Mailman 3 September 2019 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 15, 2022

Aug. 15, 2022

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 Dec. 11, 2021

Dec. 11, 2021

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 April 11, 2020

April 11, 2020

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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mass-weighted average magnetic field (QUIVERS) projected on to the plane plot
by nirmit sakre Jan. 5, 2020

Jan. 5, 2020

I would like to annotate Mass weighted Magnetic field quivers on density projection plot so that i can display the magnetic field features. Do annotate_magnetic_field() , annotate_quiver() work correctly on projection plot or do they work only on slice plot correctly. If they work on projection plot then against which quantity magnetic field quivers are weighed or not weighted?

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Ytini installation for Houdini on Windows
by uran san Dec. 17, 2019

Dec. 17, 2019

Hi guys, I am very new to Ytini's mailing list, mailing lists as well as Houdini. So please bear with me while I pick up the etiquette around this medium. With that out of the way here's my first question: After having succeeded installing Ytini for Houdini on a Mac OS X 10.14 I would now like to achieve the same with my Houdini install on a Windows 10 OS. I have tried to somewhat reproduce all steps described here http://www.ytini.com/getstarted.html#collapseTwoOut (Houdini 17.5 Tested on Mac OS X) on my Windows machine but wasn't surprised to learn that of course Houdini could not find the ytini module when I tried to import it in the python shell. Is there somebody, that could point me . in the right direction of how to install Ytini for Houdini on a Windows 10 OS environment? Not afraid of reading so even hints a re more than welcome. Many Thanks in advance Ur4n

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Update on yt governance documents/structure
by Madicken Munk Oct. 23, 2019

Oct. 23, 2019

Hi yt-users! We've been working on updating our governance model for the yt-project to help our project grow, to codify our decision-making process, and to outline the governance structure of the project. I've submitted two companion pull requests with drafts of this updated documentation: https://github.com/yt-project/governance/pull/1 and https://github.com/yt-project/ytep/pull/7 (you can see the contents of the pull requests if you click on the "files changed" tab; text highlighted in green is an addition and in red is removed) Our existing governance document is located at https://ytep.readthedocs.io/en/master/YTEPs/YTEP-1776.html The first pull request is to a new governance repository, where our governance documentation will live separately from the YTEPs (yt enhancement proposals). This will allow us to maintain and minorly update our governance without having to update YTEP. The second pull request is to the YTEP repository and generally outlines the core values and ideas we want our governance structure to reflect. Hopefully all of the things I've listed in the YTEP are reflected in the governance docs. As members of the community, I'd like to solicit feedback from all of you about these governance documents. Do these reflect our community values? Should we add anything? Do you feel everything is clear? Is this too much governance for our community right now? Is there something that's missing? As users, do you feel our governance structure is supportive to you, or do you think there is a way we could improve it to do so? Feel free to reply here or comment on the pull requests! Our governance will be better with your feedback. -Madicken

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Trying to use radial_velocity, doesn't look right
by Clayton Strawn Sept. 30, 2019

Sept. 30, 2019

Hi all, I'm trying to use "gas", "radial velocity" to compare inflows and outflows in a simulation, but the results don't really look right. using radial_velocity as a binary field, I defined new fields as follows def inflow_density(field,data): tr = data['gas','density']*((data['gas','radial_velocity'])<0).astype(float) return tr def outflow_density(field,data): tr = data['gas','density']*((data['gas','radial_velocity'])>0).astype(float) return tr A ProjectionPlot gives one side which is all inflow, one side which is all outflow. This resembles what you get if you have an incorrect bulk_velocity field, but when I correct for it like this sp = ds.sphere(center, (Rvir, "kpc")) bulk_velocity = sp.quantities.bulk_velocity() plot = yt.ProjectionPlot(ds, 0, center=center, fields=('gas','inflow_density'), width = (w,"kpc"), field_parameters={'bulk_velocity':bulk_velocity}) it doesn't change at all. Am I using this right? Thanks, Clayton

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Exporting to RADMC-3D/ Web page example
by José Mauricio Utreras Sept. 20, 2019

Sept. 20, 2019

Hi yt users! I'm not sure if this is the place to ask this but I was following The example to export to RADMC3D https://yt-astro-analysis.readthedocs.io/en/latest/radmc3d_export.html Number of processors: 4 Number of threads in use: 1 Reading global frequencies/wavelengths... Reading grid file and prepare grid tree... At line 3196 of file ./amr_module.f90 (unit = 1, file = 'amr_grid.inp') Fortran runtime error: Bad integer for item 5 in list input I've run examples from radmc3dpy webpage and those worked. I'm not sure if the problem is the format in which yt writes the amr input file or radmc3d Saludos! José Utreras

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ANN: Trident 1.2 released!
by Britton Smith Sept. 19, 2019

Sept. 19, 2019

Greetings! I'm very pleased to announce the release of Trident version 1.2! Trident is an extension of yt for creating absorption spectra from simulations. This is the first major Trident release in nearly two years. Trident 1.2 contains a number of new features, bug fixes, and minor enhancements. All are listed below. *This is the last version of Trident that will support Python 2.* All versions to follow will require the use of Python 3.5 or later. *New Features* - Add support for creating spectra in velocity space - Add ability to set wavelength limits to 'auto' - Add ability to make spectrum from data container *Bug Fixes*- off by one error in subgrid index calculation - fixing error in _ion_mass - H_p0_number_density to default, H_number_density to alias - Implements a better way of calculating the redshift on the light ray - Assures that ion_fraction field reflects on-disk fields - Fix atomic data for Si II 1260 according to Morton 2003 - A check to avoid failure when no continuum absorbers were found in the ray - Auto-addition of H_nuclei_density to a LightRay when present in the base dataset - Adding max_box_fraction as a kwarg to make_compound_ray - Updated trident_path() to be OS Independent - simplify setting up ion fields using the "local" field type - split and join filenames using os.sep instead of assuming unix - updated oscillator strengths and gamma's for Si II 1206 and Si III 1260 *Minor Enhancements*- Calculating LOS velocity with relative velocities to account for bulk motion - Enabling use of `output_absorbers_file` kwarg in SpectrumGenerator - Switching imports from yt.analysis_modules to yt_astro_analysis - Enable passing in-memory LineDatabase to SpectrumGenerator - Added equivalent width calculation to line_observables_dict - Numerous documentation updates - Updates and fixes to testing The latest version of Trident can be installed with pip: pip install trident Documentation: https://trident.readthedocs.io/en/stable/ Repository: https://github.com/trident-project/trident Trident has received contributions from 23 people. 9 people contributed changes to the latest release (underline) with 3 of those people doing so for the first time (bold). Thanks to everyone for their hard work! - Trident development team *Brendan Boyd* Lauren Corlies *Bili Dong*Hilary Egan *Nathan GoldbaumCameron HummelsBharat Kambalur*BW Keller Kacper Kowalik Erwin Lau Andrew Myers *Molly S. Peeples*Douglas Rudd Anthony Scopatz *Devin Silvia*Stephen Skory *Britton SmithClayton Strawn*Stephanie Tonnesen Matthew Turk Miguel de Val-Borro John Wise John ZuHone

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Output data selection to ascii file or fits table
by rorysmith274＠gmail.com Sept. 18, 2019

Sept. 18, 2019

Hi, I would like to use yt to make selections of data from Enzo files (e.g. gas with certain properties in a particular volume), and then output the data to an external file like an ascii or fits table, to be analysed by other codes. Can you please tell me if such a tool is already available, or how I might be able to do it otherwise? Thanks.

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Access User define function inside the yt derived field
by Prateek Gupta Sept. 17, 2019

Sept. 17, 2019

Hello all, I want to use a user-defined function (say, Maxwell distribution function) with a variable (say, p--momentum, because I want to integrate the function on that variable), and want to use density and temperature field information of each grid. This function applies individually on each grid. Please suggest me the way to do so. This could be very naive to ask but I stuck in it. That function can't be a yt-field (I think) because it has a variable, and if I want to use density and temperature field even after removing units inside the function, it will show an error, because the field is in vector form (3Dim) and the variable is scaler (basically shape miss-match error). I have to use many such functions as post-processing, please suggest me a way to achieve this goal. Many thanks and regards, -Prateek Gupta

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[yt v. 3.5.1] Issue running parallel yt script
by Andrew Cook Sept. 14, 2019

Sept. 14, 2019

Hello! I'm having issues running a yt 3.5.1 script to process an OffAxisProjectionPlot of some Enzo 2.5 data. Running mpi 4.0.1 I get this error: File "plot_time.py", line 28, in <module> val, loc = ds.find_max('density') File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/static_output.py", line 826, in find_max source.quantities.max_location(field) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 635, in __call__ rv = super(MaxLocation, self).__call__(field, sample_fields) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 591, in __call__ rv = super(SampleAtMaxFieldValues, self).__call__(field, sample_fields) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 68, in __call__ for sto, ds in parallel_objects(chunks, -1, storage = storage): File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 520, in parallel_objects to_share, datatype = 'dict', op = 'join') File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 284, in passage return func(self, *args, **kwargs) File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 723, in par_combine_object data.update(self.comm.recv(source=i, tag=0)) File "mpi4py/MPI/Comm.pyx", line 1173, in mpi4py.MPI.Comm.recv File "mpi4py/MPI/msgpickle.pxi", line 302, in mpi4py.MPI.PyMPI_recv File "mpi4py/MPI/msgpickle.pxi", line 261, in mpi4py.MPI.PyMPI_recv_match P000 yt : [ERROR ] 2019-09-14 12:26:53,382 Exception: MPI_ERR_INTERN: internal error P000 yt : [ERROR ] 2019-09-14 12:26:53,383 Error occured on rank 0. I know that someone posted a similar error recently but I don't think there was a solid solution to the problem. If anyone can help please let me know. Also i'm sorry if I didn't explain this well enough, please let me know if anything is not clear. Many thanks Andy

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Magnetic flux over a disk
by Guido Granda Muñoz Sept. 11, 2019

Sept. 11, 2019

Hello, I want to compute the magnetic flux over a disk which length is the minimum possible i.e. the resolution. I wanted to approximate this quantity using : sp=ds.disk(center,normal,(1,'pc'),(1*res,'pc')) flux=sp.calculate_flux("sqrt_magx","sqrt_magy","sqrt_magz","sqrt_magx") Where I defined the quantities sqrt_magx (root square of the magnetic field along the x direction) with units of Gauss^0.5, so the output of calculate_flux has Gauss*cm^2 units. However, it is not possible to use calculate_flux on YTDisks and only calculate_isocontour_flux is available for this data container. Do you know how I can obtain exactly the same result for the magnetic flux using the available calculate_isocontour_flux instead of the calculate_flux function? Cheers,

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SlicePlot error
by Sam Patrick Sept. 11, 2019

Sept. 11, 2019

Hi all, I've been encountering an error recently whenever I try to save a slice plot, such as: data_sets = yt.load("DD*/output_[0-9][0-9][0-9][0-9]") for ds in data_sets: filename = "density_t={:.3f}_ho.png".format(ds.current_time.in_units('Myr').value) val, loc = ds.find_max('density') print("{:.3f}".format(val)) plt = yt.SlicePlot(ds, L, field, center= loc, width= (size, 'pc')) plt.save(filename) YT seems to think issue is with the call to 'find_max' but a little experimentation shows this is not the case. I'm unable to work out any of what comes back to me asides that: File "plot.py", line 67, in <module> val, loc = ds.find_max('density') File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/static_output.py", line 826, in find_max source.quantities.max_location(field) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 635, in __call__ rv = super(MaxLocation, self).__call__(field, sample_fields) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 591, in __call__ rv = super(SampleAtMaxFieldValues, self).__call__(field, sample_fields) File "/opt/apps/pkgs/yt/3.5.1/src/yt/data_objects/derived_quantities.py", line 68, in __call__ for sto, ds in parallel_objects(chunks, -1, storage = storage): File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 520, in parallel_objects to_share, datatype = 'dict', op = 'join') File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 284, in passage return func(self, *args, **kwargs) File "/opt/apps/pkgs/yt/3.5.1/src/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 723, in par_combine_object data.update(self.comm.recv(source=i, tag=0)) File "mpi4py/MPI/Comm.pyx", line 1173, in mpi4py.MPI.Comm.recv File "mpi4py/MPI/msgpickle.pxi", line 302, in mpi4py.MPI.PyMPI_recv File "mpi4py/MPI/msgpickle.pxi", line 261, in mpi4py.MPI.PyMPI_recv_match Many thanks, Sam Patrick

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min_level and level_stats of a data container
by Guido granda muñoz Sept. 10, 2019

Sept. 10, 2019

Hello Yt users, I'm trying to obtain the maximum and minimum level of refinement of a data container in a simulation. What I am doing is the following: ds=yt.load(bname) sp_open=ds.disk(center,normal,radius,(res,'pc')) # smallest disk possible Where bname is the name of the snapshot, center, normal, radius, and res, are the desired center, normal, radius and height of the disk. I chose the resolution of the simulation as the height of the disk because I want it to represent a disk-like differential area and I the disk is located at the region of highest level of refinement. I tried to obtain the minimum and maximum levels of refinement over the sp_open subregion, however only max_level is implemented doing: sp_open.index.max_level Do you know how I can obtain the minimum level of refinement of a data container of a sub-region? Besides, when I print the level statistics of the subregion and the ones of the whole computational volume I get the same output. I print them using: sp_open.index.level_stats # subregion ds.index.level_stats # computational volume And I get: rec.array([( 1, 512, 0), ( 8, 4096, 1), ( 64, 32768, 2), ( 512, 262144, 3), ( 4096, 2097152, 4), (32768, 16777216, 5), ( 0, 0, 6), ( 0, 0, 7), ( 0, 0, 8), ( 0, 0, 9), ( 0, 0, 10), ( 0, 0, 11), ( 0, 0, 12), ( 0, 0, 13), ( 0, 0, 14), ( 0, 0, 15), ( 0, 0, 16), ( 0, 0, 17), ( 0, 0, 18), ( 0, 0, 19), ( 0, 0, 20), ( 0, 0, 21), ( 0, 0, 22), ( 0, 0, 23), ( 0, 0, 24), ( 0, 0, 25), ( 0, 0, 26), ( 0, 0, 27), ( 0, 0, 28), ( 0, 0, 29), ( 0, 0, 30), ( 0, 0, 31), ( 0, 0, 32), ( 0, 0, 33), ( 0, 0, 34), ( 0, 0, 35), ( 0, 0, 36), ( 0, 0, 37), ( 0, 0, 38), ( 0, 0, 39), ( 0, 0, 40), ( 0, 0, 41), ( 0, 0, 42), ( 0, 0, 43), ( 0, 0, 44), ( 0, 0, 45), ( 0, 0, 46), ( 0, 0, 47)], dtype=[('numgrids', '<i8'), ('numcells', '<i8'), ('level', '<i8')]) Which does not make sense to me, because the sub-region level statistics should not include coarse grids, even though this sub-region is in fact inside lower refinement regions. Shouldn't this statistics just print the lowest and highest refinement level inside the sub-region ? Thank you, -- Guido

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yt project calendar
by Britton Smith Sept. 9, 2019

Sept. 9, 2019

Greetings! We have created google calendar to keep track of yt project-related events. We'll post team meetings, workshops, or other events when people from yt are getting together. If you'd like to view it or add to your own calendar click here <https://calendar.google.com/calendar?cid=ZjJsaGJhcXAzcGRkY2xmNjRvN3RkNDBkbj…> . Britton

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AWS Certified SysOps Associate
by Kuldeep Tiwari Sept. 5, 2019

Sept. 5, 2019

Amazon has built a huge global infrastructure with 22 regions and 69 availability zones. All companies around the globe can use this globally present infrastructure to host their resources and hence they need certified, talented and skilled employees. The said expertise can only be achieved after studying the AWS Certified SysOps Associate course in Pune from a certified cloud instructor. AWS Certified SysOps Associate Training course in Pune helps one learn and understand, validate and demonstrate the expertise of hosting scalable, cost-effective and ultra-robust applications in the amazon cloud. Engineers certified on AWS Certified SysOps Associate can design a cloud infrastructure based on customer’s demand and budget. The certified engineers on AWS Certified SysOps Associate have a much upper hand as they will also be able to design a much secure and efficient infrastructure that RTO and RPO and other SLA objectives that large enterprises depend on. https://www.sevenmentor.com/aws-sysops-training-in-pune.php

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