Mailman 3 November 2016 - yt-users

Fwd: calculate the Xray emissivity
by Andrea Negri 20 Nov '16

20 Nov '16

Hi all, I'm using yt to analize ZEUS simulations. I have been able to remap all the native fields on a custom AMR grid that I created, and I load the data in the GDF format. I'm very happy with this, but when I try to calculate the Xray emissivity using this little script here: import yt from yt.analysis_modules.spectral_integrator.api import \ add_xray_emissivity_field ds=yt.load('GDFhdfaa.0000073.hdf5') xray_fields = add_xray_emissivity_field(ds, 0.2, 8.0, with_metals=False, constant_metallicity=0.5) plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') I get the error: Traceback (most recent call last): File "./xray.py", line 11, in <module> plot = yt.ProjectionPlot(ds, 'x', 'xray_luminosity_0.2_8.0_keV') File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/visualization/plot_window.py", line 1495, in __init__ max_level=max_level) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 263, in __init__ self.get_data(field) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 337, in get_data self._handle_chunk(chunk, fields, tree) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/construction_data_containers.py", line 437, in _handle_chunk d = chunk[field] * dl File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1295, in get_data self._generate_fields(fields_to_generate) File "/home/andrea/.yt-dev/yt-conda/src/yt-hg/yt/data_objects/data_containers.py", line 1346, in _generate_fields raise YTFieldUnitError(fi, fd.units) yt.utilities.exceptions.YTFieldUnitError: The field function associated with the field '('gas', 'H_number_density')' returned data with units 'dimensionless/g' but was defined with units 'cm**-3'. I tried to check the GDF frontend, but I'm able to understand if the error is there or somewhere else... You can find a very light dataset in the GDF format in attachment, if you want ot reproduce the error. You need to download both files, since in the GDF file there are some hard links to the amr2 file (still an hdf5 file). I tried both the stable and the developer version of yt, and the error is the same. Any ideas? I really think that my GDF file is correct, since I'm able to slice and project all the native fields (density, temperature, velocities...). Thanks, Andrea

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sliceplots for setting maximum temperature at the center
by turhan nasri 20 Nov '16

20 Nov '16

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

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Problem using Multiplot_yt
by rahul kashyap 20 Nov '16

20 Nov '16

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

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Annotating particles in Flash with different sizes
by Joshua Wall 20 Nov '16

20 Nov '16

Hello users, I've recently been using yt to plot gas and star Flash runs where the particle size is proportional to the log of the mass. I've noticed that using the annotate_particles method is occasionally seems to be giving me the wrong masses. Here's a plot with the annotate_particles method: ds = yt.load("./Runs/ProbStars/data/turbsph_hdf5_plt_cnt_0021") gr = yt.ProjectionPlot(ds, 'x', 'dens') gr.annotate_particles(ds.domain_width[0], p_size=np.multiply(20.0,np.log10(dd['particle_mass'].in_units('Msun').v)), col='b') gr.annotate_timestamp(corner='upper_left') gr.zoom(5) gr.save('ann_part_test.png') gr.show() Here's the plot: [image: ann_part_test.png] And if I manually add the stars (also, I'm not sure why I have to call proj.show() before the scatter plot to get this to work...): proj = yt.ProjectionPlot(ds, 'x', 'dens') proj.show() dens_plot = proj.plots['dens'] proj_ax = dens_plot.axes fig = dens_plot.figure proj_ax.scatter(dd['particle_position_y'].in_units('pc').v, dd['particle_position_z'].in_units('pc').v, s=np.multiply(20.0,np.log10(dd['particle_mass'].in_units('Msun').v)), c='k') proj_ax.set_xlim(-1.0, 1.0) proj_ax.set_ylim(-1.0, 1.0) proj.show() proj.save('man_ann_part.png') Here's the plot for this (which has the correct sized particles, note the one closest to 0,0 is about 1.4 Msun and much smaller in the plot below): [image: man_ann_part.png] I am currently re-writing my plotting routines (which I use to make movies) to account for this, but it is a lot uglier this way, especially since I run on a cluster without display and don't want to have to call proj.show() before I call for the scatter plot. I'm guessing I can probably also just call proj.save() twice with the same effect, but I haven't tested it yet. Any assistance would be appreciated, and thanks! Cordially, Josh Wall -- Joshua Wall Doctoral Candidate Department of Physics Drexel University 3141 Chestnut Street Philadelphia, PA 19104

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outputting Gadget2 files in HDF5 format to visualize in yt
by turhan nasri 19 Nov '16

19 Nov '16

Hi, I am just starting to learn the SPH simulation code Gadget2, I followed this tutorial https://astrobites.org/2011/04/02/installing-and-running-gadget-2/ and succesfully ran the simulation and got some output files. However, I needed to comment out the -DHAVE HDF5 to avoid compilation error and now I have no good way to visualize my output. I srated with SPLASH but still trying to figure out how to deal with some error there. I figured out yt has analysis tool for Gadget outputs and I would very much love to try yt. I would very appreciate if anyone tells me how to get Gadget output in HDF5 formate. I am using ubuntu 16.04LTS. I need to know how to install HDF5 or necessary package in my machine to get the HDF5 output first. laso If you tell me a little how to change the Gadget Makefile for that, that would be very nice. I am quoting some excerpt from my Makefile. #--------------------------------------- Output OPT += -DHAVE_HDF5 #OPT += -DOUTPUTPOTENTIAL #OPT += -DOUTPUTACCELERATION #OPT += -DOUTPUTCHANGEOFENTROPY #OPT += -DOUTPUTTIMESTEP #---------------------------------------------------------------------- # Here, select compile environment for the target machine. This may need # adjustment, depending on your local system. Follow the examples to add # additional target platforms, and to get things properly compiled. #---------------------------------------------------------------------- #--------------------------------------- Select some defaults CC = mpicc # sets the C-compiler OPTIMIZE = -O2 -Wall -g # sets optimization and warning flags MPICHLIB = -lmpich #--------------------------------------- Select target computer SYSTYPE="trina" #SYSTYPE="Mako" #SYSTYPE="Regatta" #SYSTYPE="RZG_LinuxCluster" #SYSTYPE="RZG_LinuxCluster-gcc" #SYSTYPE="OpteronMPA" #SYSTYPE="OPA-Cluster32" #SYSTYPE="OPA-Cluster64" #--------------------------------------- Adjust settings for target computer ifeq ($(SYSTYPE),"trina") CC = mpicc OPTIMIZE = -O3 -Wall GSL_INCL = -I/usr/local/include GSL_LIBS = -L/usr/local/lib FFTW_INCL= -I/usr/local/include FFTW_LIBS= -L/usr/local/lib MPICHLIB = -L/usr/lib endif and sorry for spaming the yt list with Gadget2 stuff. thanks Turhan

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Reminder: Python in Astronomy 2017 Deadline
by Stuart Mumford 19 Nov '16

19 Nov '16

Hello all, Applications for the Python in Astronomy 2017 conference (http://openastronomy.org/pyastro/2017/) are open until *December 9th*, 2016. The conference will be held on 8th - 12th May 2017 at the Lorentz Center in Leiden, the Netherlands. Please fill out this form <https://docs.google.com/forms/d/e/1FAIpQLSfFvzolQvW5PJRbgIoPs73t4LgMIDNX2lX…>to apply. The Python in Astronomy conferences aim to bring together a wide variety of people who currently use, develop or teach people about Python packages in the context of all forms of Astronomy. Participant selection will be made with the goal of growingthe Python in Astronomy community and we particularly encourage requests to attend from junior astronomers and people who are new to contributing to open source software. This conference is neither intended to be an introduction to Python bootcamp nor only for expert-level Python developers, but we do expect all participants to have at least a basic familiarity with Python. Please fill out the application and indicate the level of financial support you will likely require in order to attend. Once the participants have been selected, we’ll get back in touch with everyone about their specific financial support requirements. Stuart Mumford, SOC Chair Matt Craig Kelle Cruz Daniela Huppenkothen Abigail Stevens Erik Tollerud

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Gravitational Boundedness with Gas and Particles
by Jason Galyardt 17 Nov '16

17 Nov '16

Hi all, I'd like to use the yt clump finder to identify gravitationally bound clumps. However, my FLASH simulation includes both gas (on the mesh) and massive particles. I would like to use both of these gravitational sources in the determination of boundedness, but it's not clear to me that the current implementation of gravitational_binding_energy() in yt/utilities/lib/misc_utilities.pyx does this. I suspect that it would be relatively straightforward to add the ('deposit', 'io_mass') field to the gravitational_binding_energy() function, but I'm not entirely sure how to access this field in a safe manner in Cython. Has anyone already solved this problem? Thanks, Jason ----- Jason Galyardt University of Georgia

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remap spherical geometry on cartesian
by Andrea Negri 16 Nov '16

16 Nov '16

Hi all, sorry if you receive this message more than once. I'm still struggling in porting the my ZEUS data in spherical coordinates in yt. After many tests, I decided that it would by a good idea to interpolate all my arrays from the spherical (non uniform) grid to an AMR grid in cartesian (it will help me also with other software that accepts only cartesian coordinates). I wrote a python program to create an octree, but it is quite unefficient. Than, I read that it is possible to create an octree with yt. What I REALLY would like to do is to compute the octree, save all grids, all the levels in the GDF format, than with a script open the GDF format and insert in every grid the interpolated density, energy etc... I'm able to create the octree (or at least I think!) using the attached script, but I don't know how to save it in the GDF format. Could you help me? Many thanks, Andrea

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Postdoctoral position at Los Alamos National Laboratory
by Joseph Smidt 15 Nov '16

15 Nov '16

Hey everyone, Sorry to spam the mailing list, but we have a computational postdoc job ad AAS [1] some might be interested in. We welcome anyone with experience running Enzo, Gadget/Gizmo or related codes to apply. Despite the job ad's more specific reading, we are interested in a wide variety of research utilizing these codes. The advantages are a minimum starting salary of $73,600 (see lanl.gov/postdocs), nearly unlimited computational resources and a decent chance of obtaining a permanent position within 2-3 years. So sorry about the spam, but for some it might be a decent opportunity. [1] https://jobregister.aas.org/job_view?JobID=56489 -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

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Profile Plot set_ylabel
by Katharina Wollenberg 13 Nov '16

13 Nov '16

Hi together, I would like to relabel the y-axis of a profile plot. I tried the “set_ylabel”-command but got the error message that ProfilePlot does not have this attribute. I also could not find an answer when skimming through the yt Cookbook. Can anyone help me with that? Thanks in advance! 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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