Mailman 3 March 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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problem with fields that use ghost zones
by Britton Smith 29 May '12

29 May '12

Hi everyone, I'm having a problem using fields that use ghost zones. The following simple script: http://paste.yt-project.org/show/2010/ gives this error: http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/ I am working from the tip, but I get the same behavior from yt/2.3. In yt/2.2, everything is working. I am working now to narrow that range down a bit, but does anyone have an idea? Britton

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Csh environment setting bug
by Alice Coucke 27 Mar '12

27 Mar '12

Hello everyone, It looks like there is a bug with the csh environment setting. I am a Unix beginner so I might have done an error. I had to make these modifications to the install script to set up yt in a csh shell OSX Lion machine : * Disable the install of zlib. The HDF5 build failed because of some sort of version confusion. * Force the use of gcc over the newer clang compiler by setting : export CC=gcc at the top of the install script. Matplotlib-1.1.0 fails to compile with the default Lion cc which is clang based. Once installed, I had difficulties to run it. I tried to follow the Extremely Simple Data Inspection. $ yt stats $YT_DEST/src/yt-hg/tests/DD0010/moving7_0010 BUT that is what happens : yt : [ERROR ] 2012-03-23 11:17:08,651 Couldn't figure out output type for /Users/acoucke/yt-i386:/src/yt-hg/tests/DD0010/moving7_0010 Traceback (most recent call last): File "/Users/acoucke/yt-i386/bin/yt", line 9, in <module> load_entry_point('yt==2.3', 'console_scripts', 'yt')() File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 1610, in run_main sys.exit(YT.main()) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 257, in main return self.cmd(args) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd retval = self.onecmd(argv) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd return self._dispatch_cmd(handler, argv) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd return handler(argv[0], opts, *args) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 256, in arg_iterate func(self, subcmd, opts, arg) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 627, in do_stats pf = _fix_pf(arg) File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 44, in _fix_pf raise IOError IOError Then if I type : $ echo $YT_DEST /Users/acoucke/yt-i386: It seems that there is an unexpected colon here because : $ ls /Users/acoucke/yt-i386: ls: /Users/acoucke/yt-i386:: No such file or directory I have to use : setenv YT_DEST /Users/acoucke/yt-i386 to make that works. Best, Alice Coucke

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yt in macports
by erosenblum 26 Mar '12

26 Mar '12

Hi all, I tried using macports to install yt and ran into a couple of issues. First, there was a conflict because I had hdf5 installed to use flash and yt required hdf5-18. Secondly, after uninstalling hdf5 to see what would happen, I received these errors: Error: Checksum (md5) mismatch for yt-2.2.tar.gz Error: Checksum (sha1) mismatch for yt-2.2.tar.gz Error: Checksum (rmd160) mismatch for yt-2.2.tar.gz Error: Target org.macports.checksum returned: Unable to verify file checksums Error: Status 1 encountered during processing. Any ideas? Thanks! Erica

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error "Zero-length selections are not allowed"
by Jean-Claude Passy 26 Mar '12

26 Mar '12

Hi everyone, I get an error when executing the simple script below: ------------------------------------------------------------------------------ from yt.mods import * output = 'DD0010/data0010' pf = load(output) region = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.0],[1.0,1.0,1.0]) ------------------------------------------------------------------------------ I have pasted the output there: http://paste.yt-project.org/show/awqlzVK7mAhtiIVihFfC/ I think the problem is that my simulation has only 2 particles (no gas) and both particles are in subgrids so the root grid is empty: ------------------------------------------------------------------------------ [19:46:54] Obiwan:$ h5ls DD0010/data0010.cpu0000 Grid00000001 Group Grid00000002 Group Metadata Group [19:47:09] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000001 [19:47:15] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000002 particle_index Dataset {2} particle_mass Dataset {2} particle_position_x Dataset {2} particle_position_y Dataset {2} particle_position_z Dataset {2} particle_type Dataset {2} particle_velocity_x Dataset {2} particle_velocity_y Dataset {2} particle_velocity_z Dataset {2} ------------------------------------------------------------------------------ I would really appreciate if someone could help me to fix this. Thanks a lot, JC

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matpltolib warning at start
by Jean-Claude Passy 26 Mar '12

26 Mar '12

Hi everyone, nothing dramatic but I get a warning when I start iyt: --------------------------------------------------------------------------------------------------------------------- [19:25:12] lattice:$ iyt /home/jcpassy/yt-x86_64/lib/python2.7/site-packages/matplotlib/__init__.py:908: UserWarning: This call to matplotlib.use() has no effect because the the backend has already been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot, or matplotlib.backends is imported for the first time. if warn: warnings.warn(_use_error_msg) Welcome to pylab, a matplotlib-based Python environment [backend: agg]. For more information, type 'help(pylab)'. ================== | Welcome to yt! | ================== --------------------------------------------------------------------------------------------------------------------- I did not get this problem before I updated to the most recent changeset, and I reproduced the warning on two different Linux machines. If anyone has an idea about how to get rid of it, please let me know. Cheers, JC

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particle_mass
by Ali Snedden 23 Mar '12

23 Mar '12

Hello, I was trying to get the position and mass information for the dark matter (and stellar) particles in an Enzo simulation. I have tried a couple of different ways and I was curious about the units on the following method. In this case I am presumably accessing the dark matter particles (particle_type = 1) *from yt.mods import ** *pf = load("DD0252/DD0252")* *array = pf.h.find_particles_by_type(ptype=1, max_num=3)* *print "(%.5f, %.5f, %.5f) = %f\n" %(array['particle_position_x'][0], array['particle_position_y'][0], array['particle_position_z'][0], array['particle_mass'][0])* This returns *(0.01055, 0.01873, 0.00224) = 0.835448. *What are the mass units on the *0.835448*? I don't think that they are cgs, and there doesn't appear to be a conversion factor available via pf[' * ']. If I continue and enter *print pf.field_info['Density'].get_units()* *print pf.field_info['particle_mass'].get_units()* * * The 'Density' line returns *\rm{g}/\rm{cm}^3, *but the 'particle_mass' line returns nothing. So I can't get the units from here. I can, however, access the same particle (or at least a particle at the same location) by using *from yt.mods import ** *pf = load("DD0252/DD0252")* *dd = pf.h.all_data()* *print "(%f %f %f) = %f Msun, ptype= %i\n"%(dd["particle_position_x"][0], dd["particle_pos ition_y"][0], dd["particle_position_z"][0], dd["ParticleMassMsun"][0],dd["particle_type"][0])* Which returns *(0.010554 0.018727 0.002239) = 82255596.670652 Msun, ptype= 1* This seems to give reasonable values. Both methods should be equivalent ways of to access the particle (both stellar and dark matter) data, correct? So how do I get my units in solar masses when using * pf.h.find_particles_by_type()*? Thanks for your time! ~ali

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help
by Nicholas David Tillman 23 Mar '12

23 Mar '12

This is my first time using yt so bear with me please... Every time I try to upload a file as FLASH, I get an error message saying that it couldn't figure out the output type. I even went back and tried using a sample file, still got the same error message. Thanks, Nick

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opaqueness of iso-surface
by Renyue Cen 22 Mar '12

22 Mar '12

Hi, For iso-density surface I have a primitive question: how do I make certain contour level totally opaque? I can do " tf.add_gaussian(-25.5, 0.05, [1.0, 0, 0, 1.0])" but specifying alpha=1.0 in this example does not seem to make that level (red) totally opaque. Thanks, Renyue

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