Mailman 3 October 2015 - yt-users

B_div in enzo
by Cynthia Saad (Student) 07 Oct '15

07 Oct '15

Hello all, I am using enzo for 3d mhd collapse. I need to check conservation of divB=0. So i turned on BAnyl in the parameter file. Now i need to use yt for B_Div. And i'm having trouble doing so. I tried using phaseplot, but it says could not find field B_Div. One more question how may i load several data files in the same .py script? Thank you so much for taking the time to reply! Your input is really needed and mch appreciated. Cynthia Saad

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What does create_profile do?
by Yuan Li 07 Oct '15

07 Oct '15

Hi all, I have a really basic dumb question: what does yt do when it creates a profile? For example, if I do this: prof=yt.create_profile(sp,"radius",["temperature"], accumulation=False,n_bins=n_bins,weight_field="ones") Is prof["temperature"].value the arithmetic average of the temperatures of all the cells within each radius bin? The reason why I ask is because when I create a profile plot of "CoolingRate" (my derived field) using yt, and compare that with the one I create with tracer particles, they look different at low temperatures. Since I put one particle in the center of each cell, I assume that the two methods should give the same results. Did I make a silly mistake somewhere or does yt do some sort of smoothing to the data? Thank you! Yuan

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RadMC3DWriter and Ramses data
by Marc Schartmann 06 Oct '15

06 Oct '15

Dear all, I am trying to export the density distribution from a RAMSES run to RADMC-3D using RadMC3DWriter. Whereas the example with the “StarParticle” data set works perfectly, it fails for any RAMSES data I tried (e.g. the “ramses_mhd_amr” one). Below is the output, complaining about a missing attribute in the RAMSES frontend. I am not a yt expert, any help with how to fix this would be appreciated. Thanks a lot. Best wishes, Marc >>> writer = RadMC3DWriter(ds) yt : [INFO ] 2015-10-05 14:20:04,236 Loading field plugins. yt : [INFO ] 2015-10-05 14:20:04,237 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-10-05 14:20:04,237 Loaded astro (15 new fields) yt : [INFO ] 2015-10-05 14:20:04,237 Loaded cosmology (22 new fields) yt : [INFO ] 2015-10-05 14:20:04,238 Loaded fluid (63 new fields) yt : [INFO ] 2015-10-05 14:20:04,238 Loaded fluid_vector (95 new fields) yt : [INFO ] 2015-10-05 14:20:04,239 Loaded geometric (111 new fields) yt : [INFO ] 2015-10-05 14:20:04,239 Loaded local (111 new fields) yt : [INFO ] 2015-10-05 14:20:04,239 Loaded magnetic_field (119 new fields) yt : [INFO ] 2015-10-05 14:20:04,239 Loaded my_plugins (119 new fields) yt : [INFO ] 2015-10-05 14:20:04,239 Loaded species (121 new fields) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py", line 148, in __init__ sorted_grids = sorted(ds.index.grids, key=lambda x: x.Level) AttributeError: 'RAMSESIndex' object has no attribute 'grids'

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Issue regarding Volume Rendering
by Reju Sam John 06 Oct '15

06 Oct '15

Hi all, I am trying to do some volume rendering with the following script. tf = yt.ColorTransferFunction((-29, -24)) tf.add_layers(4, w=0.01) cam = ds.camera([5.020844896e-01, 4.934331785e-01, 4.921018057e-01], [0.0, 0.0, 1.0], (20, 'Mpc'), 640, tf, fields=["density"], log_fields="False", no_ghost=False) image = cam.snapshot(fn="density_vol_"+fn_i+".png") cam.save_image(image, clip_ratio=4, transparent=False) cam.show(clip_ratio=4) But the problem is that the image saved using cam.save_image() is different from the one displayed by cam.show(clip_ratio=4) Displayed image using cam.show(clip_ratio=4) download.png <https://drive.google.com/file/d/0B6l5iRWTUbHWa054VDVNOFY1bGpqVklqYlA3ZEhzaz…> Saved image using cam.save_image() density_vol_10.png <https://drive.google.com/file/d/0B6l5iRWTUbHWUmhXVGZfY0xiMXBGUW81Szh0LU0yZF…> Why this is happening ? How to save the same image as of displayed one? Thank you Reju Sam John -- Reju Sam John

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interactive yt
by Guido granda muñoz 05 Oct '15

05 Oct '15

Hello, I have installed yt in a cluster and something is wrong with the ineteractive yt. This is what I got: iyt ^C Traceback (most recent call last): File "/home/guidomunoz/yt-x86_64/bin/iyt", line 6, in <module> exec(compile(open(__file__).read(), __file__, 'exec')) File "/home/guidomunoz/yt-x86_64/src/yt-hg/scripts/iyt", line 56, in <module> display_banner = True) File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/terminal/interactiveshell.py", line 328, in __init__ **kwargs File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 465, in __init__ self.init_history() File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 1521, in init_history self.history_manager = HistoryManager(shell=self, parent=self) File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 490, in __init__ **traits) File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 184, in __init__ self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 92, in catch_corrupt_db self.init_db() File "<string>", line 2, in init_db File "/home/guidomunoz/yt-x86_64/lib/python2.7/site-packages/IPython/core/history.py", line 85, in catch_corrupt_db return f(self, *a, **kw) KeyboardInterrupt How can I solve ths]is problem? Thanks, -- Guido

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Re: [yt-users] yt-users Digest, Vol 92, Issue 1
by Professor Maller 01 Oct '15

01 Oct '15

Also if your issue is just that you only want the prompt when you are using yt you can just execute deactivate which will stop the prompt and the yt environment. You will then have to activate it again when you want yt to work. Ari On Thu, Oct 1, 2015 at 1:48 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. how to remove (yt-x86_64) prefix? (Tianyu Liu) > 2. Re: how to remove (yt-x86_64) prefix? (Michael Zingale) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 30 Sep 2015 21:20:26 -0400 > From: Tianyu Liu <kingcrimsontianyu(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] how to remove (yt-x86_64) prefix? > Message-ID: <560C8A5A.80605(a)gmail.com> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear forum, > I'm a new user (yt age: 1 day).Since the file [install_dir]/bin/activate > was sourced, I have seen``(yt-x86_64)'' prepended to every single line > of my bash shell. May Iknow how to remove it?Thanks. > -- > > Best regards, > Tianyu Liu > > Ph.D., Nuclear Engineering and Science > Computer Scientist of Department of Mechanical, Aerospace, and Nuclear > Engineering (MANE) > Rensselaer Radiation Measurement and Dosimetry Group (RRMDG) > <http://www.rpi.edu/dept/radsafe/public_html/index.htm> > Rensselaer Polytechnic Institute (RPI) > Room 1-18, NES Building, 3021 Tibbits Ave. > Troy, NY 12180, USA > Personal website: http://tianyuliukingcrimson.wordpress.com > > /The rusted chains of prison moons are shattered by the sun. > I walk a road, horizons change, the tournament's begun. > The purple piper plays his tune, the choir softly sing; > Three lullabies in an ancient tongue, for the court of the crimson king. > / > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Wed, 30 Sep 2015 21:26:37 -0400 > From: Michael Zingale <michael.zingale(a)stonybrook.edu> > To: liut10(a)rpi.edu, Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] how to remove (yt-x86_64) prefix? > Message-ID: > <CAGO1_wqd-H9A0+1= > NUwEfoOPUHNWZpbFpeYWyjjQ9FApnH3UNA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > looking at the script, it seems that if you > define VIRTUAL_ENV_DISABLE_PROMPT=1 it will not change your prompt. > > You could also always just reset the prompt (the PS1 environment variable) > > On Wed, Sep 30, 2015 at 9:20 PM, Tianyu Liu <kingcrimsontianyu(a)gmail.com> > wrote: > > > Dear forum, > > I'm a new user (yt age: 1 day). Since the file > [install_dir]/bin/activate was > > sourced, I have seen ``(yt-x86_64)'' prepended to every single line of my > > bash shell. May I know how to remove it? Thanks. > > -- > > > > Best regards, > > Tianyu Liu > > > > Ph.D., Nuclear Engineering and Science > > Computer Scientist of Department of Mechanical, Aerospace, and Nuclear > > Engineering (MANE) > > Rensselaer Radiation Measurement and Dosimetry Group (RRMDG) > > <http://www.rpi.edu/dept/radsafe/public_html/index.htm> > > Rensselaer Polytechnic Institute (RPI) > > Room 1-18, NES Building, 3021 Tibbits Ave. > > Troy, NY 12180, USA > > Personal website: <http://tianyuliukingcrimson.wordpress.com> > > http://tianyuliukingcrimson.wordpress.com > > > > > > > > > > *The rusted chains of prison moons are shattered by the sun. I walk a > > road, horizons change, the tournament's begun. The purple piper plays his > > tune, the choir softly sing; Three lullabies in an ancient tongue, for > the > > court of the crimson king. * > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > -- > 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 > github: http://github.com/zingale > -------------- 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 92, Issue 1 > *************************************** >

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how to remove (yt-x86_64) prefix?
by Tianyu Liu 01 Oct '15

01 Oct '15

Dear forum, I'm a new user (yt age: 1 day).Since the file [install_dir]/bin/activate was sourced, I have seen``(yt-x86_64)'' prepended to every single line of my bash shell. May Iknow how to remove it?Thanks. -- Best regards, Tianyu Liu Ph.D., Nuclear Engineering and Science Computer Scientist of Department of Mechanical, Aerospace, and Nuclear Engineering (MANE) Rensselaer Radiation Measurement and Dosimetry Group (RRMDG) <http://www.rpi.edu/dept/radsafe/public_html/index.htm> Rensselaer Polytechnic Institute (RPI) Room 1-18, NES Building, 3021 Tibbits Ave. Troy, NY 12180, USA Personal website: http://tianyuliukingcrimson.wordpress.com /The rusted chains of prison moons are shattered by the sun. I walk a road, horizons change, the tournament's begun. The purple piper plays his tune, the choir softly sing; Three lullabies in an ancient tongue, for the court of the crimson king. /

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