 'NoneType' object is not iterable ------ I recall it worked when I was using yt 2.x version a few months ago. The problem seems to appear for the current yt. The tests with enzo I ran were MHDCTOrszangTang in 2D, ShearingBox in 3D (there are no particles). Any clues? Cheers, Kit

4 3

need to set omega_baryon in yt-3
by Brian O'Shea 19 Aug '14

19 Aug '14

Hi folks, I am using yt-3, and attempting to make a ProjectionPlot of the derived field 'baryon_overdensity' (using an Enzo dataset). The line in question is this: plot1 = yt.ProjectionPlot(ds,'z',"baryon_overdensity",weight_field="baryon_overdensity",center=c,data_source=my_region) (with c, my_region being previously defined). When I do this, it complains: yt.fields.field_exceptions.NeedsParameter: (['omega_baryon']) which certainly makes sense from a physical perspective, and which Enzo doesn't natively carry around. I tried to set this by hand:

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Accessing colormap colors
by Massimo Gaspari 18 Aug '14

18 Aug '14

Hi all, I'd like to plot a line with a given color taken from a given colormap. I am trying to access e.g. pylab.cm.jet(0.5) in order to get the tuple to put in pylab.plot(…, ... , color = …) However it gives me the error: TypeError: 'dict' object is not callable If I remove the import line from yt.mods import * it works fine though. Should I call something else within yt environment? By the way, is there another quick way to access a given colormap color? Thanks, Max

1 0

Question about 2D phase plot limits
by Brian O'Shea 18 Aug '14

18 Aug '14

Hi folks, I'm using yt 2.6 (well, the most up-to-date version of yt 2.x), and am attempting to manually set the limits on a 2D phase plot. Unfortunately, I can't find anything in the docs, and the one IPython notebook solution linked to is defunct. So, if I want to manually set the x and y limits on a plot generated using PhasePlot - i.e., with the command: phase = PhasePlot(ad, "Baryon_Overdensity", "Temperature", "CellMassMsun", weight_field=None, fractional=True) What is the best way to do this? Thanks! --Brian

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color bar label in multiple panel projection plot
by Desika Narayanan 15 Aug '14

15 Aug '14

Hi All, I'm trying to make a plot similar to the pre-fab projection time-series example described here: http://yt-project.org/doc/cookbook/complex_plots.html#time-series-multipanel I'd love it if the colorbar label didn't say "PartType0_smoothed_density" or whatever, but rather something physical. In the past, I've been able to (thanks to Nathan's advice) access the matplotlib primitives for a single projection plot via something like: > px = ProjectionPlot(ds1,'x',("deposit","PartType0_smoothed_density")) > plot = px.plots[('deposit','PartType0_smoothed_density')] > colorbar_axes = plot.cax > colorbar_axes.set_ylabel("N$_H$ g cm$^{-2}$") So, similarly, I thought I could try something like: >plot.cax.set_ylabel("N$_H$ g cm$^{-2}$") in the above time-series example, but it doesn't seem to adjust the colorbar label. I'm sure I'm missing something obvious but can't seem to figure it out - any help would be greatly appreciated. thanks! desika

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probably a dumb question about yt-3.0
by Eric Hallman 15 Aug '14

15 Aug '14

Good morning, I'm getting back to using yt for cosmological analysis after a layoff, and I'm now on yt-3.0, which I hadn't been using in the past. So I needed to do a quick halo finding on a small dataset, and the cookbook script fails immediately. I'm absolutely certain I'm doing something stupid, but I don't know what it is, since I've only issued two commands, they are the first two in the script, and they fail. Can someone tell me what I'm doing wrong? My problem here is that this error is so basic to the operation that I'm not sure exactly how to dig into it. Thanks. Here are the commands, and the output: >>> import yt >>> from yt.analysis_modules.halo_analysis.api import HaloCatalog Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named halo_analysis.api And here is my version info: torque:RD0009 hallman$ yt version yt module located at: /Users/hallman/work/yt-x86_64/lib/python2.7/site-packages/yt-3.0-py2.7-macosx-10.4-x86_64.egg The supplemental repositories are located at: /Users/hallman/work/yt-x86_64/src/yt-supplemental The current version and changeset for the code is: --- Version = 3.0 Changeset = cf867eab0515 stable ---

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Re: [yt-users] yt-users Digest, Vol 78, Issue 39
by Professor Maller 15 Aug '14

15 Aug '14

Hi Matt, ds.field_info.create_cooling_fields("") done directly after loading gives an error no field_info. I do a ds.field_list first to so that ds.field_info exists, then ds.field_info.create_cooling_fields("") gives no error, but also no changes that I can see. That is nothing is added to ds.derived_field_lists and doing dd=ds.all_data() HI=dd[('gas','HI')] gives could not find field '('gas','HI')' For others, I'm trying to get the ionization state information from the cooling??.dat files, this run has no ionization information in the hydro output files. Thanks, Ari On Fri, Aug 15, 2014 at 4:21 AM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: yt-users Digest, Vol 78, Issue 38 (Professor Maller) > 2. Re: yt-users Digest, Vol 78, Issue 38 (Matthew Turk) > 3. " cannot import name YTDomainOverflow" after hg update to an > earlier version (Hao Wang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Aug 2014 14:56:22 -0400 > From: Professor Maller <amaller(a)citytech.cuny.edu> > To: yt-users(a)lists.spacepope.org > Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38 > Message-ID: > <CACCSjdMFbhvsBhpH3ybzvW= > dEGSkMRYBetsJG-deSEjyiqztHg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Matt, > > Those fields are not in my derived field list. That is > ds.derived_field_list. Do I have to add them in some way? Or is there a way > to check if yt didn't find the cooling??.dat files? > > Thanks, > > Ari > > > On Thu, Aug 14, 2014 at 1:54 PM, <yt-users-request(a)lists.spacepope.org> > wrote: > > > Send yt-users mailing list submissions to > > yt-users(a)lists.spacepope.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > or, via email, send a message with subject or body 'help' to > > yt-users-request(a)lists.spacepope.org > > > > You can reach the person managing the list at > > yt-users-owner(a)lists.spacepope.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of yt-users digest..." > > > > > > Today's Topics: > > > > 1. ionization states in ramses data sets (Professor Maller) > > 2. Re: ionization states in ramses data sets (Geoffrey So) > > 3. Re: ionization states in ramses data sets (Matthew Turk) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 14 Aug 2014 13:12:11 -0400 > > From: Professor Maller <amaller(a)citytech.cuny.edu> > > To: yt-users(a)lists.spacepope.org > > Subject: [yt-users] ionization states in ramses data sets > > Message-ID: > > < > > CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi, > > > > Does anyone have code to create derived fields of ionization states, e.g. > > HI, for ramses data sets? If that's a no, does anyone have an example > of a > > derived field where you have to read in a table and interpolate the field > > values. > > > > Thanks, > > > > Ari > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 14 Aug 2014 10:19:49 -0700 > > From: Geoffrey So <gsiisg(a)gmail.com> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] ionization states in ramses data sets > > Message-ID: > > < > > CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi, > > > > according to > > http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html? > > > > what worked for me for enzo data is the following > > > > def _HINeutralFraction(field, data): > > return data['HI_Density']/(data['HI_Density']+data['HII_Density']) > > > > add_field('HINeutralFraction',function=_HINeutralFraction, > > units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}") > > > > unless there's something strange with ramses dataset, the above should > > work. > > > > From > > G.S. > > > > > > On Thu, Aug 14, 2014 at 10:12 AM, Professor Maller < > > amaller(a)citytech.cuny.edu> wrote: > > > > > Hi, > > > > > > Does anyone have code to create derived fields of ionization states, > e.g. > > > HI, for ramses data sets? If that's a no, does anyone have an example > > of a > > > derived field where you have to read in a table and interpolate the > field > > > values. > > > > > > Thanks, > > > > > > Ari > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 14 Aug 2014 12:22:16 -0500 > > From: Matthew Turk <matthewturk(a)gmail.com> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] ionization states in ramses data sets > > Message-ID: > > <CALO3= > > 5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ(a)mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi Ari, > > > > My reading of yt/frontends/ramses/fields.py is that this should be > > implemented already, using the cooling_%05i.dat files. If it's able > > to find those files, it will create the appropriate derived fields > > from them -- specifically, I think it can do Electron, HI, HII, HeI, > > HeII, and HeIII. Is it not creating those? > > > > On Thu, Aug 14, 2014 at 12:12 PM, Professor Maller > > <amaller(a)citytech.cuny.edu> wrote: > > > Hi, > > > > > > Does anyone have code to create derived fields of ionization states, > e.g. > > > HI, for ramses data sets? If that's a no, does anyone have an example > > of a > > > derived field where you have to read in a table and interpolate the > field > > > values. > > > > > > Thanks, > > > > > > Ari > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > ------------------------------ > > > > End of yt-users Digest, Vol 78, Issue 38 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Thu, 14 Aug 2014 14:05:04 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] yt-users Digest, Vol 78, Issue 38 > Message-ID: > <CALO3= > 5EBSnthcHi+SzWTvWvmTbj7751MjPQ_+tVK4+GDes2OHA(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Ari, > > Looks to me like it may actually not be enabled by default for some > reason. Can you try calling: > > ds.field_info.create_cooling_fields("") > > and seeing if that adds the correct fields? If so, I'll update the > code to do this automatically. > > -Matt > > On Thu, Aug 14, 2014 at 1:56 PM, Professor Maller > <amaller(a)citytech.cuny.edu> wrote: > > Hi Matt, > > > > Those fields are not in my derived field list. That is > > ds.derived_field_list. Do I have to add them in some way? Or is there a > way > > to check if yt didn't find the cooling??.dat files? > > > > Thanks, > > > > Ari > > > > > > On Thu, Aug 14, 2014 at 1:54 PM, <yt-users-request(a)lists.spacepope.org> > > wrote: > >> > >> Send yt-users mailing list submissions to > >> yt-users(a)lists.spacepope.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> or, via email, send a message with subject or body 'help' to > >> yt-users-request(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)lists.spacepope.org > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of yt-users digest..." > >> > >> > >> Today's Topics: > >> > >> 1. ionization states in ramses data sets (Professor Maller) > >> 2. Re: ionization states in ramses data sets (Geoffrey So) > >> 3. Re: ionization states in ramses data sets (Matthew Turk) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 14 Aug 2014 13:12:11 -0400 > >> From: Professor Maller <amaller(a)citytech.cuny.edu> > >> To: yt-users(a)lists.spacepope.org > >> Subject: [yt-users] ionization states in ramses data sets > >> Message-ID: > >> > >> <CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Hi, > >> > >> Does anyone have code to create derived fields of ionization states, > e.g. > >> HI, for ramses data sets? If that's a no, does anyone have an example > of > >> a > >> derived field where you have to read in a table and interpolate the > field > >> values. > >> > >> Thanks, > >> > >> Ari > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: > >> < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Thu, 14 Aug 2014 10:19:49 -0700 > >> From: Geoffrey So <gsiisg(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] ionization states in ramses data sets > >> Message-ID: > >> > >> <CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Hi, > >> > >> according to > >> http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html? > >> > >> what worked for me for enzo data is the following > >> > >> def _HINeutralFraction(field, data): > >> return data['HI_Density']/(data['HI_Density']+data['HII_Density']) > >> > >> add_field('HINeutralFraction',function=_HINeutralFraction, > >> units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}") > >> > >> unless there's something strange with ramses dataset, the above should > >> work. > >> > >> From > >> G.S. > >> > >> > >> On Thu, Aug 14, 2014 at 10:12 AM, Professor Maller < > >> amaller(a)citytech.cuny.edu> wrote: > >> > >> > Hi, > >> > > >> > Does anyone have code to create derived fields of ionization states, > >> > e.g. > >> > HI, for ramses data sets? If that's a no, does anyone have an example > >> > of a > >> > derived field where you have to read in a table and interpolate the > >> > field > >> > values. > >> > > >> > Thanks, > >> > > >> > Ari > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> > > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: > >> < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Thu, 14 Aug 2014 12:22:16 -0500 > >> From: Matthew Turk <matthewturk(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] ionization states in ramses data sets > >> Message-ID: > >> > >> <CALO3=5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ(a)mail.gmail.com> > >> Content-Type: text/plain; charset=UTF-8 > >> > >> Hi Ari, > >> > >> My reading of yt/frontends/ramses/fields.py is that this should be > >> implemented already, using the cooling_%05i.dat files. If it's able > >> to find those files, it will create the appropriate derived fields > >> from them -- specifically, I think it can do Electron, HI, HII, HeI, > >> HeII, and HeIII. Is it not creating those? > >> > >> On Thu, Aug 14, 2014 at 12:12 PM, Professor Maller > >> <amaller(a)citytech.cuny.edu> wrote: > >> > Hi, > >> > > >> > Does anyone have code to create derived fields of ionization states, > >> > e.g. > >> > HI, for ramses data sets? If that's a no, does anyone have an example > >> > of a > >> > derived field where you have to read in a table and interpolate the > >> > field > >> > values. > >> > > >> > Thanks, > >> > > >> > Ari > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> End of yt-users Digest, Vol 78, Issue 38 > >> **************************************** > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Message: 3 > Date: Fri, 15 Aug 2014 16:21:05 +0800 > From: Hao Wang <hwang.phy(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] " cannot import name YTDomainOverflow" after hg > update to an earlier version > Message-ID: > <CAD_YEuC99LOH2p8n8zfdrLEZ7= > 7__QNjSeEis3nyz2mEio5SSQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I was using YT when some error messages appeared; since this happened > immediately after I updated yt, I tried to "hg update 13651" to an earlier > version. > > It turned out to be a big mistake -- suddenly every command I tried (yt; yt > update; hg update; and yt notebook) gave the following error: > ======================================= > Traceback (most recent call last): > File "/home/hao/projects/yt/bin/yt", line 9, in <module> > load_entry_point('yt==3.0dev', 'console_scripts', 'yt')() > File > > "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", > line 337, in load_entry_point > return get_distribution(dist).load_entry_point(group, name) > File > > "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", > line 2311, in load_entry_point > return ep.load() > File > > "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", > line 2017, in load > entry = __import__(self.module_name, globals(),globals(), ['__name__']) > File "/home/hao/projects/yt/src/yt-hg/yt/utilities/command_line.py", line > 19, in <module> > from yt.mods import * > File "/home/hao/projects/yt/src/yt-hg/yt/mods.py", line 50, in <module> > from yt.data_objects.api import \ > File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/api.py", line 13, > in <module> > from grid_patch import \ > File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/grid_patch.py", > line 25, in <module> > from yt.data_objects.data_containers import YTFieldData > File > "/home/hao/projects/yt/src/yt-hg/yt/data_objects/data_containers.py", line > 31, in <module> > from yt.data_objects.derived_quantities import GridChildMaskWrapper > File > "/home/hao/projects/yt/src/yt-hg/yt/data_objects/derived_quantities.py", > line 26, in <module> > from yt.utilities.parallel_tools.parallel_analysis_interface import \ > File > > "/home/hao/projects/yt/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 29, in <module> > from yt.utilities.lib import \ > File "/home/hao/projects/yt/src/yt-hg/yt/utilities/lib/__init__.py", line > 21, in <module> > from .geometry_utils import * > File "geometry_utils.pyx", line 22, in init > yt.utilities.lib.geometry_utils (yt/utilities/lib/geometry_utils.c:10907) > ImportError: cannot import name YTDomainOverflow > ======================================== > Anything to do to fix the damage besides a reinstallation? > > Thanks! > > Hao > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 78, Issue 39 > **************************************** >

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'object not found' and 'out of bounds' errors
by Hao Wang 15 Aug '14

15 Aug '14

Hi all, I was plotting Enzo outputs with yt (version = 3.0, changeset = cf867eab0515), and obtained the following errors messages: 1). For DD0000 (the name of the output files) the error message and backtrace: http://paste.yt-project.org/show/5044/ 2). For DD0001 files: http://paste.yt-project.org/show/5045/ >From 0002, all output files produce figures that looked normal. Any ideas what happened? Thanks! Hao

2 1

ionization states in ramses data sets
by Professor Maller 15 Aug '14

15 Aug '14

Hi, Does anyone have code to create derived fields of ionization states, e.g. HI, for ramses data sets? If that's a no, does anyone have an example of a derived field where you have to read in a table and interpolate the field values. Thanks, Ari

4 3

" cannot import name YTDomainOverflow" after hg update to an earlier version
by Hao Wang 15 Aug '14

15 Aug '14

Hi all, I was using YT when some error messages appeared; since this happened immediately after I updated yt, I tried to "hg update 13651" to an earlier version. It turned out to be a big mistake -- suddenly every command I tried (yt; yt update; hg update; and yt notebook) gave the following error: ======================================= Traceback (most recent call last): File "/home/hao/projects/yt/bin/yt", line 9, in <module> load_entry_point('yt==3.0dev', 'console_scripts', 'yt')() File "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 337, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 2311, in load_entry_point return ep.load() File "/home/hao/projects/yt/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/pkg_resources.py", line 2017, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/hao/projects/yt/src/yt-hg/yt/utilities/command_line.py", line 19, in <module> from yt.mods import * File "/home/hao/projects/yt/src/yt-hg/yt/mods.py", line 50, in <module> from yt.data_objects.api import \ File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/api.py", line 13, in <module> from grid_patch import \ File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/grid_patch.py", line 25, in <module> from yt.data_objects.data_containers import YTFieldData File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/data_containers.py", line 31, in <module> from yt.data_objects.derived_quantities import GridChildMaskWrapper File "/home/hao/projects/yt/src/yt-hg/yt/data_objects/derived_quantities.py", line 26, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/home/hao/projects/yt/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 29, in <module> from yt.utilities.lib import \ File "/home/hao/projects/yt/src/yt-hg/yt/utilities/lib/__init__.py", line 21, in <module> from .geometry_utils import * File "geometry_utils.pyx", line 22, in init yt.utilities.lib.geometry_utils (yt/utilities/lib/geometry_utils.c:10907) ImportError: cannot import name YTDomainOverflow ======================================== Anything to do to fix the damage besides a reinstallation? Thanks! Hao

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Re: [yt-users] yt-users Digest, Vol 78, Issue 38
by Professor Maller 14 Aug '14

14 Aug '14

Hi Matt, Those fields are not in my derived field list. That is ds.derived_field_list. Do I have to add them in some way? Or is there a way to check if yt didn't find the cooling??.dat files? Thanks, Ari On Thu, Aug 14, 2014 at 1:54 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. ionization states in ramses data sets (Professor Maller) > 2. Re: ionization states in ramses data sets (Geoffrey So) > 3. Re: ionization states in ramses data sets (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Aug 2014 13:12:11 -0400 > From: Professor Maller <amaller(a)citytech.cuny.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] ionization states in ramses data sets > Message-ID: > < > CACCSjdOxDp+Mmgae1XLYJJvC7vJn52Xu59ppUA+p0mq7Fggz8A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > Does anyone have code to create derived fields of ionization states, e.g. > HI, for ramses data sets? If that's a no, does anyone have an example of a > derived field where you have to read in a table and interpolate the field > values. > > Thanks, > > Ari > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Thu, 14 Aug 2014 10:19:49 -0700 > From: Geoffrey So <gsiisg(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] ionization states in ramses data sets > Message-ID: > < > CAM-dO+DM+ygbGg3GG9vrxjSn+JM9mGGgHDXA1UEJu1KYpnJJqw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > according to > http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html? > > what worked for me for enzo data is the following > > def _HINeutralFraction(field, data): > return data['HI_Density']/(data['HI_Density']+data['HII_Density']) > > add_field('HINeutralFraction',function=_HINeutralFraction, > units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}") > > unless there's something strange with ramses dataset, the above should > work. > > From > G.S. > > > On Thu, Aug 14, 2014 at 10:12 AM, Professor Maller < > amaller(a)citytech.cuny.edu> wrote: > > > Hi, > > > > Does anyone have code to create derived fields of ionization states, e.g. > > HI, for ramses data sets? If that's a no, does anyone have an example > of a > > derived field where you have to read in a table and interpolate the field > > values. > > > > Thanks, > > > > Ari > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Thu, 14 Aug 2014 12:22:16 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] ionization states in ramses data sets > Message-ID: > <CALO3= > 5HE+5eFNfXaWqJ_ApFCZeE_Sy73EEj+O5y7CuqMiVQ9sQ(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Ari, > > My reading of yt/frontends/ramses/fields.py is that this should be > implemented already, using the cooling_%05i.dat files. If it's able > to find those files, it will create the appropriate derived fields > from them -- specifically, I think it can do Electron, HI, HII, HeI, > HeII, and HeIII. Is it not creating those? > > On Thu, Aug 14, 2014 at 12:12 PM, Professor Maller > <amaller(a)citytech.cuny.edu> wrote: > > Hi, > > > > Does anyone have code to create derived fields of ionization states, e.g. > > HI, for ramses data sets? If that's a no, does anyone have an example > of a > > derived field where you have to read in a table and interpolate the field > > values. > > > > Thanks, > > > > Ari > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 78, Issue 38 > **************************************** >

2 1

Problems using Rockstar in yt
by David Sullivan 14 Aug '14

14 Aug '14

Hi Britton, all, That took care of my issues, now it’s run successfully. Just one more question: as I’m using RAMSES I create a DatasetSeries using: es = yt.load('../output_*/info_*.txt’) rh = RockstarHaloFinder(es, num_readers=1, num_writers=2) Is there a way for me to add a dark matter only filter as done here for an enzo dataset: # create a particle filter to remove star particles @yt.particle_filter("dark_matter", requires=["creation_time"]) def _dm_filter(pfilter, data): return data["creation_time"] < 0.0 def setup_ds(ds): ds.add_particle_filter("dark_matter”) es = yt.simulation("enzo_tiny_cosmology/32Mpc_32.enzo", "Enzo") es.get_time_series(setup_function=setup_ds, redshift_data=False) rh = RockstarHaloFinder(es, num_readers=1, num_writers=2, particle_type="dark_matter") I’ve looked at the docs on particle filtering but I can’t add filters to the DatasetSeries object I have. Many thanks for the help so far! David On 12 Aug 2014, at 12:44, yt-users-request(a)lists.spacepope.org wrote: > Hi Cameron, David, > > Cameron, you are correct, on Mac systems you need to set DYLD_LIBRARY_PATH > instead of LD_LIBRARY_PATH. The fact that this causes vi and other things > to fail is apparently an OS X bug (I found some discussions of it on the > internet) and has nothing to do with yt. I went through a similar thing > and had to resort to having a separate terminal for running rockstar that I > didn't try to do anything else in. For what it's worth, this behavior > seems to have been fixed. I am on OS X 10.8.5 and no longer have the issue > of things crashing in a terminal where I have edited DYLD_LIBRARY_PATH. > > On the second issue that you both reported, the problem is the way in which > one tells yt to run in parallel depends on how you import yt. > > If you do "from yt.mods import *", the parallelism is enabled by adding the > --parallel flag on the command line. However, if you do "import yt", then > parallelism is enabled by doing "yt.enable_parallelism()" directly below > the import statement within your script. > > I looked at the latest documentation on parallelism ( > http://yt-project.org/doc/analyzing/parallel_computation.html) and is > discusses the use of yt.enable_parallelism(), but not the old way that > works with "from yt.mods import *". There should probably be a short > discussion added of how this has changed. Additionally, let's make sure > that the yt-rockstar docs get any needed additions there as well. > > Britton

3 2

yt/mpi4py on oak ridge cray machines
by David Sullivan 13 Aug '14

13 Aug '14

Hi all, I’ve been trying to build yt and mpi4py on the cray machines at oak ridge and came across this old thread in the mailing list: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-December/0… I was just wondering if anyone had managed this since? If so, what the best approach is (system python or install script)? Many thanks, David

6 6

Re: [yt-users] Problems using Rockstar in yt
by David Sullivan 13 Aug '14

13 Aug '14

Hi all, I also get the same error as Cameron when trying to run rockstar with mpi: http://paste.yt-project.org/show/5019/ I’m using a ramses dataset (not sure if this is supported, but couldn’t see any clear evidence that it isn’t) and the following script: mpirun -np 4 --mca btl ^openib python run_rockstar.py --parallel http://paste.yt-project.org/show/5020/ I followed the same install instructions as Cameron, but I’m using a Linux cluster running CentOS. Appreciate any help! Cheers, David On 12 Aug 2014, at 10:04, yt-users-request(a)lists.spacepope.org wrote: > Message: 3 > Date: Tue, 12 Aug 2014 02:04:10 -0700 > From: Sam Skillman <samskillman(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Problems using Rockstar in yt > Message-ID: > <CAB4=1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Cameron, > > Are you running in MPI? You need to run with at least 3 MPI tasks for > Rockstar to work properly. > > Sam > > > On Mon, Aug 11, 2014 at 6:41 PM, Cameron Hummels <chummels(a)gmail.com> wrote: > >> Hello, >> >> I'm trying to use Rockstar with the new HaloCatalog functionality in yt >> 3.0, but I'm encountering some problems. For reference, this is an OS X >> box with the "yt" branch. I've tested it on two OS X systems to the same >> result. >> >> I modified my install_script.py to have it install Rockstar as described >> here: >> >> >> http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html… >> >> Then, after rerunning my install script for the `yt` branch (ie yt-3.1 >> dev) I tried to run the script provided here in order to generate a halo >> catalog using HOP: >> >> >> http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_transition.h… >> >> It can create the catalog fine with finder_method='hop', but when I change >> it to finder_method='rockstar', I get failures. This is the traceback: >> >> http://paste.yt-project.org/show/TE2DW8gc50urchv4JnUk >> >> In the traceback, it claims that it cannot access librockstar.so, but this >> library exists in the yt-x86_64/lib directory, which is explicitly in from >> my $LD_LIBRARY_PATH. I can seemingly get it to work, if I add that path to >> my $DYLD_LIBRARY_PATH environment variable, but then a bunch of other >> things break (like vi). Not sure what to do here. >> >> But assuming there is no vi problem here, even then, when I run the script >> above, I get failures. Here is the traceback: >> >> http://paste.yt-project.org/show/rCOT1eVT1szR1T6DEUDb >> >> I'm not sure what to do here. I've also tried running rockstar external >> to yt on an enzo dataset, but it doesn't appear that the version we install >> as part of yt allows it to work on HDF5 datasets. >> >> Has anyone run into any of these problems before? I'm at a bit of a loss >> as to how to proceed on any of these fronts. >> >> Cameron >> >> >> -- >> Cameron Hummels >> Postdoctoral Researcher >> Steward Observatory >> University of Arizona >> http://chummels.org >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>

6 7

ANN: YT v0.1.0, a Julia wrapper for yt 3.0
by John ZuHone 12 Aug '14

12 Aug '14

Hi yt-er's, I just wanted to email the list and let everyone know about a new package I've developed called YT (yes, in caps), which as of today has its first release as v0.1.0. YT is a wrapper for yt for the Julia programming language. Julia is a new(-ish) high-level, high-performance dynamic programming language for technical computing. If you want to learn more about Julia, visit http://julialang.org. One of the most important things to note about Julia is that it has a "just-in-time" compiler, so it can be very fast (within a factor of few of C speed in some cases). There is also a lot of interoperability between Julia and Python, including wrappers for Matplotlib and Sympy, and even an extension of the IPython (soon to be Jupyter) notebook! A short summary of what YT exposes from yt in Julia: * Datasets * Some data objects (e.g., spheres, rectangular regions, slices, projections, profiles, etc.) * YTArrays and YTQuantities * Simple visualization tools (e.g., SlicePlot, ProjectionPlot, FixedResolutionBuffer) To find out more about the YT package, visit the documentation: http://www.jzuhone.com/yt_julia or the GitHub project page: http://github.com/jzuhone/YT.jl Thanks for reading, and sorry for the spam. Best, John Z

1 0

Problems using Rockstar in yt
by Cameron Hummels 12 Aug '14

12 Aug '14

Hello, I'm trying to use Rockstar with the new HaloCatalog functionality in yt 3.0, but I'm encountering some problems. For reference, this is an OS X box with the "yt" branch. I've tested it on two OS X systems to the same result. I modified my install_script.py to have it install Rockstar as described here: http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html… Then, after rerunning my install script for the `yt` branch (ie yt-3.1 dev) I tried to run the script provided here in order to generate a halo catalog using HOP: http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_transition.h… It can create the catalog fine with finder_method='hop', but when I change it to finder_method='rockstar', I get failures. This is the traceback: http://paste.yt-project.org/show/TE2DW8gc50urchv4JnUk In the traceback, it claims that it cannot access librockstar.so, but this library exists in the yt-x86_64/lib directory, which is explicitly in from my $LD_LIBRARY_PATH. I can seemingly get it to work, if I add that path to my $DYLD_LIBRARY_PATH environment variable, but then a bunch of other things break (like vi). Not sure what to do here. But assuming there is no vi problem here, even then, when I run the script above, I get failures. Here is the traceback: http://paste.yt-project.org/show/rCOT1eVT1szR1T6DEUDb I'm not sure what to do here. I've also tried running rockstar external to yt on an enzo dataset, but it doesn't appear that the version we install as part of yt allows it to work on HDF5 datasets. Has anyone run into any of these problems before? I'm at a bit of a loss as to how to proceed on any of these fronts. Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

2 1

ANN: DistArray 0.5 release
by Kurt Smith 11 Aug '14

11 Aug '14

==================================================== DistArray 0.5 release ==================================================== **Documentation:** http://distarray.readthedocs.org **License:** Three-clause BSD **Python versions:** 2.7, 3.3, and 3.4 **OS support:** \*nix and Mac OS X What is DistArray? ------------------ DistArray aims to bring the ease-of-use of NumPy to data-parallel high-performance computing. It provides distributed multi-dimensional NumPy arrays, distributed ufuncs, and distributed IO capabilities. It can efficiently interoperate with external distributed libraries like Trilinos. DistArray works with NumPy and builds on top of it in a flexible and natural way. 0.5 Release ----------- Noteworthy improvements in this release include: * closer alignment with NumPy's API, * support for Python 3.4 (existing support for Python 2.7 and 3.3), * a performance-oriented MPI-only mode for deployment on clusters and supercomputers, * a way to register user-defined functions to be callable locally on worker processes, * more consistent naming of sub-packages, * testing with MPICH2 (already tested against OpenMPI), * improved and expanded examples, * installed version testable via ``distarray.test()``, and * performance and scaling improvements. With this release, DistArray ready for real-world testing and deployment. The project is still evolving rapidly and we appreciate the continued input from the larger scientific-Python community. Existing features ----------------- DistArray: * supports NumPy-like slicing, reductions, and ufuncs on distributed multidimensional arrays; * has a client-engine process design -- data resides on the worker processes, commands are initiated from master; * allows full control over what is executed on the worker processes and integrates transparently with the master process; * allows direct communication between workers, bypassing the master process for scalability; * integrates with IPython.parallel for interactive creation and exploration of distributed data; * supports distributed ufuncs (currently without broadcasting); * builds on and leverages MPI via MPI4Py in a transparent and user-friendly way; * has basic support for unstructured arrays; * supports user-controllable array distributions across workers (block, cyclic, block-cyclic, and unstructured) on a per-axis basis; * has a straightforward API to control how an array is distributed; * has basic plotting support for visualization of array distributions; * separates the array’s distribution from the array’s data -- useful for slicing, reductions, redistribution, broadcasting, and other operations; * implements distributed random arrays; * supports ``.npy``-like flat-file IO and hdf5 parallel IO (via ``h5py``); leverages MPI-based IO parallelism in an easy-to-use and transparent way; and * supports the distributed array protocol [protocol]_, which allows independently developed parallel libraries to share distributed arrays without copying, analogous to the PEP-3118 new buffer protocol. Planned features and roadmap ---------------------------- Near-term features and improvements include: * array re-distribution capabilities; * lazy evaluation and deferred computation for latency hiding; * interoperation with Trilinos [Trilinos]_; and * distributed broadcasting support. The longer-term roadmap includes: * Integration with other packages [petsc]_ that subscribe to the distributed array protocol [protocol]_; * Distributed fancy indexing; * Out-of-core computations; * Support for distributed sorting and other non-trivial distributed algorithms; and * End-user control over communication and temporary array creation, and other performance aspects of distributed computations. History and funding ------------------- Brian Granger started DistArray as a NASA-funded SBIR project in 2008. Enthought picked it up as part of a DOE Phase II SBIR [SBIR]_ to provide a generally useful distributed array package. It builds on NumPy, MPI, MPI4Py, IPython, IPython.parallel, and interfaces with the Trilinos suite of distributed HPC solvers (via PyTrilinos [Trilinos]_). This material is based upon work supported by the Department of Energy under Award Number DE-SC0007699. This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. .. [protocol] http://distributed-array-protocol.readthedocs.org/en/rel-0.10.0/ .. [Trilinos] http://trilinos.org/ .. [petsc] http://www.mcs.anl.gov/petsc/ .. [SBIR] http://www.sbir.gov/sbirsearch/detail/410257 -- Kurt W. Smith, Ph.D. <ksmith(a)enthought.com> Enthought, Inc. <http://www.enthought.com> | 512.536.1057

1 0

Slice Plot Gadget Problem
by Jared Coughlin 11 Aug '14

11 Aug '14

Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error: IndexError: index 32767 is out of bounds for axis 0 with size 32767 Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! -Jared

4 11

will yt 2.6 analysis scripts works for yt 3.0 ?
by Reju Sam John 11 Aug '14

11 Aug '14

Dear All, My yt version is --- Version = 2.6.1 Changeset = c7bae05dd4ef --- If I update it to 3.0 with the command: yt update --all , will my old analysis scripts(written for 2.6 ) works? Thank you. -- Reju Sam John

2 2

lagrangian volume of ICs?
by Brian O'Shea 10 Aug '14

10 Aug '14

Hi folks, I'm going back to resimulate some cosmological simulations with a nested-grid setup, and can't seem to figure out how to get yt to tell me where all of the dark matter particles in a given halo start out at high redshift. It seems that something like this used to exist in the Hub (i.e., http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-August/001…), but that is not around any more. Would somebody mind sharing such a tool if they have already coded it up? Thanks! --Brian

3 4

yt-3.0 density gradient
by Lile Wang 08 Aug '14

08 Aug '14

Hi all, I am just worried about the problem associated to the density gradient field in yt-3.0. When I was trying to get the gradient of density field along z (actually any) direction, I got this error message (last few lines) when calling data[ 'density_gradient_z' ]: ~/lilew/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in selector(self) 529 if sclass is None: 530 raise YTDataSelectorNotImplemented(self._type_name) --> 531 self._selector = sclass(self) 532 return self._selector 533 ~/lilew/yt-x86_64/src/yt-hg/yt/geometry/selection_routines.so in yt.geometry.selection_routines.RegionSelector.__init__ (yt/geometry/selection_routines.c:20276)() RuntimeError: Error: bad Region in non-periodic domain along dimension 0. Region left edge = -0.01171875 code_length, Region right edge = 0.13671875 code_lengthDataset left edge = 0. 0 code_length, Dataset right edge = 1.0 code_length Similar things happen for the pressure gradient. The data input was generated by Enzo with AMR. In comparison, it works well with yt-2.6, where I refer to the gradient by data[ 'gradDensityZ' ]. Any ideas are appreciated. Thanks! Cheers, Lile ----------------------------------------------------------- Lile 'Patrick' Wang Dept. of Astroph. Sci., Princeton University, NJ 08544 USA Website : http://www.astro.princeton.edu/~lilew/ <http://www.astro.princeton.edu/%7Elilew/> Tel (Mobile): +1-(734)-834-3936 Tel (GVoice): +1-(510)-926-6831 -----------------------------------------------------------

2 2

ANN: Enzo 2.4 Release
by Nathan Goldbaum 08 Aug '14

08 Aug '14

We are pleased to announce the release of version 2.4 of the Enzo code. This is a periodic release that includes all changes committed to the Enzo BitBucket repository since July 2013. This release contains some new features and a number of enhancements and bugfixes. Enzo now has bindings to version 1.0 of the grackle chemistry and cooling library. Grackle is based on Enzo's own cooling and chemistry code and includes updated rate and chemistry tables, as well a number of enhancements and new features that are not available in Enzo's native chemistry and cooling modules. Enzo's solvers and physics modules have also seen improvements, including updates for the GPU MHD solver, the FLD solver, and the MHD-CT solver, the Jeans pressure floor, the Cen & Ostriker star particle, tracer particles, and particle splitting. There have also been a number of infrastructure improvements, including a new progress meter script (which allows the user to monitor simulations during runtime), updates for geometric refinement regions and the shear refinement criterion, improved control over the frequency of hierarchy rebuilds, updates for test problem initialization (which is now more memory efficient), and improvements to the GalaxySimulation, KelvinHelmholtz, and CosmologySimulation problem types. There is also a new rotating turbulent sphere problem type. There have also been a number of significant bugfixes, including several that may increase the stability and efficiency of production multi-physics simulations. We urge all users to update to the latest version if they are using Enzo 2.3 or earlier. While one can obtain the release by downloading a tar file, we strong encourage all users to use enzo from a clone of the mercurial repository, which will facilitate reproducible work with the code. For more information about enzo, see http://enzo-project.org. For the release notes and changelog, see http://enzo-project.org/ReleaseNotes.html On behalf of the Enzo collaboration, Nathan Goldbuam

1 0

Generation of smoothing lengths from coordinates of tracer particles
by Amos Manneschmidt 08 Aug '14

08 Aug '14

Hello, I am a student researcher working on the Chimera project. Part of my work involves creating density maps from tracer particles that accurately represent what we get directly interpolated to the grid from chimera code. If I can do this I know I can make accurate element abundance maps for up to 150 species. We are limited by computing resources to creating maps for only 14 species directly. Here is a video of the best conservative density plot I have been able to come up with thus far. The smoothing lengths for the tracers are found in a round-about way right now that is less than ideal. Is there a way in yt to create smoothing lengths using just particle coordinates like this? (IE the complex nearest neighbor math I would rather not code myself if I don’t have to) Thanks, Amos M

2 2

doing SPH smoothing without smoothing lengths (or with them inputted manually)
by Brendan Griffen 08 Aug '14

08 Aug '14

Hi, As I understand yt is able to construct an array based on cloud-in-cell assignment but not using sph assignment. Each particle must have their own smoothing lengths. Could a rudimentary smoothing length be assigned within yt if particles don't already have a smoothing length? The volume rendering looks great for gas with a 'density' field but if I want to create a sph smoothed field also called 'density' for the dark matter particles, my only option for particle data at this point is cloud in cell assignment? This looks OK for large scale full homogeneous runs but for zoom-ins cloud in cell looks pretty terrible. Or could you even feed yt the smoothing lengths (say output from subfind) as a vector which yt then uses for the sph assignment? This might be a good first step as I already have the smoothing lengths pre-calculated in hsml files from subfind. Thanks. Brendan

2 1

coLaboratory Chrome App
by Sam Skillman 08 Aug '14

08 Aug '14

Hi all, Some of you might be interested in a few news bits today: http://googleresearch.blogspot.com/2014/08/doing-data-science-with-colabora… and http://www.symmetrymagazine.org/article/august-2014/open-access-to-the-univ… What's even cooler than the fact that you can now load up an ipython notebook that runs sandboxed in your Chrome browser is that because Matt is the one compiling all these python tools into the Chrome app, we went ahead and included a very recent version of yt 3.0! Then we went a bit further, and baked in thingking ( https://bitbucket.org/zeropy/thingking) and some DarkSky tools, so when you put it all together now anyone and everyone can access data from the DarkSky simulations. If you install the chrome app ( https://chrome.google.com/webstore/detail/colaboratory-notebook/pianggobfjc…) then check out some examples: Dark Sky Examples <https://docs.google.com/folderview?id=0B7ET8zdoN208T1ZRNnk4cUJ0YnM&usp=driv…> We (Matt, Mike Warren, and I) would love to hear feedback if you try things out. I expect there will some growing pains with the interface, but we're all pretty excited about finally getting this out. Congrats to Matt and the Chrome/Jupyter teams! Cheers, Sam

2 1

troubles with derived field: 1+1 is not equal to 2
by Antoine Strugarek 08 Aug '14

08 Aug '14

Hello, I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on. I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields: def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB'] Then I add them to my yt object: ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False) and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots. I must be missing something here but I really don’t get it. Many thanks in advance for your help! Antoine Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek(a)astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek(a)cea.fr --------------------------------------------------------------------

3 8

yt python import error
by Romeel Davé 07 Aug '14

07 Aug '14

Has anyone seen an error like this? I go into python and say "import yt" and it gives http://paste.yt-project.org/show/4994/ The problem seems to be with PyUnicodeUCS2_DecodeUTF8, and it also appears when i try to pip install scipy using yt's python. I am using anaconda, and uname -a gives Linux ursa.uwc.ac.za 3.9.10-100.fc17.x86_64 #1 SMP Sun Jul 14 01:31:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux romeel

3 3

Animation of annotated projection plot
by Hao Wang 05 Aug '14

05 Aug '14

Hi all, I have been trying to make a movie out of annotated projection plots but encountered the following problem: ------------error message----------------------------- File "...../yt/src/yt-hg/yt/visualization/plot_modifications.py", line 1157, in _get_region LE[zax] = data.center[zax] - self.width*0.5 TypeError: 'NoneType' object has no attribute '__getitem__' -------------------------------------------------------------- I pasted the script (copied from the yt Cookbook) I used below. It worked fine without the "prj.annotate_particles(1.0)" line. The annotation itself works too -- the figure looks good in the IPython notebook. ======Script (anim.py)================================== import matplotlib.animation as anim from matplotlib.backends.backend_agg import FigureCanvasAgg from yt.mods import * prj = ProjectionPlot(load('DD0000/DD0000.hierarchy'), "z", 'Density') prj.annotate_particles(1.0) # adding this line causes error fig = prj.plots['Density'].figure fig.canvas = FigureCanvasAgg(fig) def animate(i): filename = './DD%04i/' % i + 'DD%04i' % i + '.hierarchy' pf = load(filename) prj._switch_pf(pf) density_ani = anim.FuncAnimation(fig, animate, frames=100, interval=100, blit=False) density_ani.save('density_animation.mp4') ==================== Could anyone point out the problem? Thanks in advance, Hao

2 1

Current branches post yt-3.0 and "yt update"
by Matthew Turk 05 Aug '14

05 Aug '14

Hi all, I wanted to write with a brief update on a few things. Now that yt-3.0 has been released, we have changed the way named branches work in the yt repository. * yt-2.x => This is what used to be the "yt" branch, and is legacy yt 2.x support. * yt-3.0 => This branch is deprecated, but not closed, and will not be undergoing regular updates * yt => This is the new development branch, which is now "yt 3.0" This will become yt 3.1. * stable => This is the stable branch (as before) which now corresponds to yt-3.0 stable releases. If you do not use the "yt update" functionality, you may disregard the remainder of this email. If you have been running yt 2.x, and want to stay on yt 2.x, you will need to make a one-time modification to your source directory. NOTE : ANY UNCOMMITTED CHANGES WILL BE WIPED OUT BY THIS COMMAND. 1) Activate your yt environment (typically via the activate script) 2) cd $YT_DEST/src/yt-hg 3) hg pull 4) hg up -C yt-2.x That will switch you to the yt-2.x branch. If you have been running yt 3.0, you will need to make a similar modification: 1) Activate your yt environment (typically via the activate script) 2) cd $YT_DEST/src/yt-hg 3) hg pull 4) hg up -C yt Hope that helps! -Matt

1 0

Loading gadget snapshot
by Jared Coughlin 04 Aug '14

04 Aug '14

Hello! I'm a grad student working with gadget, and someone told me today about version 3, which supports gadget! I have never used yt before, as it has never supported sph before, so if this is a really stupid question, please forgive me. I followed the bootcamp examples just fine, and then tried to load in a gadget snapshot (obtained from the sample datasets portion of yt's website) by doing yt.load("snapshot_010"). I got the following error: yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('snapshot_010',) {}, but could not load! Then I tried yt.load("snapshot_010", "gadget_binary"), but got the same error. Clearly, I am misunderstanding something very important here. I looked at the source and saw the GadgetBinaryFile class, so I know it can be done, I just can't figure out how. Very sorry for the bother. Any help would be greatly appreciated! Thank you very much! -Jared

4 4

Cutting region confusion
by Stephanie Tonnesen 04 Aug '14

04 Aug '14

Hi all, I am trying to get the total mass in a disk region of my simulation. I am using athena data and yt 2.7-dev. I thought I was defining the region in the same way using two methods: alld = pf.h.all_data() tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25","grid['z'] < 0.1925","grid['z'] > -0.1925","grid['cyl_Rcode'] < 1.2"]) disk = pf.h.disk([0.0,0.0,0.0],[0.0,0.0,1.0],1.2,0.385) tdp25 = disk.cut_region(["grid['specific_scalar[0]'] > 0.25"]) but when I print the total mass I get answers that differ by 10% print tracerp25.quantities["TotalQuantity"]("CellMassMsun") print tdp25.quantities["TotalQuantity"]("CellMassMsun") >>[8019047231.5192223] >>[8886968784.4710732] Can someone point out where my difference is? Thanks! Stephanie

4 6

updated to latest change set - now can't load gadget data
by Brendan Griffen 04 Aug '14

04 Aug '14

Hi, I just did: loadyt; cd $YT_DEST/src/yt-hg; hg pull http://bitbucket.org/MatthewTurk/yt-3.0; hg up; python2.7 setup.py build_ext -i I then did the following (which worked previously): pf = load(basepath+ext+'.0.hdf5') yt : [INFO ] 2014-08-04 14:11:07,101 Calculating time from 2.128e-02 to be 1.671e+15 seconds yt : [INFO ] 2014-08-04 14:11:07,102 Assuming length units are in Mpc/h (comoving) yt : [INFO ] 2014-08-04 14:11:07,102 Parameters: current_time = 1.67110631651e+15 yt : [INFO ] 2014-08-04 14:11:07,102 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2014-08-04 14:11:07,103 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-08-04 14:11:07,103 Parameters: domain_right_edge = [ 100. 100. 100.] yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: cosmological_simulation = 1 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: current_redshift = 45.999999479 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: omega_lambda = 0.6825 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: omega_matter = 0.3175 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: hubble_constant = 0.6711 yt : [INFO ] 2014-08-04 14:11:07,285 Allocating for 1.074e+09 particles yt : [INFO ] 2014-08-04 14:14:25,748 Identified 6.401e+07 octs yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Coordinates') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'ParticleIDs') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Potential') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Velocities') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Masses') to list of fields yt : [INFO ] 2014-08-04 14:14:26,095 Adding unknown field ('all', 'Potential') to list of fields --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /nfs/blank/h4231/bgriffen/data/lib/yt-x86_64/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where) 202 else: 203 filename = fname --> 204 __builtin__.execfile(filename, *where) /nfs/blank/h4231/bgriffen/work/projects/caterpillar/c2ray/code/submitcic/ytcic.py in <module>() ---> 59 rho_crit_0 = pf.cosmology.critical_density(0.) AttributeError: 'GadgetHDF5StaticOutput' object has no attribute 'cosmology' It seems the data has no attributes now? Brendan

2 3

ANN: yt-3.0 released!
by Matthew Turk 04 Aug '14

04 Aug '14

The yt community is proud to announce the release of yt 3.0. yt (http://yt-project.org) is an open source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical simulations and nuclear engineering simulations. This release of yt features an entirely rewritten infrastructure for data ingestion, indexing, and representation. While past versions of yt were focused on analysis and visualization of data structured as regular grids, this release features full support for particle (discrete point) data such as N-body and SPH data, irregular hexahedral mesh data, and data organized via octrees. This infrastructure will be extended in future versions for high-fidelity representation of unstructured mesh datasets. Highlighted changes in yt 3.0: * Units now permeate the code base, enabling self-consistent unit transformations of all arrays and quantities returned by yt. * Particle data is now supported using a lightweight octree. SPH data can be smoothed onto an adaptively-defined mesh using standard SPH smoothing * Support for octree AMR codes * Preliminary Support for non-Cartesian data, such as cylindrical, spherical, and geographical * Revamped analysis framework for halos and halo catalogs, including direct ingestion and analysis of halo catalogs of several different formats * Support for multi-fluid datasets and datasets containing multiple particle types * Flexible support for dynamically defining new particle types using filters on existing particle types or by combining different particle types. * Vastly improved support for loading generic grid, AMR, hexahedral mesh, and particle without hand-coding a frontend for a particular data format. * New frontends for ART, ARTIO, Boxlib, Chombo, FITS, GDF, Subfind, Rockstar, Pluto, RAMSES, SDF, Gadget, OWLS, PyNE, Tipsy, as well as rewritten frontends for Enzo, FLASH, Athena, and generic data. * First release to support installation of yt on Windows * Extended capabilities for construction of simulated observations, and new facilities for analyzing and visualizing FITS images and cube data * Many performance improvements This release is the first of several; while most functionality from the previous generation of yt has been updated to work with yt 3.0, it does not yet have feature parity in all respects. While the core of yt is stable, we suggest the support for analysis modules and volume rendering be viewed as a late-stage beta, with a series of additional releases (3.1, 3.2, etc) appearing over the course of the next year to improve support in these areas. For more information, including installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt-3.0 at http://yt-project.org/docs/3.0 yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. yt 3.0 features contributions from over 60 individuals, constituting almost 5000 commits. For many contributors, this is the first release featuring their work. Please forward this announcement on to any interested parties, and look for information soon about upcoming workshops focused on yt and applying it to your data. Thank you,

1 0

units error in cloud-in-cell construction in yt
by Brendan Griffen 04 Aug '14

04 Aug '14

Hi, I've been trying to construct a CiC mesh but couldn't get an answer comparable with theory for the mean density of the mesh yt gave me. I've put all the relevant code and output in a pastebin here: http://pastebin.com/hbVM0rYN I've spoken with Britton Smith and he thinks the physical size of the mesh might be wrong by a factor of (1+z) which translates to the densities all being off by (1+z)^3. There also seems to be a missing h**3 somewhere which brings everything in "rough" alignment. I've run it for two redshifts z = 46 and z = 0 and put the output in the above pastebin. I've added a correction where I forcefully put /(1+z)^3 term at the end and it gives reasonable results. I've also added another two values including the missing /h**3 term. Can this be corrected or can someone tell me where I went wrong in what I'm doing? Thanks! Brendan

3 2

critical density calculation from yt
by Brendan Griffen 02 Aug '14

02 Aug '14

Hi, I'm using the cosmology.critical_density(z) calculation from yt and I was wondering what is the exact type of critical density? Is it baryon critical density? That is what I need. Thanks. Brendan

2 1