Mailman 3 June 2015 - yt-users

Ploting particles with FLASH
by Andrew James Emerick June 5, 2015

June 5, 2015

Hi everyone, I just tried to make a simple projection plot of gas density in FLASH, while overplotting tracer particles using the annotate_particles callback: proj = yt.ProjectionPlot(ds,'z','density',center='m',weight_field='density') proj.annotate_particles((1.0,'kpc')) I got an error while doing this, however: http://paste.yt-project.org/show/5599/ The error occurs during the annotate_particles callback. I played around with the width argument, but it did not help. Is this functionality supported with FLASH data? Thanks, Andrew E. -- Graduate Student Columbia University Department of Astronomy

2 4

Ray Profiling
by John Regan June 4, 2015

June 4, 2015

Hi All, I can't seem to figure out how to create 1D profiles anymore! I created a ray object and I'd like to profile it. I used BinnedProfile1D in the past but that seems to be deprecated now and ProfilePlot is throwing errors at me. I have a simple script here that creates a ray and tries to 1D profile it http://paste.yt-project.org/show/5591/ It spits this error at me Traceback (most recent call last): File "H2Rates.py", line 86, in <module> plot = yt.ProfilePlot(my_ray, "density", ["temperature"]) File "/homeappl/home/regan/appl_taito/YT/3.1/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.py", line 217, in __init__ logs=logs)] File "/homeappl/home/regan/appl_taito/YT/3.1/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 1478, in create_profile for f, l in zip(bin_fields, logs)] AttributeError: 'YTRay' object has no attribute 'quantities' Cheers, John

2 3

About creating derived fields
by 孫伯符 June 4, 2015

June 4, 2015

Hello, all, I am new to yt Project. I want to create new derived fields. I have two data arrays: one for vertex coordinate, and the other for vertex indexes of face. I also create two datasets of particle type: one for vertex coordinate, and the other for face info. For face dataset, the particle position is the coordinate of face center, which is calculated from data arrays. # Associate data with fields data = dict(particle_position_x=face_pos[0], particle_position_y=face_pos[1], particle_position_z=face_pos[2]) # Create bounding box bbox = utility.create_bounding_box(face_pos) # Create dataset for face ds_face = yt.load_particles(data, bbox=bbox) (p.s. utility.create_bounding_box() is user-defined function by me) I create three derived fields (before loading the data): neighbor vertex index 1-3, for future use. The problem is that I want to feed the value from face data array. How do I access other data array in derived field function. # Define 1st neighbor index @derived_field(name="neighbor_index_1") def _neighbor_index_1(field, data): If this is not a good way to create the relationship for vertices, please give me suggestions. Besides, after that, I want to render the mesh given the vertex coordinate and face info. Is there a function to do this? Thank you very much. [?] Best regards, Mew

2 2

Problem with Rockstar + time series in yt 3.2-dev
by Brian O'Shea June 3, 2015

June 3, 2015

Hi folks, I'm having some problems creating a time series of halo catalogs with Rockstar on a small cosmology run, using the tip of yt 3.2-dev (changeset a2b03516ed2c) with mpi4py v1.3.1 (and OpenMPI v1.4.3) installed on a local Linux cluster. I'm pretty confident that it has something specifically to do with a time series. When I use this script to call rockstar on a single dataset: http://paste.yt-project.org/show/5586/ with this command line: mpirun -np 8 --mca btl ^openib python new_rockstar_ts.py --parallel everything works just fine, and does so for every RDNNNN dataset. However, when I uncomment lines 40-44 and comment out lines 47-53 in the same script (i.e., like this: http://paste.yt-project.org/show/5587/) so that the code now uses a time series of all of the RDNNNN datasets rather than a single dataset, and use the same command line, I immediately get a seg fault that appears to be related to the mpi4py package: http://paste.yt-project.org/show/5588/ The datasets that I'm using for the time series can be found here: http://galactica.pa.msu.edu/~bwoshea/data/datasets/rockstar_timeseries.tar.… (total size ~300 MB). Does anybody have any idea what's going on? Thanks! --Brian

3 4

Guess what's back?
by Matthew Turk June 3, 2015

June 3, 2015

The mailing list archives! http://lists.spacepope.org/pipermail/yt-users-spacepope.org/ Hooray!

3 3

Profile plot of a 2d projection FRB object
by Ben Thompson June 3, 2015

June 3, 2015

Hello everyone. I was wondering if anyone has had experience with producing a profile plot from a 2d projection object (FRB object). Essentially, what I am trying to do is plot the stellar surface density of a galaxy as a function of radius. This is achieved by doing the following from a disk YT object called cylinder (in which the origional simulation object is called shot) center = cylinder.get_field_parameter("center") normal = cylinder.get_field_parameter("normal") image_width = (100,"kpc") three_image_width = YTArray((image_width[0], image_width[0], image_width[0]),image_width[1]) left = center - image_width right = center + image_width region = shot.region(center, left, right) proj = yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc") the error arrises here prof = yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None ) where I get the error /gpfs/home/........./profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional) 1304 else: 1305 raise NotImplementedError -> 1306 bin_fields = data_source._determine_fields(bin_fields) 1307 fields = data_source._determine_fields(fields) 1308 if units is not None: AttributeError: 'FixedResolutionBuffer' object has no attribute '_determine_fields' Any ideas how to get around this error? Also some other things to add as a postscript. Since how the projection works, if I provide weights=None as a keyword argument within the ProjectionPlot object, I get a surface density (g/cm^2). But also a "cylindrical_r" in cm^2 as well. I *think* the way to get around this is to do another projection where weights="ones", get the radius values out of that profile.. and then in matplotlib, useing the surface density array from the former profile, and the radius bin array from the latter... Produce a plot of the surface density as a function of radius from those two arrays (I might check by hand afterwards to see if this does the trick). This seems kinda convoluted so I am wondering if there is an easier way than this. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

8 16

ANN: Grackle 2.1 release
by Britton Smith June 2, 2015

June 2, 2015

Greetings everyone, I am pleased to announce the release of version 2.1 of the Grackle chemistry and cooling library. The Grackle is a library for chemistry and radiative cooling in astrophysical simulations. This release contains a number of enhancements to the existing functionality. These updates are as follows: * The calculation of the mean molecular weight and temperature fields in tabulated mode now properly considers the effects of photo-ionization from the UV backgrounds. Note, the input data files have been updated to include a mean molecular weight field. The new files must be used for all tabulated mode calculations using Grackle version 2.1 and later. * The chemistry network has been updated to include the H2I+ + H- -> H+ + H2 reaction in the H- update. * The value of the solar metal mass fraction has been updated to be consistent with the photo-ionization code, Cloudy. The value has been changed from 0.02041 to 0.01295. * The build system has been converted to using libtool. Shared and static libraries will both be built automatically. * A python script, cooling_cell.py, has been added to simulate the cooling of a single cell over a period of time. This can be used as a benchmark to test implementations in simulation codes. These are the first set of improvements made only to the 2.x branch of Grackle. From here on out, only the 2.x and higher versions will be updated. Those using version 1.1 and earlier are encouraged to update to the latest version. As always: The Grackle can be obtained at: https://bitbucket.org/grackle/grackle The documentation can be seen here: http://grackle.readthedocs.org/ Stay cool! Britton on behalf the Grackle dev team

1 0

Overlaying matplotlib plots on yt plots
by DORIS LEE June 2, 2015

June 2, 2015

Hi all, I have been trying to plot a circle of a given radius around the boundary of a collapsing cloud to track its evolution. Usually in matplotlib, I would just draw a circle using a xy meshgrid, but if I do this using matplotlib the circle would be on a separate figure and not overlaid on the yt plot. So I tried using a PlotWindow to separate the data and the yt plot but I get this error: In [92]:yt.visualization.plot_window.PlotWindow(proj,(-1e5,1e5,-1e5,1e5)) AttributeError: 'ProjectionPlot' object has no attribute '_key_fields' In general, is there to get my RAMSES data loaded into yt as a numpy array with actual numbers in them then feed it into matplotlib to do this task? or alternatively, is there a simpler way to do this directly on yt using annotate_contour or some other yt function? Thank you. Regards, Doris ---- Code for generating the attached plot, the green boundary line is in theory what I am trying to draw. ds= yt.load("../../bin/output_00002/info_00002.txt") proj = yt.ProjectionPlot(ds, "y", "density",window_size=10) proj.set_cmap("density","rainbow") proj.annotate_velocity() proj.show()

3 3

ramses dataset structure
by Desika Narayanan June 2, 2015

June 2, 2015

Hi All, I have a couple of very super basic questions about how Ramses data sets are organized which I think are all related (and rooted in my total ignorance of Ramses outputs). 1. How should I interpret the particle data outputs from a Ramses data set? http://paste.yt-project.org/show/5579 on a yt example data set, I get a total particle mass of total particle mass = 1.13468176647e+16 Msun What particles does this encompass? It seems large even for dark matter and stars. 2. Relatedly - is there an obvious way to extract just the information about stars from a ramses data set? (Assuming the particles are made up of only dark matter and stars...though maybe I have that wrong?) 3. If I run the same script with the Output 00101 (Cosmology output) from the yt Ramses data sets, I find that a derived field list doesn't list anything that's obviously for the gas. Unless this is the 'deposit' fields (which my gadget-centric brain thinks is related to an octree deposition somehow). Thanks! -desika

2 2

tab completion broken
by Juan Camilo Ibanez Mejia June 2, 2015

June 2, 2015

Hi all, I've been hesitant about moving to the newer versions of yt and am still using yt2.6. Although I'm finally starting to move to the newer version, but I'm not sure if I broke the tab completion help or something because I dont get information about the functions anymore. Below I send two snapshots, one for yt2.6 and one for the latest stable version yt3.1 [cid:7F12DE07-5B99-45C7-8B6A-7E4167E43A5F@internal.amnh.org] [cid:C87186F7-D1E9-45EB-AAEE-C398EE99BB20@internal.amnh.org] Is there something I am missing in the installation, or update, that I missed ? thanks for your help Juan -------------------------------------------------- Juan Camilo Ibáñez-Mejia PhD student in Physics. Institut für Theoretische Astrophysik, Zentrum für Astronomie Heidelberg jibanez(a)zah.uni-heidelberg.de<mailto:jibanez@zah.uni-heidelberg.de> American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> ----------------------------------------------------

4 6