yt-users March 2017

yt-users@python.org

21 participants
25 discussions

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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Import of crystallographic charge density data
by Matthew Horton 29 Mar '17

29 Mar '17

Hello all, I’m a new user to yt looking for some general guidance. 1. I have files describing the charge density in a crystal (CHGCAR files for any DFT/VASP users on the mailing list). I can import these with yt as generic (periodic) unigrid data, however the axes are not always orthogonal… In cubic crystals, `yt.load_uniform_grid` works perfectly, but in some crystals this would give a distorted visualization. What would be the best way to import this kind of data? 2. Regarding units, the units in my file are nominally fractional electrons per grid cell volume, e/Angstrom^3 … importing into yt as a density field, what units should I use? Would be good to keep the data in its natural units, rather than converting to SI/cgs, because they’d be very very small floats otherwise. I tried 'unit_system = yt.UnitSystem('custom', 'Angstrom', 'g', 's’)' and this works as expected for the length units in my plots, but how do I set the custom Charge unit? What ‘units’ string would I then use for the density field? It doesn’t seem to want to accept ‘Angstrom’, ‘C’ etc. Many thanks for any help! Best regards, Matthew

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Particle Velocity Magnitude without bulk velocity correction
by Reju Sam John 29 Mar '17

29 Mar '17

Dear all, I tried the following defination of Particle Velocity Magnitude without bulk velocity correction. def _ParticleVelocityMagnitudenoBVcor(field, data): return ( data["particle_velocity_x"]**2.0 + \ data["particle_velocity_y"]**2.0 + \ data["particle_velocity_z"]**2.0 )**(1.0/2.0) add_field("ParticleVelocityMagnitudenoBVcor", function=_ParticleVelocityMagnitudenoBVcor, take_log=False, units=r"\rm{cm/s}" ) and tried to calculate the weighted average value of it with the following line vrms_dm_no_bv_cor = sphere.quantities["WeightedAverageQuantity"]("ParticleVelocityMagnitudenoBVcor", "ParticleMass") But I am getting the following error IndexError: too many indices for array What could be the reason? How can I compute Particle Velocity Magnitude without bulk velocity correction? Thanks -- Reju Sam John

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phaseplot set zlim
by Stephanie Tonnesen 28 Mar '17

28 Mar '17

Hi yt-users, I am trying to make some nice looking phaseplots, and want to set the mass range that I show in the figure. I use set_zlim and instead of only showing the cells that call into that mass range, it just changes the color coding. You can see the attached for what I am talking about. Is there a way to have phaseplot only show me the cells that have "cell_mass" larger that 1e36 (or whatever I happen to set)? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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miniconda installation issue
by Wolfram Schmidt 28 Mar '17

28 Mar '17

Hi, I have encountered a problem when installing yt using the miniconda python distribution on a remote host. After downloading and installing various packages, the installation process gets stuck here (see also attached log file): EXECUTING: /home/h/hzfbhsws/yt-conda/bin/conda install -c conda-forge --yes yt Fetching package metadata ........... Solving package specifications: . CondaError: CondaHTTPError: HTTP None None for url <https://conda.anaconda.org/conda-forge/linux-64/conda-env-2.6.0-0.tar.bz2> Elapsed: None Indeed when I try wget https://conda.anaconda.org/conda-forge/linux-64/conda-env-2.6.0-0.tar.bz2 on the host on which I have been running the installation, the following error message is thrown: Connecting to s3.amazonaws.com|54.231.40.130|:443... failed: No route to host. On the local host (i.e. my PC), there is no problem with downloading the conda-env package with wget: Saving to: ‘conda-env-2.6.0-0.tar.bz2’ conda-env-2.6.0-0.tar.bz2 100%[===================================================================>] 1017 --.-KB/s in 0s 2017-03-28 12:18:08 (37,9 MB/s) - ‘conda-env-2.6.0-0.tar.bz2’ saved [1017/1017] Maybe the problem is related to port 443 on the host on which I want to install yt. In any case, how can I circumvent this? I can put the required package into the yt-conda/pkgs directory, but I haven't figured out how to tell the installation script to use the existing file rather than attempting to download it. Best regards, Wolfram

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Stacked temperature profiles
by Thor Andreas Seiff Ellewsen 17 Mar '17

17 Mar '17

Hi everyone. I'm currently working on making temperature and density profiles from some ramses simulations. I'd like to make these profiles the average radial profile of the halos in the simulation. I think the included rockstar in yt supports this in some form, but my halo catalog is made using AHF and then imported from an ascii file. To do this I need help with two things: The first one is how to scale the radius of each profile to the corresponding virial radius. The other is how to actually average all these profiles. Is this something that can be done? I will be trying to compare the resulting profile with the same for different simulations in the end, but I don't expect to have any big problems with that. The code I'm currently using for this can be found at http://paste.yt-project.org/show/7058/ Best, Andreas Ellewsen

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Re: [yt-users] cutting plane not working or changed
by Nathan Goldbaum 16 Mar '17

16 Mar '17

Yes, using a conda environment should work. It's up to you how you want to manage your install. The nightly conda builds might be useful for this purpose: http://yt-project.org/doc/installing.html#installing-yt-using-anaconda On Thu, Mar 16, 2017 at 7:55 AM Slavin, Jonathan <jslavin(a)cfa.harvard.edu> wrote: > Hi Nathan, > > As you can probably tell, our e-mails of yesterday crossed. > > I am willing to use the development branch of yt, though I'd prefer if > I could use it alongside the stable branch instead of replacing it. I > currently use anaconda. I suppose the way to go about that would be > to create a new environment. Maybe this is the motivation I need to > finally move to python 3.x. Any suggestions? > > Jon > > On Wed, Mar 15, 2017 at 5:06 PM, <yt-users-request(a)lists.spacepope.org> > wrote: > > Date: Wed, 15 Mar 2017 13:42:36 -0500 > > From: Nathan Goldbaum <nathan12343(a)gmail.com> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] cutting plane not working or changed > > Message-ID: > > < > CAJXewOkmpm6U9XpeDu+Xgjf4xTLBig_4Ery1tPetKi4ThPkzYA(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Ah, apologies for not checking how yt behaves on a stable release. I'm > able > > to reproduce the behavior you're seeing on yt 3.3.5. It looks like this > > behavior doesn't manifest itself on the yt branch, so it looks like some > > changes we've made have "fixed" this since we branched off for yt 3.4 > last > > summer. I suspect this has something to do with the pixelizers being > > rewritten to use compositing but I'd need to check in detail with hg > bisect > > to be sure. > > > > Can you try testing out the development version of yt? You should be able > > to build yt from source by uninstalling your current version of yt, > cloning > > the repository, checking out the "yt" branch, and running "python > setup.py > > develop". See this page for more details: > > > > > http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-f… > > > > Is the new behavior (wtihout the NaNs) what you expect? > > > > I might try to backport this to the stable branch, but given that a lot > of > > code has changed in the pixelizers it might be difficult to backport just > > this fix. Would you be ok with running on the development branch for now? > > I'd ideally like to get yt 3.4.0 out the door by this summer. > > > > > -- > ________________________________________________________ > Jonathan D. Slavin Harvard-Smithsonian CfA > jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 > phone: (617) 496-7981 Cambridge, MA 02138-1516 > cell: (781) 363-0035 USA > ________________________________________________________ >

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Re: [yt-users] cutting plane not working or changed
by Slavin, Jonathan 15 Mar '17

15 Mar '17

Hi Nathan, I think this may have to do with pixelization_routines.pyx. I noticed that the version I have (i.e. 3.3.5) differs significantly from that under the main yt branch on bitbucket, which seems more recent. (Is that the development branch?) In particular the 3.3.5 version is lacking "NOTE ON ROWS AND COLUMNS" in pixelize_off_axis_cartesian and associates the width with rows and height with columns: px_dx = width / (<np.float64_t> rows) px_dy = height / (<np.float64_t> cols) In the newer version the argument list is different and instead there is px_dx = width / (<np.float64_t> buff.shape[1]) px_dy = height / (<np.float64_t> buff.shape[0]) where, I believe buff corresponds to the argument to resolution, so resolution should be (h,w) which seems to contrast with the situation in the stable branch version. Jon On Wed, Mar 15, 2017 at 2:00 PM, <yt-users-request(a)lists.spacepope.org> wrote: > > Date: Wed, 15 Mar 2017 14:00:17 -0400 > From: "Slavin, Jonathan" <jslavin(a)cfa.harvard.edu> > To: yt-users(a)lists.spacepope.org > Subject: Re: [yt-users] cutting plane not working or changed > Message-ID: > <CACcRS=fo5KiYBdnu3EvEyuq5vA-UGFK4jRK1soPM-5E1LPWa-w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > ?Hi Nathan, > > I finally got around to testing your code on LodegIt that uses the > IsolatedGalaxy data. I ran it as is except I added some plotting > statements (using matplotlib) at the end. I again do get the problem of > NaNs: > > ?In [2]: run slice_prob_test.py > Parsing Hierarchy : 100%|??????????????????| 173/173 [00:00<00:00, > 23359.45it/s] > /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/visualization/fixed_resolution.py:546: > RuntimeWarning: invalid value encountered in divide > bounds).transpose() > (nan g/cm**3, nan g/cm**3) > True > > ?Where the (nan g/cm**3... line is from the print(image.max()... > statement. Also np.any(np.isnan(image)) returns True. The image that is > produced is shown in the attached png file. > > The RuntimeWarning is apparently associated with this statement: > ?buff = pixelize_off_axis_cartesian( > self.data_source['x'], > self.data_source['y'], self.data_source['z'], > self.data_source['px'], > self.data_source['py'], > self.data_source['pdx'], > self.data_source['pdy'], self.data_source['pdz'], > self.data_source.center, > self.data_source._inv_mat, indices, > self.data_source[item], > self.buff_size[0], self.buff_size[1], > bounds).transpose() > > ?which is in the __getitem__ method of ?the ObliqueFixedResolutionBuffer > class. That's about all I could tell you at this point. > > The package versions I'm using are yt 3.3.5, python 2.7.12, matplotlib > 2.0.0 (running on Linux CentOS 6.8 if that matters). > > ?Regards, > Jon? > > > > On Fri, Mar 10, 2017 at 4:05 PM, <yt-users-request(a)lists.spacepope.org> > wrote: > > > Date: Fri, 10 Mar 2017 12:14:55 -0800 > > From: Nathan Goldbaum <nathan12343(a)gmail.com> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] cutting plane not working or changed behavior > > Message-ID: > > <CAJXewOmWwY1CU4nrafG5_=GrAScGBnq=VMNxxh3s0OUzDzaGVw@ > > mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Jonathan, > > > > I'm not able to reproduce the behavior you're seeing with a test dataset > > (e.g. see http://paste.yt-project.org/show/7080/, this uses a dataset from > > yt-project.org/data). > > > > Is there any chance you can share a dataset that triggers this? > > Alternatively, can you reproduce this using one of the test datasets on > > yt-project.org/data? > > > > The yt curldrop might be useful to share a dataset that triggers the issue > > you're seeing, see docs.hub.yt. If you're not comfortable sharing the > > dataset publicly, feel free to share it with me off-list. > > > > -Nathan > > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Re: [yt-users] cutting plane not working or changed
by Slavin, Jonathan 15 Mar '17

15 Mar '17

Hi Nathan, I finally got around to testing your code on LodegIt that uses the IsolatedGalaxy data. I ran it as is except I added some plotting statements (using matplotlib) at the end. I again do get the problem of NaNs: In [2]: run slice_prob_test.py Parsing Hierarchy : 100%|██████████████████| 173/173 [00:00<00:00, 23359.45it/s] /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/visualization/fixed_resolution.py:546: RuntimeWarning: invalid value encountered in divide bounds).transpose() (nan g/cm**3, nan g/cm**3) True Where the (nan g/cm**3... line is from the print(image.max()... statement. Also np.any(np.isnan(image)) returns True. The image that is produced is shown in the attached png file. The RuntimeWarning is apparently associated with this statement: buff = pixelize_off_axis_cartesian( self.data_source['x'], self.data_source['y'], self.data_source['z'], self.data_source['px'], self.data_source['py'], self.data_source['pdx'], self.data_source['pdy'], self.data_source['pdz'], self.data_source.center, self.data_source._inv_mat, indices, self.data_source[item], self.buff_size[0], self.buff_size[1], bounds).transpose() which is in the __getitem__ method of the ObliqueFixedResolutionBuffer class. That's about all I could tell you at this point. The package versions I'm using are yt 3.3.5, python 2.7.12, matplotlib 2.0.0 (running on Linux CentOS 6.8 if that matters). Regards, Jon On Fri, Mar 10, 2017 at 4:05 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Fri, 10 Mar 2017 12:14:55 -0800 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] cutting plane not working or changed behavior > Message-ID: > <CAJXewOmWwY1CU4nrafG5_=GrAScGBnq=VMNxxh3s0OUzDzaGVw@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jonathan, > > I'm not able to reproduce the behavior you're seeing with a test dataset > (e.g. see http://paste.yt-project.org/show/7080/, this uses a dataset from > yt-project.org/data). > > Is there any chance you can share a dataset that triggers this? > Alternatively, can you reproduce this using one of the test datasets on > yt-project.org/data? > > The yt curldrop might be useful to share a dataset that triggers the issue > you're seeing, see docs.hub.yt. If you're not comfortable sharing the > dataset publicly, feel free to share it with me off-list. > > -Nathan > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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yt-users March 2017