Mailman 3 November 2017 - yt-users

Readline on Pleiades
by David Collins 22 Nov '17

22 Nov '17

Hi, Everybody! I'm running yt on Pleiades, and I'm running into a readline error (below) Has anyone else run into this, and do you know what I can do to fix this? This is a recent build, not from source. Thanks! pleiades:~/yt3_scripts>python Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Traceback (most recent call last): File "/etc/pythonstart", line 7, in <module> import readline ImportError: /u/dccolli1/local-yt-2017-09-28/yt-conda/lib/python2.7/lib- dynload/../../libreadline.so.6: undefined symbol: PC >>> -- -- Sent from a computer.

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ANN: Trident CGM/IGM Analysis Code v1.1 Released
by Cameron Hummels 19 Nov '17

19 Nov '17

On behalf of the Trident development team, I am happy to announce a new stable release of Trident, a python-based code suite for analyzing astrophysical hydro simulations to investigate the CGM/IGM and produce synthetic absorption spectra. This release is accompanied by a shift in development from mercurial/bitbucket to git/github, continuous integration and testing with travis, and a number of bugfixes and additional features. Our changelog (below) has a full description of the changes in this version. Full installation instructions are available in our documentation, as are instructions for a number of common use cases in working with your datasets: e.g., adding arbitrary ion fields, making column density maps, calculating column densities of individual sightlines, generating absorption line spectra. There has also been recent development in the yt community to treat particle-based datasets more natively rather than by depositing to a grid and then processing. This effort, nicknamed "*demeshening*", is being led by Nathan Goldbaum, Meagan Lang, and Matt Turk, with Trident contributions by Bili Dong and myself. Not only does it get more accurate results, but it is faster and uses less memory since particle fields don't need to be deposited to a global grid. This code is now in beta, and users are encouraged to use it and give bug reports. There are full instructions for installation of it available in the Trident docs, and we expect the next stable release of Trident will incorporate it. Please don't hesitate to contact the mailing list with any questions or problems you may encounter with the code, and I encourage you to share this announcement with other scientists who may be interested in using Trident. *Trident Page:* http://trident-project.org *Trident Code:* https://github.com/trident-project/trident/ *Trident Docs:* https://trident.readthedocs.io/en/latest/ *Trident Paper*: http://adsabs.harvard.edu/abs/2017ApJ...847...59H *Changelog to Trident 1.1:* https://trident.readthedocs.io/en/latest/changelog.html *Installation Docs for beta "demeshened" yt and Trident:* https://nbviewer.jupyter.org/url/trident-project.org/notebooks/trident_deme… --The Trident Developer Team: Cameron Hummels Britton Smith Devin Silvia Matthew Turk Nathan Goldbaum Kacper Kowalik Lauren Corlies Bili Dong Hilary Egan Clayton Strawn -- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org

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how to add halo quantity
by Daegene Koh 17 Nov '17

17 Nov '17

Hi all, I’m trying to add a new quantity to a halo catalog following the docs as such, 23 def _total_mass(halo): 24 gasmass, dmmass = halo.data_object.quantities.total_mass() 25 return gasmass+dmmass 26 27 add_quantity('total_mass',_total_mass) 28 hc.add_quantity('total_mass’) however, it seems at add_quantity is not defined. How do I go about doing this? Cheers, DK

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Re: [yt-users] yt-users Digest, Vol 117, Issue 22
by Matias Enrique Suazo Campos 15 Nov '17

15 Nov '17

Thanks Everybody!!! There was no problem after all :P I hope this to be useful for someone else. Matías Suazo, MSc student at Universidad de Chile 2017-11-14 17:42 GMT-03:00 <yt-users-request(a)lists.spacepope.org>: > 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: Projection (Jos? Mauricio Utreras) > 2. Re: Projection (Nathan Goldbaum) > 3. Re: Projection (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Nov 2017 15:45:23 -0300 > From: Jos? Mauricio Utreras <jutreras(a)ug.uchile.cl> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Projection > Message-ID: > <CANhQbF5OzXEhNzguuXR8iNRrAryy74iQ=sVg8zZg5QCzyzqvJg@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi everyone, > > I got the same result using the IsolatedGalaxy dataset > > ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc')) > proj=ds.proj('density',axis='z',weight_field='density', > data_source=disk,method='integrate') > proj['density'] > >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3 > > 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>: > > Can I get one of you to open an issue? > > > > https://github.com/yt-project/yt/issues/new > > > > If you can, please include a script to reproduce the problem, making use > of > > one of the public datasets on yt-project.org/data. > > > > -Nathan > > > > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick > > <aje2123(a)columbia.edu > >> wrote: > > > >> Hello Matias and Nathan, > >> > >> I was able to reproduce this error on my own Enzo data set(s) using > >> similar code. I did a little more playing around and it looks like it > >> only > >> breaks when having a weight_field. weight_field = None seems to be O.K. > . > >> It also occurs for the "region" objects, in addition to the disk. > >> Interestingly, as Matias pointed out, doing something like this works: > >> > >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0]) > >> proj=ds.proj('density',axis='z',weight_field='density',data_ > >> source=region,method='integrate') > >> > >> but this does not: > >> > >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] ) > >> proj =ds.proj('density',axis='z',weight_field='density',data_ > >> source=region,method='integrate') > >> > >> In short, this indeed appears to be a bug, and possibly not specific to > a > >> single dataset. > >> > >> > >> > >> > >> Andrew > >> > >> > >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum < > nathan12343(a)gmail.com> > >> wrote: > >> > >>> This sounds like a bug. I don't think you should ever get back NaNs > from > >>> a projection operation. > >>> > >>> Is there any chance you can share the dataset that's triggering this > >>> behavior? > >>> > >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos < > >>> matias.suazo(a)ug.uchile.cl> wrote: > >>> > >>>> Dear YT users, > >>>> > >>>> I'm trying to make a density projection, in the following lines I show > >>>> you the lines that I have. > >>>> > >>>> #Ramses output > >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap) > >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc')) > >>>> proj=ds.proj('density',axis='z',weight_field='density',data_ > >>>> source=disk,method='integrate') > >>>> > >>>> However when I print proj["density"] I get a list of nan, however when > >>>> I > >>>> use the whole domain as my data_source I get reasonable numbers. > >>>> > >>>> Thanks, > >>>> Mat?as Suazo > >>>> MSc student at Universidad de Chile > >>>> > >>>> _______________________________________________ > >>>> 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 > >>> > >>> > >> > >> > >> -- > >> NSF Graduate Fellow > >> Columbia University > >> Department of Astronomy > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 Nov 2017 13:04:04 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Projection > Message-ID: > <CAJXewOm3f91Z66L8WPYZ3ztnVx=BPaKAO9FuZ1Lq28qJZHNVZg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Ah, so this isn't actually a bug. There's even a comment in the code > indicating that this is the intended behavior: > > https://github.com/yt-project/yt/blob/master/yt/data_ > objects/construction_data_containers.py#L373 > > So the choices about what to do here are, in my opinion: > > * Change this behavior to fill the array with zeros instead of NaNs > * Improve the documentation to make this choice clearer > > I'm not sure offhand what is the best approach, especially given that > changing this behavior would be a backward compatibility break. > > For the original question: your data aren't all NaNs I suspect. E.g. take a > look at this example script: > > import yt > import numpy as np > ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc')) > proj = ds.proj('density', axis='z', weight_field='density', > data_source=disk, > method='integrate') > dens_proj = proj['density'] > print(dens_proj[np.isfinite(dens_proj)]) > print(np.nanmax(dens_proj)) > print(np.nanmin(dens_proj)) > > Which prints out values in regions where the projection isn't filled with > NaNs. > > > On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras < > jutreras(a)ug.uchile.cl> wrote: > > > Hi everyone, > > > > I got the same result using the IsolatedGalaxy dataset > > > > ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > > disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc')) > > proj=ds.proj('density',axis='z',weight_field='density', > > data_source=disk,method='integrate') > > proj['density'] > > >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3 > > > > 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>: > > > Can I get one of you to open an issue? > > > > > > https://github.com/yt-project/yt/issues/new > > > > > > If you can, please include a script to reproduce the problem, making > use > > of > > > one of the public datasets on yt-project.org/data. > > > > > > -Nathan > > > > > > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick > > > <aje2123(a)columbia.edu > > >> wrote: > > > > > >> Hello Matias and Nathan, > > >> > > >> I was able to reproduce this error on my own Enzo data set(s) using > > >> similar code. I did a little more playing around and it looks like it > > >> only > > >> breaks when having a weight_field. weight_field = None seems to be > O.K. > > . > > >> It also occurs for the "region" objects, in addition to the disk. > > >> Interestingly, as Matias pointed out, doing something like this works: > > >> > > >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0]) > > >> proj=ds.proj('density',axis='z',weight_field='density',data_ > > >> source=region,method='integrate') > > >> > > >> but this does not: > > >> > > >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] ) > > >> proj =ds.proj('density',axis='z',weight_field='density',data_ > > >> source=region,method='integrate') > > >> > > >> In short, this indeed appears to be a bug, and possibly not specific > to > > a > > >> single dataset. > > >> > > >> > > >> > > >> > > >> Andrew > > >> > > >> > > >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum < > > nathan12343(a)gmail.com> > > >> wrote: > > >> > > >>> This sounds like a bug. I don't think you should ever get back NaNs > > from > > >>> a projection operation. > > >>> > > >>> Is there any chance you can share the dataset that's triggering this > > >>> behavior? > > >>> > > >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos < > > >>> matias.suazo(a)ug.uchile.cl> wrote: > > >>> > > >>>> Dear YT users, > > >>>> > > >>>> I'm trying to make a density projection, in the following lines I > show > > >>>> you the lines that I have. > > >>>> > > >>>> #Ramses output > > >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap) > > >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc')) > > >>>> proj=ds.proj('density',axis='z',weight_field='density',data_ > > >>>> source=disk,method='integrate') > > >>>> > > >>>> However when I print proj["density"] I get a list of nan, however > when > > >>>> I > > >>>> use the whole domain as my data_source I get reasonable numbers. > > >>>> > > >>>> Thanks, > > >>>> Mat?as Suazo > > >>>> MSc student at Universidad de Chile > > >>>> > > >>>> _______________________________________________ > > >>>> 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 > > >>> > > >>> > > >> > > >> > > >> -- > > >> NSF Graduate Fellow > > >> Columbia University > > >> Department of Astronomy > > >> > > >> _______________________________________________ > > >> 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20171114/0e8395d8/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Tue, 14 Nov 2017 14:42:01 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Projection > Message-ID: > <CALO3=5GimZpK9u2i40ZWfECXx3btj1GFT1jLO+6OhVn6_DqQGg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Tue, Nov 14, 2017 at 1:04 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > > Ah, so this isn't actually a bug. There's even a comment in the code > > indicating that this is the intended behavior: > > > > https://github.com/yt-project/yt/blob/master/yt/data_ > > objects/construction_data_containers.py#L373 > > > > So the choices about what to do here are, in my opinion: > > > > * Change this behavior to fill the array with zeros instead of NaNs > > > > I think this would give the wrong impression, especially for things like > weighted average velocity fields. > > > > * Improve the documentation to make this choice clearer > > > > Probably a good thing. > > I think I would suggest another option, which would be to filter it based > on which values are non-NaN. In the cases identified in the emails, I > would *suspect* that what's happening is that there are elements in the > quad tree that are initialized from the tree initialization step (which > just looks at the mesh from the container, not the selected elements in the > mesh) and left at zero following initialization. We could either have a > "touched" flag on all of the mesh elements (i.e., "has this been touched by > data, or is it left at initialized value) and filter in the conversion of > the quad tree to the flat arrays, or we could filter in the python code > based on NaNs. My preference would be to filter it in the creation of the > flat arrays, as then it will be uniformly applied even without weight > fields. > > > > > > I'm not sure offhand what is the best approach, especially given that > > changing this behavior would be a backward compatibility break. > > > > I think filtering NaNs is not a big change in compatibility. I think we'd > just need to make sure that the cmap normalization has the same behavior > for missing values as for NaN values, which I think it does. > > > > > > For the original question: your data aren't all NaNs I suspect. E.g. take > > a look at this example script: > > > > import yt > > import numpy as np > > ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > > disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc')) > > proj = ds.proj('density', axis='z', weight_field='density', > > data_source=disk, > > method='integrate') > > dens_proj = proj['density'] > > print(dens_proj[np.isfinite(dens_proj)]) > > print(np.nanmax(dens_proj)) > > print(np.nanmin(dens_proj)) > > > > Which prints out values in regions where the projection isn't filled with > > NaNs. > > > > > > On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras < > > jutreras(a)ug.uchile.cl> wrote: > > > >> Hi everyone, > >> > >> I got the same result using the IsolatedGalaxy dataset > >> > >> ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') > >> disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc')) > >> proj=ds.proj('density',axis='z',weight_field='density',data_ > >> source=disk,method='integrate') > >> proj['density'] > >> >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3 > >> > >> 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343(a)gmail.com>: > >> > Can I get one of you to open an issue? > >> > > >> > https://github.com/yt-project/yt/issues/new > >> > > >> > If you can, please include a script to reproduce the problem, making > >> use of > >> > one of the public datasets on yt-project.org/data. > >> > > >> > -Nathan > >> > > >> > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick > >> > <aje2123(a)columbia.edu > >> >> wrote: > >> > > >> >> Hello Matias and Nathan, > >> >> > >> >> I was able to reproduce this error on my own Enzo data set(s) using > >> >> similar code. I did a little more playing around and it looks like it > >> >> only > >> >> breaks when having a weight_field. weight_field = None seems to be > >> O.K. . > >> >> It also occurs for the "region" objects, in addition to the disk. > >> >> Interestingly, as Matias pointed out, doing something like this > works: > >> >> > >> >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0]) > >> >> proj=ds.proj('density',axis='z',weight_field='density',data_ > >> >> source=region,method='integrate') > >> >> > >> >> but this does not: > >> >> > >> >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] ) > >> >> proj =ds.proj('density',axis='z',weight_field='density',data_ > >> >> source=region,method='integrate') > >> >> > >> >> In short, this indeed appears to be a bug, and possibly not specific > >> to a > >> >> single dataset. > >> >> > >> >> > >> >> > >> >> > >> >> Andrew > >> >> > >> >> > >> >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum < > >> nathan12343(a)gmail.com> > >> >> wrote: > >> >> > >> >>> This sounds like a bug. I don't think you should ever get back NaNs > >> from > >> >>> a projection operation. > >> >>> > >> >>> Is there any chance you can share the dataset that's triggering this > >> >>> behavior? > >> >>> > >> >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos < > >> >>> matias.suazo(a)ug.uchile.cl> wrote: > >> >>> > >> >>>> Dear YT users, > >> >>>> > >> >>>> I'm trying to make a density projection, in the following lines I > >> show > >> >>>> you the lines that I have. > >> >>>> > >> >>>> #Ramses output > >> >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap) > >> >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc')) > >> >>>> proj=ds.proj('density',axis='z',weight_field='density',data_ > >> >>>> source=disk,method='integrate') > >> >>>> > >> >>>> However when I print proj["density"] I get a list of nan, however > >> when > >> >>>> I > >> >>>> use the whole domain as my data_source I get reasonable numbers. > >> >>>> > >> >>>> Thanks, > >> >>>> Mat?as Suazo > >> >>>> MSc student at Universidad de Chile > >> >>>> > >> >>>> _______________________________________________ > >> >>>> 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 > >> >>> > >> >>> > >> >> > >> >> > >> >> -- > >> >> NSF Graduate Fellow > >> >> Columbia University > >> >> Department of Astronomy > >> >> > >> >> _______________________________________________ > >> >> 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 > >> > > > > > > _______________________________________________ > > 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/20171114/49378c57/attachment.html> > > ------------------------------ > > 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 117, Issue 22 > ***************************************** >

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Projection
by Matias Enrique Suazo Campos 14 Nov '17

14 Nov '17

Dear YT users, I'm trying to make a density projection, in the following lines I show you the lines that I have. #Ramses output ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap) disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc')) proj=ds.proj('density',axis='z',weight_field='density',data_source=disk,method='integrate') However when I print proj["density"] I get a list of nan, however when I use the whole domain as my data_source I get reasonable numbers. Thanks, Matías Suazo MSc student at Universidad de Chile

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2 ProfilePlot problems
by Stephanie Tonnesen 08 Nov '17

08 Nov '17

Hi yt-users! I have two ProfilePlot issues. I have updated to yt version 3.5 dev0 to try and get the standard_error on a ProfilePlot, but now am running into other problems. Basically, I am trying to get the same result two ways, and have run into two problems. 1) The linewidth call no longer works. This code worked in my old yt version, but now gives me an error unless I take out the linewidth command: profiles = [] labels = [] plot_specs = [] linest = ['-','--','-.','-','--'] cols = ['red','red','red','green','green'] lws = ['2','2','2','2','2'] i =0 while i < len(loop): ds = yt.load("/mnt/ceph/users/stonnesen/data1/"+loopfile[i]+"/DD"+loop[i]+"/"+loopfile[i]+loop[i]) disk = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(2,"kpc")) profiles.append(yt.create_profile( data_source=disk, bin_fields=["radius"], fields=["density"], n_bins=52, units=dict(radius="kpc", density="g/cm**3"), logs=dict(radius=False), weight_field='ones', extrema=dict(radius=(0,40)), )) labels.append("%s" % looptext[i]) plot_specs.append(dict(linestyle=linest[i],linewidth=lws[i],color=cols[i])) i = i+1 plot = yt.ProfilePlot.from_profiles(profiles,labels=labels,plot_specs=plot_specs) plot.set_ylim('density',1e-27,1e-22) plot.save() I get this error: yt : [INFO ] 2017-11-06 16:44:12,585 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "yt_diskprofile_oplotdiffruns.py", line 61, in <module> plot = yt.ProfilePlot.from_profiles(profiles,labels=labels,plot_specs=plot_specs) File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py", line 443, in from_profiles return cls._initialize_instance(obj, profiles, labels, plot_specs, y_log) File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py", line 393, in _initialize_instance obj._setup_plots() File "/mnt/home/stonnesen/yt-conda/yt/yt/visualization/profile_plotter.py", line 355, in _setup_plots label=self.label[i], **self.plot_spec[i]) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1710, in inner return func(ax, *args, **kwargs) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 1437, in plot for line in self._get_lines(*args, **kwargs): File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 404, in _grab_next_args for seg in self._plot_args(this, kwargs): File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 394, in _plot_args seg = func(x[:, j % ncx], y[:, j % ncy], kw, kwargs) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 301, in _makeline seg = mlines.Line2D(x, y, **kw) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py", line 396, in __init__ self.set_linestyle(linestyle) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py", line 1115, in set_linestyle self._us_dashOffset, self._us_dashSeq, self._linewidth) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/matplotlib/lines.py", line 69, in _scale_dashes scaled_offset = offset * lw TypeError: can't multiply sequence by non-int of type 'float' 2) the plot copying the cookbook example ( http://yt-project.org/doc/cookbook/simple_plots.html?highlight=profileplot%…) is giving me 0s and nans instead of the correct values: profiles = [] labels = [] plot_specs = [] linest = ['-','--','-.','-','--'] cols = ['red','red','red','green','green'] lw = ['2','2','2','2','2'] i =0 while i < len(loop): ds = yt.load("/mnt/ceph/users/stonnesen/data1/"+loopfile[i]+"/DD"+loop[i]+"/"+loopfile[i]+loop[i]) disk = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(2,"kpc")) prof = yt.create_profile(disk,'radius',('gas','density'), units={'radius':'kpc'}, extrema={'radius':((0.0,'kpc'),(40.0,'kpc'))},weight_field='ones') radius = prof.x mean = prof['gas','density'] std = prof.standard_deviation['gas','density'] plt.semilogy(radius,mean,color=cols[i])#,linewidth=lw[i],linestyle=linest[i]) print (mean) print (radius) labels.append("%s" % looptext[i]) i = i+1 plt.ylim(1e-27,1e-21) plt.xlabel('r (kpc)') plt.ylabel(r'density') plt.legend() plt.savefig('density_profiles_gasmassmatch.png') plt.clf() The mean values are all zero, and the radius values are all nan. The code will finish (unless I use the linewidth command), but of course the plots have nothing on them!! Any ideas for these issues? I would be happy to send my full scripts or output files. Thanks! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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postdoc opportunities in multi-dimensional stellar hydro
by Michael Zingale 06 Nov '17

06 Nov '17

Hi all, As the yt community has a lot of astro-ers working on multi-d simulations, I am writing to let you know about three postdoc opportunities in computational stellar / nuclear astrophysics working on multidimensional hydrodynamics. These positions are part of a larger DOE SciDAC collaboration involving multiple institutions and exploring R-process, stellar evolution, neutron star mergers, and new algorithms. Here are links for 3 open positions (at Stony Brook, MSU, and Princeton): SBU: https://jobregister.aas.org/ad/4dcea4f9 MSU: https://astro.natsci.msu.edu/news-events/job-postings/research-associate-in… Princeton: https://web.astro.princeton.edu/jobs#Supernova%20Theory Best, 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 github: http://github.com/zingale

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Re: [yt-users] profile plots combining different datasets
by Nathan Goldbaum 04 Nov '17

04 Nov '17

I wonder what would break if we got rid of this error: In [5]: dobj = ds.all_data() + ds2.all_data() --------------------------------------------------------------------------- YTBooleanObjectsWrongDataset Traceback (most recent call last) ~/Documents/yt-git-fixes/yt/mods.py in <module>() ----> 1 dobj = ds.all_data() + ds2.all_data() ~/Documents/yt-git-fixes/yt/data_objects/data_containers.py in __add__(self, other) 1423 1424 def __add__(self, other): -> 1425 return self.__or__(other) 1426 1427 def __sub__(self, other): ~/Documents/yt-git-fixes/yt/data_objects/data_containers.py in __or__(self, other) 1399 raise YTBooleanObjectError(other) 1400 if self.ds is not other.ds: -> 1401 raise YTBooleanObjectsWrongDataset() 1402 # Should maybe do something with field parameters here 1403 return YTBooleanContainer("OR", self, other, ds = self.ds) YTBooleanObjectsWrongDataset: Boolean data objects must share a common dataset object.

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profile plots combining different datasets
by ｔyuta 03 Nov '17

03 Nov '17

Dear yt-users, Hi, I want to ask you about profile plot. I'm analyzing Enzo data, and I'm trying to plot metallicity-cellmass of different 12 datasets into one curve. I can plot 12 curves on one image, but that's not what I want. Does anyone know some good way, or links to documentation? I've attached the 12-curve plot. I want to sum up all the curves to get one curve. Thanks, Y.T.[image: 埋め込み画像 2]

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1D Profile standard deviation
by Stephanie Tonnesen 03 Nov '17

03 Nov '17

Hi yt-users! I am trying to make a profile plot of the standard deviation of the gas density of a galaxy for a few outputs. I *think* I am closely following the cookbook example: http://yt-project.org/doc/cookbook/simple_plots.html?highlight=profileplot%… but am getting an error: AttributeError: 'Profile1D' object has no attribute 'standard_deviation' Here is a code snippet, and I will attach the whole ugly script in case I missed anything that someone needs to see (ignore the strange indents below, cut and paste does not love me): ds = yt.load("/data001/stonnes/"+loopfile[i]+"/DD"+loop[i]+"/"+loopfile[i]+loop[i]) disk1 = ds.disk([0.5,0.5,0.5],[0,0,-1.0],(40,"kpc"),(2,"kpc")) disk = disk1.cut_region(["obj['Metal_Density']/obj['density'] > 0.05"]) prof = yt.create_profile(disk, 'radius',('gas','density'), n_bins=52, units={'radius':'kpc'}, weight_field='ones', extrema={'radius':((0.0,'kpc'),(40.0,'kpc'))}, ) radius = prof.x mean = prof['gas','density'] std = prof.standard_deviation['gas','density'] plt.semilogy(radius,mean,color=cols[i],linewidth=lw[i],linestyle=linest[i],label=looptext[i]) plt.ylim(1e-27,1e-21) plt.xlabel('r (kpc)') plt.ylabel(r'density (g/cm$^3$)') plt.legend() I am using yt version 3.4-dev, and the line that gets the error is: std = prof.standard_deviation['gas','density'] Any help is much appreciated! Thanks, Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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