Mailman 3 November 2016 - 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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Re: [yt-users] FLASH Time Series Analysis with Particle Files
by Jason Galyardt 01 Dec '16

01 Dec '16

Hi John & Nathan, Yes, I'm having trouble using the time series analysis machinery with my FLASH simulations. I've checked that the plot files and particle files all have the same current_time variable, so there's no issue there. I'm using a development version of yt with a changeset ID of 5cf30893afdf. This changeset includes Nathan's changes supporting cut_region functionality for FLASH plot files. Here's what I see when I try to do a time series analysis: ########################### In [9]: ts = yt.load("mysim_hdf5_plt_cnt_*", particle_filename="mysim_hdf5_part_*") In [10]: for ds in ts: print ds.current_time ....: --------------------------------------------------------------------------- IOError Traceback (most recent call last) <ipython-input-10-fccd01bb5065> in <module>() ----> 1 for ds in ts: 2 print ds.current_time 3 /home/emrys/yt/yt/data_objects/time_series.pyc in __iter__(self) 179 for o in self._pre_outputs: 180 if isinstance(o, string_types): --> 181 ds = self._load(o, **self.kwargs) 182 self._setup_function(ds) 183 yield ds /home/emrys/yt/yt/data_objects/time_series.pyc in _load(self, output_fn, **kwargs) 396 elif self._mixed_dataset_types: 397 return load(output_fn, **kwargs) --> 398 ds = load(output_fn, **kwargs) 399 self._dataset_cls = ds.__class__ 400 return ds /home/emrys/yt/yt/convenience.pyc in load(*args, **kwargs) 84 candidates = find_lowest_subclasses(candidates) 85 if len(candidates) == 1: ---> 86 return candidates[0](*args, **kwargs) 87 if len(candidates) == 0: 88 if ytcfg.get("yt", "enzo_db") != '' \ /home/emrys/yt/yt/frontends/flash/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, particle_filename, units_override, unit_system) 209 self._particle_handle = HDF5FileHandler(self.particle_filename) 210 except: --> 211 raise IOError(self.particle_filename) 212 # Check if the particle file has the same time 213 if self._particle_handle != self._handle: IOError: mysim_hdf5_part_* ########################### It looks to me like HDF5FileHandler() just does not like the wildcard. I've also tried, unsuccessfully, to feed a list of particle files to yt.load(). I thought perhaps that I should be using the DatasetSeries framework directly, but I'm not clear on how to pass in the list of particle files, as DatasetSeries does not understand the particle_filename keyword argument. Any ideas? Thanks, Jason On Wed, Nov 30, 2016 at 1:57 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. FLASH Time Series Analysis with Particle Files (Jason Galyardt) > 2. Re: FLASH Time Series Analysis with Particle Files > (Nathan Goldbaum) > 3. Re: FLASH Time Series Analysis with Particle Files (John Zuhone) > > > ---------- Forwarded message ---------- > From: Jason Galyardt <jason.galyardt(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Wed, 30 Nov 2016 10:16:44 -0500 > Subject: [yt-users] FLASH Time Series Analysis with Particle Files > Dear yt-users, > > In May 2015, there was some traffic on this list concerning errors in time > series analysis on FLASH simulations that include both plot files and > particle files. Does anyone have an update on the status of this issue? > > Thanks, > Jason > > ------ > Jason Galyardt > University of Georgia > > > > ---------- Forwarded message ---------- > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Wed, 30 Nov 2016 09:32:37 -0600 > Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files > Hi Jason, > > As far as I'm aware this should be working now. Are you having trouble? > > -Nathan > > On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <jason.galyardt(a)gmail.com> > wrote: > >> Dear yt-users, >> >> In May 2015, there was some traffic on this list concerning errors in >> time series analysis on FLASH simulations that include both plot files and >> particle files. Does anyone have an update on the status of this issue? >> >> Thanks, >> Jason >> >> ------ >> Jason Galyardt >> University of Georgia >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > ---------- Forwarded message ---------- > From: John Zuhone <jzuhone(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Wed, 30 Nov 2016 11:32:09 -0500 > Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files > Yes, my understanding is that this is working, provided that your files > have the same basename and the times of the files are the same. > > On Nov 30, 2016, at 10:32 AM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > Hi Jason, > > As far as I'm aware this should be working now. Are you having trouble? > > -Nathan > > On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <jason.galyardt(a)gmail.com> > wrote: > >> Dear yt-users, >> >> In May 2015, there was some traffic on this list concerning errors in >> time series analysis on FLASH simulations that include both plot files and >> particle files. Does anyone have an update on the status of this issue? >> >> Thanks, >> Jason >> >> ------ >> Jason Galyardt >> University of Georgia >> >> >> _______________________________________________ >> 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 > >

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FLASH Time Series Analysis with Particle Files
by Jason Galyardt 30 Nov '16

30 Nov '16

Dear yt-users, In May 2015, there was some traffic on this list concerning errors in time series analysis on FLASH simulations that include both plot files and particle files. Does anyone have an update on the status of this issue? Thanks, Jason ------ Jason Galyardt University of Georgia

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volume rendering ramses output
by mohammad safarzadeh 25 Nov '16

25 Nov '16

Hello, I am trying to do a simple volume rendering on a ramses cosmological output by following the simple recipe that yt provides, but I get an AMRKDTree error. Can I not volume render a ramses output? I am using the latest version of YT. here is my simple code that fails: ds=yt.load(filename) sc = yt.create_scene(ds, field=('gas', 'density')) sc.camera.resolution = (1024, 1024) sc.camera.focus = ds.arr([0.3, 0.3, 0.3], 'unitary') sc.camera.position = ds.arr([0, 0, 0], 'unitary') sc.render() ---> 37 sc.render() RuntimeError: AMRKDTree does not support particle or octree-based data. Thank you very much, -- Mohammadtaher Safarzadeh, Ph.D.

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Bin 1D spherically averaged profiles uniformly on log radius
by Marco Surace 25 Nov '16

25 Nov '16

Hi all, I have been using yt.ProfilePlot to create 1D spherically averaged profiles of say the gas temperature in a simulation as a function of radius, starting from the centre of a halo out to a given radius. Does anyone know how I can bin the data uniformly in log radius? This would improve the resolution at smaller radii. It currently does not bin the data uniformly in linear or log radius. I haven't found an option with ProfilePlot for affecting the binning. Best wishes, Marco

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Question about tunneling through ssh
by JASMIN HISON SHIN 23 Nov '16

23 Nov '16

Hi Everyone, I am wondering why I cannot tunnel YT plots through ssh. I am using ssh -Y user(a)somehpcc.edu, then doing ssh -Y to the node. I can send xclock through to the XQuartz on the Mac that I am using and display plots made through iyt, but p.show() is not showing anything. I am using yt version = 3.3.1. Could someone please help me troubleshoot this? Sincerely, Jasmin

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Problems when using YTSphere.max(...)
by Katharina Wollenberg 23 Nov '16

23 Nov '16

Hi together, I want to find out, among others, temperature and pressure values corresponding to a maximum density value within a spherical volume. I thought about using YTSphere.max(…) or YTSphere.argmax(…) for this purpose. However, in both cases I get the Attribute error “ “YTSphere” object has no attribute “max” “ . What might be the error origin? Have I forgotten something obvious? Regards, Katharina ------------------------------------------------------- Katharina Wollenberg PhD Student in Astronomy Zentrum für Astronomie der Universität Heidelberg (ZAH) Institute of Theoretical Astrophysics (ITA) Albert-Ueberle-Str. 2 69120 Heidelberg Germany

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Volume render
by Sushilkumar 21 Nov '16

21 Nov '16

Dear yt: I am using volume render to visualizing the gradient in field lines. Is there a way that I can add more sensitivity, in terms of colors to my final image? Currently the gradient seems very limited and cannot differentiate between near and far fields. Drive link is below Thanks in advance https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc On Sun, Nov 20, 2016 at 11:44 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: Problem using Multiplot_yt (John Wise) > 2. Re: Problem using Multiplot_yt (John Wise) > 3. sliceplots for setting maximum temperature at the center > (turhan nasri) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 20 Nov 2016 08:34:09 -0500 > From: John Wise <jwise(a)physics.gatech.edu> > To: <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Problem using Multiplot_yt > Message-ID: <15643110-1f4b-460c-c80e-2e85b0fdb18d(a)physics.gatech.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > Hi Rahul, > > I can confirm that this is a bug with multiplot_yt. I'll get back to > the list once I find a fix. In the meantime, can you create an issue on > bitbucket? > > Thanks, > John > > On 11/20/2016 12:51 AM, rahul kashyap wrote: > > Some attempts which didn't work. The callback is pasted on > > http://paste.yt-project.org/show/6931/ > > > > I tried putting fields in the call > > > > eps_fig = eps.multiplot_yt(2, 2, s,["density","temperature", > > "velocity_magnitude","pressure"], bare_axes=True) > > > > I also tried putting a break point in the yt/visualization/eps_writer.py > > > > figure = multiplot(ncol, nrow, yt_plots=plots, fields=fields, **kwargs) > > > > > > > > > > On Sun, Nov 20, 2016 at 12:35 AM, rahul kashyap > > <rahulkashyap411(a)gmail.com <mailto:rahulkashyap411@gmail.com>> wrote: > > > > Hi, > > > > After doing > > > > import yt.visualization.eps_writer as eps > > from yt.visualization.eps_writer import multiplot_yt > > s = yt.SlicePlot(ds, "z", ["density","temperature", > > "velocity_magnitude","pressure"], center="max") > > > > This works for me > > > > eps_fig = eps.single_plot(s) > > eps_fig.save_fig('zoom', format='eps') > > eps_fig.save_fig('zoom-pdf', format='pdf') > > > > *But, the code below doesn't work for me; error is "YTFieldNotFound: > > Could not find field '('io', 0)' in super3d_hdf5_plt_cnt_0000."* > > > > s.set_width(2.e9, 'cm') > > eps_fig = eps.multiplot_yt(2, 2, s, bare_axes=True) #not working > now > > #eps_fig.scale_line(0.2, '5 kpc') > > eps_fig.save_fig('multi', format='eps') > > > > Any help would be appreciated, Thanks > > -Rahul Kashyap > > > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > -- > John Wise > Associate Professor of Physics > Center for Relativistic Astrophysics, Georgia Tech > http://cosmo.gatech.edu > > > ------------------------------ > > Message: 2 > Date: Sun, 20 Nov 2016 08:55:12 -0500 > From: John Wise <jwise(a)physics.gatech.edu> > To: <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Problem using Multiplot_yt > Message-ID: <b7bf57b5-3aaa-d243-f77c-8ba56b519d68(a)physics.gatech.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > Hi again, > > The fix was easier than I thought. Can you test it out? If you > installed yt with "INST_YT_SOURCE=1" in the install script, then you can > issue the following commands in the yt source directory > > hg pull -u -r 9373defa8ed5 https://bitbucket.org/jwise77/yt > python setup.py develop > > and see if your script now works. It works for me with a similar script > as you posted. > > If you're using the conda installation, then you can follow the > instructions in this previous email. > > http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/2016-October/008277.html > > Let us know what you find. > Thanks, > John > > > On 11/20/2016 08:34 AM, John Wise wrote: > > Hi Rahul, > > > > I can confirm that this is a bug with multiplot_yt. I'll get back to > > the list once I find a fix. In the meantime, can you create an issue on > > bitbucket? > > > > Thanks, > > John > > > > On 11/20/2016 12:51 AM, rahul kashyap wrote: > >> Some attempts which didn't work. The callback is pasted on > >> http://paste.yt-project.org/show/6931/ > >> > >> I tried putting fields in the call > >> > >> eps_fig = eps.multiplot_yt(2, 2, s,["density","temperature", > >> "velocity_magnitude","pressure"], bare_axes=True) > >> > >> I also tried putting a break point in the yt/visualization/eps_writer.py > >> > >> figure = multiplot(ncol, nrow, yt_plots=plots, fields=fields, **kwargs) > >> > >> > >> > >> > >> On Sun, Nov 20, 2016 at 12:35 AM, rahul kashyap > >> <rahulkashyap411(a)gmail.com <mailto:rahulkashyap411@gmail.com>> wrote: > >> > >> Hi, > >> > >> After doing > >> > >> import yt.visualization.eps_writer as eps > >> from yt.visualization.eps_writer import multiplot_yt > >> s = yt.SlicePlot(ds, "z", ["density","temperature", > >> "velocity_magnitude","pressure"], center="max") > >> > >> This works for me > >> > >> eps_fig = eps.single_plot(s) > >> eps_fig.save_fig('zoom', format='eps') > >> eps_fig.save_fig('zoom-pdf', format='pdf') > >> > >> *But, the code below doesn't work for me; error is "YTFieldNotFound: > >> Could not find field '('io', 0)' in super3d_hdf5_plt_cnt_0000."* > >> > >> s.set_width(2.e9, 'cm') > >> eps_fig = eps.multiplot_yt(2, 2, s, bare_axes=True) #not > >> working now > >> #eps_fig.scale_line(0.2, '5 kpc') > >> eps_fig.save_fig('multi', format='eps') > >> > >> Any help would be appreciated, Thanks > >> -Rahul Kashyap > >> > >> > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > > > -- > John Wise > Associate Professor of Physics > Center for Relativistic Astrophysics, Georgia Tech > http://cosmo.gatech.edu > > > ------------------------------ > > Message: 3 > Date: Sat, 19 Nov 2016 20:33:01 -0500 > From: turhan nasri <turhannasri(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] sliceplots for setting maximum temperature at the > center > Message-ID: > <CANPWr5iqWXTAk9i5drdSRTVD4D6s9i5+o0oZCUhq-UZNwZ2QUA@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi people, > > I wanted to to get slices for temperature and temperature gradient > magnitude setting the maximum temperature at the center. I used yt's > feature: > > v,c = pf.h.find_max('temperature') #set center at max_temp > > and got the slices, however, my slice outputs clearly show the maximum > temperature was not set at center. I am sharing the python code for the > slices and also my output files. > this code worked when I created density slices and max_dens was set at > center, I don't see it isn't working out for temperature. Thanks for your > help > > Turhan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20161119/9e9c84a2/attachment.htm> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: super3d_hdf5_chk_0047_3slice_temperature.png > Type: image/png > Size: 89139 bytes > Desc: not available > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20161119/9e9c84a2/attachment.png> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: super3d_hdf5_chk_0047_3slice_temperature_gradient_magnitude (7).png > Type: image/png > Size: 107028 bytes > Desc: not available > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20161119/9e9c84a2/attachment-0001.png> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: slice.py > Type: text/x-python > Size: 3813 bytes > Desc: not available > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20161119/9e9c84a2/attachment.py> > > ------------------------------ > > 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 105, Issue 28 > ***************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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