Mailman 3 October 2011 - 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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in-situ visualization possible with yt?
by Matthieu Dorier 09 Nov '11

09 Nov '11

Hello, I'm trying to make in-situ visualization available for a simulation, and I'm considering different softwares for that (VisIt, YT,...). I've never used YT, so my question is: is it possible to add some code in a simulation (written in C++) to have some kind of distributed rendering engine using YT, just like VisIt does with code-instrumentation? Thanks, Matthieu -- Matthieu Dorier ENS Cachan, antenne de Bretagne Département informatique et télécommunication http://perso.eleves.bretagne.ens-cachan.fr/~mdori307/wiki/

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multi-field volume projection?
by Stephen Skory 31 Oct '11

31 Oct '11

Hi all, I may be asking something that is obvious to others, but it's not to me. It is it possible to have more than one data field displayed in a single volume projection image? Say, each with a different color map? If so, how? Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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field parameters and extract_connected_sets
by Elizabeth Tasker 26 Oct '11

26 Oct '11

Hi, Is there a way of passing field parameters to extract_connected_sets? Currently, print dd["NegEscapeVelocity"] works fine but contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0, maxv, log_space=False) complains it can't find the set field variables. Elizabeth

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Enzo 2.1 Public Release
by Christine Simpson 18 Oct '11

18 Oct '11

Enzo 2.1 Oct. 17, 2011 We are proud to announce the public release of Enzo version 2.1. New with this release is an extensive answer testing facility, additional physics capabilities, and AMR performance enhancements. New physics capabilities include isotropic and anisotropic heat conduction, X-ray ionization/heating, massive black hole particles, 4th-order accurate gravity solver, distributed stellar feedback, shock tracking, and improved molecular hydrogen chemistry. Performance improvements include Hilbert curve dynamic load balancing, faster ray tracing, and ray merging. We have improved Enzo’s inline analysis using the yt project, as well as user documentation for the entire Enzo codebase. We have also simplified the generation of multi-mesh cosmological initial conditions. In addition to code upgrades, we have upgraded and reorganized our online repositories and documentation. The Enzo Project’s main website is now http://enzo-project.org/ . Links and information can be found here for both developers and general users. Our stable releases will continue to live on our Google code website: http://code.google.com/p/enzo/ . Users can clone a mercurial repository of our stable release code or download a tarball of the code (http://code.google.com/p/enzo/downloads/list ). A simple quick-start guide can also be found here: http://code.google.com/p/enzo/wiki/EnzoBootCamp . We will now support versioned documentation for all stable releases since Enzo 2.0 in addition to the development code on enzo-project.org. The documentation for Enzo 2.1 is located here: http://enzo-project.org/docs/2.1/. Development will now move to our new Bitbucket repository where all users are encouraged to make contributions to the code by forking the main repository, located at https://bitbucket.org/enzo/enzo-dev . An explanation of new developer guidelines can be found here: http://enzo-project.org/docs/2.1/developer_guide/index.html . The current release of Enzo 2.1 features contributions, bug fixes and enhancements from an additional ten individuals (over the course of 2700 changesets) since Enzo 2.0, and through our new development infrastructure we are expanding our ability to solicit and review contributions. Main website: http://enzo-project.org/ Mailing List: https://groups.google.com/forum/#!forum/enzo-users Stable repository: http://code.google.com/p/enzo/ Tarball of Enzo 2.1.0: http://code.google.com/p/enzo/downloads/list Enzo Boot Camp (a quick-start guide): http://code.google.com/p/enzo/wiki/EnzoBootCamp Enzo 2.1.0 documentation: http://enzo-project.org/docs/2.1/ Developer’s repository: https://bitbucket.org/enzo/enzo-dev/overview Developer’s guidlines: http://enzo-project.org/docs/2.1/developer_guide/index.html The Enzo Development Team

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Smooth ENZO datacube to lower resolution
by Anthony Harness 13 Oct '11

13 Oct '11

I have a 1536^3 ENZO datacube that I want to smooth to essentially become a 512^3 datacube. I want to be able to still use the datacube to do further analysis with yt, so I need the format of the data not to change. I only need to smooth the data of 3 fields, but I need to keep the Derived Quantities and parallel capabilities of yt. Is there any yt implementation that can do this or any other suggestions? Thanks, Anthony

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Installing YT to co-exist with existing Python packages
by Sam Geen 13 Oct '11

13 Oct '11

Hi, I don't know how widely this has been discussed (sorry if it has and I've just missed it), but how easy would it be to install YT such that it interacts with my existing Python packages? Is the easiest thing simply to re-install everything to the YT directory and re-update the PYTHONPATH environment variable for any packages not in the default Python path, or is there a better way to allow YT and my existing Python packages to co-exist without activating/deactivating YT? Thanks! Sam

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trouble with callback on phase plot
by Christine Simpson 03 Oct '11

03 Oct '11

Hi all, I'm having trouble adding text through a callback onto a phase plot. I tried this code: pc.add_phase_sphere(r200[j],'kpc',["Density","Temperature","CellMassMsun"],weight = None) pc.set_zlim(1.0e-2,1.0e5) pc.set_xlim(1.0e-30,5.0e-19) pc.set_ylim(10.0,1.0e7) pc.plots[-1].modify["text"]([0.92,0.92],redshift_string) pc.save("output_%(file_num)s_branch_%yt-users(a)lists.spacepope.org(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) And I get this error: Traceback (most recent call last): File "test_phase_plots.py", line 41, in <module> pc.save("output_%(file_num)s_branch_%(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 157, in save override=override, force_save=force_save)) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 108, in save_image self._redraw_image() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 903, in _redraw_image self._run_callbacks() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 800, in _run_callbacks cb(self) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 910, in __call__ y = plot.image._A.shape[1] * self.pos[1] IndexError: tuple index out of range The error arises in the save command, but the problem only happens when I add the modify["text"] command. Any ideas? Christine

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Re: [yt-users] log-linear phase plot (David Collins)
by Wolfram Schmidt 03 Oct '11

03 Oct '11

Hi Dave, thanks a lot, setting y_log=False does the trick! Wolfram > ------------------------------ > > Message: 3 > Date: Fri, 30 Sep 2011 16:32:58 -0600 > From: David Collins <dcollins(a)physics.ucsd.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] log-linear phase plot > Message-ID: > <CAGva0oysAaoEf8cPXxCevTtJqjcQX55n15Bixsx2WPMFD3TzXQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > I've run into this as well. I believe you need to give > add_phase_object the log value by hand, with > > x_log=False > > Cheers, > d. > > On Fri, Sep 30, 2011 at 3:52 PM, Geoffrey So <gsiisg(a)gmail.com> wrote: >> Just wondering, if FieldOne is already logged, do you still want the limits >> to encompass 1 to 1e10, have you tried something like (1e9,1e10) ? >> From >> G.S. >> >> On Fri, Sep 30, 2011 at 2:37 PM, Wolfram Schmidt >> <schmidt(a)astro.physik.uni-goettingen.de> wrote: >>> >>> Hi everyone, >>> >>> I defined two fields, say, FieldOne and FieldTwo, to make 2D phase plot. >>> FieldOne is logarithmic by default, FieldTwo is linear (i.e., I set >>> take_log=False in add_field). >>> >>> I want to produce a phase plot with logarithmic bins for FieldOne and >>> linear bins for FieldTwo, where the range of FieldTwo is [-10,10] >>> >>> I thought that >>> >>> pc.add_phase_object(dd, ["FieldOne", "FieldTwo", "CellMass"], weight=None, >>> x_bins=100,y_bins=100, \ >>> ? ? ? ? ? ? ? ? ? ?x_bounds=[1e0,1e10], y_bounds=[-10,10]) >>> >>> might do the job, but ?yt returns the error message: >>> >>> Warning: invalid value encountered in log10 >>> yt : [ERROR ? ?] 2011-09-30 16:55:05,610 Your min/max values for x, y have >>> given me a nan. >>> yt : [ERROR ? ?] 2011-09-30 16:55:05,610 Usually this means you are asking >>> for log, with a zero bound. >>> Traceback (most recent call last): >>> ?File "stability.py", line 352, in <module> >>> ? ?x_bounds=[1e0,1e10], y_bounds=[-10,10]) >>> ?File >>> "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/visualization/plot_collection.py", >>> line 1149, in add_phase_object >>> ? ?lazy_reader) >>> ?File >>> "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/data_objects/profiles.py", >>> line 408, in __init__ >>> ? ?raise ValueError >>> ValueError >>> >>> It appears that add_phase_object treats FieldTwo logarithmically, although >>> it is linear. >>> >>> So how can I do a log-linear phase plot? >>> >>> Best, >>> Wolfram >>> _______________________________________________ >>> yt-users mailing list >>> yt-users(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > >

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yt-users October 2011