Mailman 3 April 2018 - yt-users

The key words of "primoridal_index" in HaloMassFcn
by lianxiaoli87＠sjtu.edu.cn 19 Apr '18

19 Apr '18

Dear all: The key words of 'primoridal_index' in function of HaloMassFcn cannot be set during my work, and the traceback and error are: Traceback (most recent call last): File "./hmf.py", line 9, in <module> hmf = HaloMassFcn(simulation_ds=ds,halos_ds=my_halos,primoridal_index=0.9667,log_mass_min=13.0,log_mass_max=15.5,fitting_function=4,this_redshift=0.0) TypeError: __init__() got an unexpected keyword argument 'primoridal_index' Who know the reason for the key work of 'primoridal_index' in HaloMassFcn?

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Cool images or results made with yt?
by Nathan Goldbaum 18 Apr '18

18 Apr '18

Hi all, As some of you may know, my participation in yt development is partially funded by an NSF SI2-SSI grant. I'll be going to my first PI meeting for the grant in a couple of weeks where I'll be presenting a poster summarizing the present state of and future plans for the yt community. As part of this poster I'd like to highlight cool things people have used yt to accomplish. I'm particularly interested in visually appealing examples since this will be on a poster. You will of course be credited and cited for your work. Please feel free to reply to this thread on or off-list to me directly with more detail. Thanks for your help! -Nathan

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YT Python Installation Help
by Nomita Vazirani 16 Apr '18

16 Apr '18

Hello, I am trying to install YT Python on my scientific linux computer. The installation stops at some point and gives me a failure message. I am new to python and don't know what the issue is. I have copied the end of my log file below. Please let me know if you know what I should be doing differently. Sincerely, Nomita V. ^Mjupyter_console 5.2.0 | 0% ^Mjupyter_console 5.2.0###4 | 35% ^Mjupyter_console 5.2.0#######5 | 75% ^Mjupyter_console 5.2.0########7 | 88% ^Mjupyter_console 5.2.0#########6 | 97% ^Mjupyter_console 5.2.0########## | 100% ^Mbackcall 0.1.0 | 0% ^Mbackcall 0.1.0#######5 | 75% ^Mbackcall 0.1.0########9 | 90% ^Mbackcall 0.1.0########## | 100% ^Mhtml5lib 1.0.1 | 0% ^Mhtml5lib 1.0.1#3 | 13% ^Mhtml5lib 1.0.1#######5 | 75% ^Mhtml5lib 1.0.1######### | 90% ^Mhtml5lib 1.0.1########## | 100% ^Mwidgetsnbextension 3.2.1 | 0% ^Mwidgetsnbextension 3.2.1 | 1% ^Mwidgetsnbextension 3.2.1###9 | 40% ^Mwidgetsnbextension 3.2.1#######5 | 75% ^Mwidgetsnbextension 3.2.1########4 | 85% ^Mwidgetsnbextension 3.2.1#########1 | 91% ^Mwidgetsnbextension 3.2.1#########7 | 97% ^Mwidgetsnbextension 3.2.1#########8 | 98% ^Mlibgcc 7.2.0 | 0% ^Mlibgcc 7.2.03 | 4% ^Mlibgcc 7.2.0#######5 | 75% ^Mlibgcc 7.2.0########6 | 87% ^Mlibgcc 7.2.0#########5 | 95% ^Mlibgcc 7.2.0########## | 100% ^Mgettext 0.19.8.1 | 0% ^Mgettext 0.19.8.1 | 0% ^Mgettext 0.19.8.18 | 8% ^Mgettext 0.19.8.1##1 | 21% ^Mgettext 0.19.8.1###4 | 34% ^Mgettext 0.19.8.1####7 | 48% ^Mgettext 0.19.8.1######1 | 61% ^Mgettext 0.19.8.1#######4 | 75% ^Mgettext 0.19.8.1#######5 | 75% ^Mqt 5.6.2 | 0% ^Mnotebook 5.4.1 | 0% ^Mfontconfig 2.12.6 | 0% ^Mpexpect 4.5.0 | 0% ^Mtestpath 0.3.1 | 0% ^Mnbformat 4.4.0 | 0% ^Mzeromq 4.2.5 | 0% ^Mlibsodium 1.0.16 | 0% ^Mpyqt 5.6.0 | 0% ^Mpcre 8.41 | 0% ^Mentrypoints 0.2.3 | 0% ^Mgst-plugins-base 1.8.0 | 0% ^Micu 58.2 | 0% ^Mxorg-libxdmcp 1.1.2 | 0% ^Mjpeg 9b | 0% ^Mlibiconv 1.15 | 0% ^Mlibxcb 1.13 | 0% ^Msend2trash 1.5.0 | 0% ^Mlibpng 1.6.34 | 0% ^Mterminado 0.8.1 | 0% ^Mipython 6.3.1 | 0% ^Mnbconvert 5.3.1 | 0% ^Mfreetype 2.8.1 | 0% ^Mpandoc 2.1.3 | 0% ^Mwebencodings 0.5 | 0% ^Mparso 0.1.1 | 0% ^Mgmp 6.1.2 | 0% OSError(122, 'Disk quota exceeded') OSError(28, 'No space left on device') OSError(28, 'No space left on device') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') ## Package Plan ## environment location: /home/grad3/nomitav/Desktop/ytpython/yt-conda added / updated specs: - jupyter The following packages will be downloaded: package | build ---------------------------|----------------- gstreamer-1.8.0 | 1 3.3 MB conda-forge jupyter-1.0.0 | py_1 6 KB conda-forge pandocfilters-1.4.1 | py36_0 13 KB conda-forge wcwidth-0.1.7 | py36_0 23 KB conda-forge jupyter_core-4.4.0 | py_0 44 KB conda-forge pygments-2.2.0 | py36_0 1.3 MB conda-forge sip-4.18 | py36_1 263 KB conda-forge ptyprocess-0.5.2 | py36_0 22 KB conda-forge qtconsole-4.3.1 | py36_0 149 KB conda-forge pickleshare-0.7.4 | py36_0 11 KB conda-forge dbus-1.10.22 | 0 1.6 MB conda-forge jinja2-2.10 | py36_0 183 KB conda-forge ipywidgets-7.2.1 | py36_0 146 KB conda-forge SError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') The following packages will be downloaded: package | build ---------------------------|----------------- gstreamer-1.8.0 | 1 3.3 MB conda-forge jupyter-1.0.0 | py_1 6 KB conda-forge pandocfilters-1.4.1 | py36_0 13 KB conda-forge wcwidth-0.1.7 | py36_0 23 KB conda-forge jupyter_core-4.4.0 | py_0 44 KB conda-forge pygments-2.2.0 | py36_0 1.3 MB conda-forge sip-4.18 | py36_1 263 KB conda-forge ptyprocess-0.5.2 | py36_0 22 KB conda-forge qtconsole-4.3.1 | py36_0 149 KB conda-forge pickleshare-0.7.4 | py36_0 11 KB conda-forge dbus-1.10.22 | 0 1.6 MB conda-forge jinja2-2.10 | py36_0 183 KB conda-forge ipywidgets-7.2.1 | py36_0 146 KB conda-forge SError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') ## Package Plan ## environment location: /home/grad3/nomitav/Desktop/ytpython/yt-conda added / updated specs: - jupyter The following packages will be downloaded: package | build ---------------------------|----------------- gstreamer-1.8.0 | 1 3.3 MB conda-forge jupyter-1.0.0 | py_1 6 KB conda-forge pandocfilters-1.4.1 | py36_0 13 KB conda-forge wcwidth-0.1.7 | py36_0 23 KB conda-forge jupyter_core-4.4.0 | py_0 44 KB conda-forge pygments-2.2.0 | py36_0 1.3 MB conda-forge sip-4.18 | py36_1 263 KB conda-forge ptyprocess-0.5.2 | py36_0 22 KB conda-forge qtconsole-4.3.1 | py36_0 149 KB conda-forge pickleshare-0.7.4 | py36_0 11 KB conda-forge dbus-1.10.22 | 0 1.6 MB conda-forge jinja2-2.10 | py36_0 183 KB conda-forge ipywidgets-7.2.1 | py36_0 146 KB conda-forge SError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') OSError(122, 'Disk quota exceeded') ## Package Plan ## environment location: /home/grad3/nomitav/Desktop/ytpython/yt-conda added / updated specs: - jupyter The following packages will be downloaded: package | build ---------------------------|----------------- gstreamer-1.8.0 | 1 3.3 MB conda-forge jupyter-1.0.0 | py_1 6 KB conda-forge pandocfilters-1.4.1 | py36_0 13 KB conda-forge wcwidth-0.1.7 | py36_0 23 KB conda-forge jupyter_core-4.4.0 | py_0 44 KB conda-forge pygments-2.2.0 | py36_0 1.3 MB conda-forge sip-4.18 | py36_1 263 KB conda-forge ptyprocess-0.5.2 | py36_0 22 KB conda-forge qtconsole-4.3.1 | py36_0 149 KB conda-forge pickleshare-0.7.4 | py36_0 11 KB conda-forge dbus-1.10.22 | 0 1.6 MB conda-forge jinja2-2.10 | py36_0 183 KB conda-forge ipywidgets-7.2.1 | py36_0 146 KB conda-forge

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The key words of primoridal_index in HaloMassFcn
by 连晓丽 15 Apr '18

15 Apr '18

Dear all: The key words of 'primoridal_index' in function of HaloMassFcn cannot be set during my work, and the traceback and error are: Traceback (most recent call last): File "./hmf.py", line 9, in <module> hmf = HaloMassFcn(simulation_ds=ds,halos_ds=my_halos,primoridal_index=0.9667,log_mass_min=13.0,log_mass_max=15.5,fitting_function=4,this_redshift=0.0) TypeError: __init__() got an unexpected keyword argument 'primoridal_index' Who know the reason for the key work of 'primoridal_index' in HaloMassFcn? Thank you! Xiaoli Lian

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Failure of loading YT with the most recent version checkout from github
by Stephanie Ho 08 Apr '18

08 Apr '18

Hi, I just tried to checkout and update to the most update version from github. However, yt cannot even be loaded, as it appears some functions are missing. Please see the error message below. ---> 10 import yt 11 import yt.units as units 12 import pylab /Users/stephaniehho/yt-git/yt/__init__.py in <module>() 60 savetxt 61 ---> 62 from yt.fields.api import \ 63 field_plugins, \ 64 DerivedField, \ /Users/stephaniehho/yt-git/yt/fields/api.py in <module>() 17 field_plugins 18 ---> 19 from . import angular_momentum 20 from . import astro_fields 21 from . import cosmology_fields /Users/stephaniehho/yt-git/yt/fields/angular_momentum.py in <module>() 24 register_field_plugin 25 ---> 26 from .vector_operations import \ 27 create_magnitude_field 28 /Users/stephaniehho/yt-git/yt/fields/vector_operations.py in <module>() 30 handle_mks_cgs 31 ---> 32 from yt.utilities.lib.misc_utilities import obtain_relative_velocity_vector 33 34 def get_bulk(data, basename, unit): ImportError: cannot import name obtain_relative_velocity_vector ############## Checking the yt version then also fails, as it shows a similar/related error message. File "/Users/stephaniehho/anaconda2/bin/yt", line 4, in <module> import yt.utilities.command_line File "/Users/stephaniehho/yt-git/yt/__init__.py", line 62, in <module> from yt.fields.api import \ File "/Users/stephaniehho/yt-git/yt/fields/api.py", line 19, in <module> from . import angular_momentum File "/Users/stephaniehho/yt-git/yt/fields/angular_momentum.py", line 26, in <module> from .vector_operations import \ File "/Users/stephaniehho/yt-git/yt/fields/vector_operations.py", line 32, in <module> from yt.utilities.lib.misc_utilities import obtain_relative_velocity_vector ImportError: cannot import name obtain_relative_velocity_vector I just checked out within the last 30 minutes. I therefore wonder does anyone face a similar error. Thanks, Stephanie

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Unexpected Change in Defined Quantity
by Stephanie Ho 08 Apr '18

08 Apr '18

Hi, I define a quantity with radius = ds.quan(0.05,'Mpc'). I then use this radius to create a data object (a sphere). However, this radius changes automatically without any new calculation or assignment. See the simple code below. eagle_fname = './data/snapshot_028_z000p000/snap_028_z000p000.0.hdf5' unit_base = {'UnitLength_in_cm' : 3.085678e+24, 'UnitMass_in_g' : 1.989e+43, 'UnitVelocity_in_cm_per_s' : 100000.0} ds = yt.load(eagle_fname,unit_base=unit_base) center = ds.arr(np.array([12.08809,4.474372,1.4133347]),'Mpccm') radius = ds.quan(0.05,'Mpc') cc = ds.sphere(center,(radius,'Mpc')) print 'radius: ', radius print 'Number of particle in cc: ', len(cc['PartType0', 'ParticleIDs']) print 'radius: ', radius ########## The output results: radius: 0.05 Mpc Number of particle in cc: 3699 radius: 0.0338849953984 Mpc I am not sure what trigger this unexpected change; what I have done is just to extract a quantity from the data object. Thanks, Stephanie

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NaNs from Xray emissivity calculation with EAGLE data
by Andrea Negri 04 Apr '18

04 Apr '18

Hi all, I am just getting started with yt, what I want to do is a easy calculation of the X-ray luminosity in some EAGLE galaxies. I was following the approach explained in http://yt-project.org/doc/analyzing/analysis_modules/xray_emission_fields.h… by using data taken from http://yt-project.org/data/ (in particular snapshot_028_z000p000 and apec_emissivity_v2.h5). My script is fairly simple, however the output is always NaN. Am I doing something wrong? The version of yt I'm using the 3.4.1, and the script is the following #------------------------------------ # -*- coding: utf-8 -*- import yt import time t0 = time.time() # all data taken from http://yt-project.org/data/ ds = yt.load('snapshot_028_z000p000/snap_028_z000p000.0.hdf5') xray_fields = yt.add_xray_emissivity_field(ds, 0.5, 7.0, table_type='apec') t1 = time.time() print('read time=', t1-t0) sp = ds.all_data() t2 = time.time() print('selection time=', t2-t1) Lx = sp.quantities.total_quantity("xray_luminosity_0.5_7.0_keV") t3 = time.time() print('Lx time=', t3-t2) print ('Lx in erg/s =',Lx) #------------------------------------ Many thanks in advance for your help. Cheers, Andrea -- Dr. Andrea Negri Instituto de Astrofísica de Canarias (IAC) Calle Vía Láctea, s/n, 38205 San Cristóbal de La Laguna, Tenerife, Spain E-mail: anegri(a)iac.es Skype: andreanegri86 Hangouts: negri.andre(a)gmail.com --------------------------------------------------------------------------------------------- ADVERTENCIA: Sobre la privacidad y cumplimiento de la Ley de Protección de Datos, acceda a http://www.iac.es/disclaimer.php WARNING: For more information on privacy and fulfilment of the Law concerning the Protection of Data, consult http://www.iac.es/disclaimer.php?lang=en

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Re: Question on saving OffAxisSlicePlot as dataset and ploting
by Nathan Goldbaum 03 Apr '18

03 Apr '18

Hi Huanqing, I'm replying to the mailing list so others can see this discussion. On Tue, Apr 3, 2018 at 3:34 PM, Huanqing <hqchen(a)oddjob.uchicago.edu> wrote: > Hi Nathan, > > Thanks for your prompt reply, but in your ipynb, you didn’t really load > saved_ds (In [6]) right? > Oops, you're right. Apologies for the typo. > > When I do > plot=yt.SlicePlot(saved_ds,[1,1,1],density) > plt.show() > > It says SlicePlot can only plot fields that are defined on a mesh but > received the following particle fields: [(‘all’,’density’)] > I don't see that, here's what happens when I correct the mistake you pointed out in my notebook: https://gist.github.com/ngoldbaum/2b33e46dddcac6453cdb9cac71d9c46f Which yt version are you using? Which sort of data are you dealing with? I'm using yt 3.4.1 and the example I shared uses Enzo data. > > Thanks, > Huanqing > > On Apr 3, 2018, at 11:17 AM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > I remembered just now I had to manually whitelist this e-mail last night > because you're not on the mailing list. Just in case you didn't see my > reply to the list, see below. Please subscribe to the mailing list to > participate further. > > -Nathan > > On Tue, Apr 3, 2018 at 11:04 AM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > >> Hi Huanqing, >> >> Take a look at the following notebook, which I created using a dataset >> from yt-project.org and yt 3.4.1 on python 3.6: >> >> https://gist.github.com/ngoldbaum/2712f5ae826d6b95bb3833ef27be541d >> >> Does this not work for your dataset? >> >> -Nathan >> >> On Mon, Apr 2, 2018 at 8:52 PM, Huanqing <hqchen(a)oddjob.uchicago.edu> >> wrote: >> >>> Hi, >>> >>> I have a question on save OffAxisSlicePlot. My original dataset is very >>> large so every time it takes a long time to make a slice. I wish to save it >>> as dataset so I can quickly reload it to plot. However, after I reload it >>> and use OffAxisSlicePlot, it says “received the following particle fields: >>> (‘gas’,’density’). I had a look at the source code ( >>> http://yt-project.org/doc/_modules/yt/visualization/plot_wi >>> ndow.html#OffAxisSlicePlot) and it has a step to validate_mesh_fields, >>> in which the comments says ytdata plot datasets load mesh data as a >>> particle field. >>> >>> I wonder how to get rid of this error and plot the saved slice dataset? >>> >>> Thank you very much! >>> Huanqing >>> >>> _______________________________________________ >>> yt-users mailing list -- yt-users(a)python.org >>> To unsubscribe send an email to yt-users-leave(a)python.org >>> >>> >> > >

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ANN: Grackle 3.1 released!
by Andrew Emerick 03 Apr '18

03 Apr '18

Hello! We are excited to announce the release of Grackle 3.1! The Grackle is a library for chemistry and radiative cooling in astrophysical simulations and models. Grackle 3.1 is fully backward compatible with Grackle 3.0 and comes with a number of new features and bugfixes. *Major enhancements:* * New metal cooling tables that include atomic self-shielding corrections for both Haardt & Madau and Faucher-Giguere tables. These tables have “_shielded” appended to the filenames. * H2 self-shielding of Lyman-Werner radiation using the Wolcott-Green et al. (2011) model. Length scales for H2 column density can be calculated using 1) neighboring grid zones (grid codes only), 2) a user-supplied array of lengths, or 3) the local Jeans length. * pygrackle Python wrapper now compatible with Python 3. Pygrackle works with Python 3.4 and later. Python 2.7 is still supported. *Minor enhancements:* * Added low-temperature (T < 30 K) term to (HI + HII -> H2II + p) rate. * Allow UV background parameters, UVbackground_redshift_on, UVbackground_redshift_fullon, UVbackground_redshift_drop, and UVbackground_redshift_on, to be user-settable and make redshift-dependent ramping factor symmetric in redshift. * Single consistent tolerance value used in solver. * Volumetric and specific heating arrays now setable from Python interface. * Documentation improvements. * Automated testing using Bitbucket Pipelines. *Added/updated machine make files:* * NCSA Blue Waters * Caltech Wheeler *Bugfixes:* * Fixed scaling and unit conversion issues with volumetric and specific heating rate arrays and added tests. * Fixed scaling issue of metal cooling rates. Metal cooling rates will change by a factor of (1 / 0.76). * Source code format fixes for radiative transfer fields * Fixed issue where NaNs occurred in atomic self-shielding when redshift is greater than turn-on redshift for UV background. * Fixed OpenMP compilation errors. * Fixed memory allocation in C example. * Fixed precision issues with radiation transfer field variables. * Fixed bug in answer testing where some tests were not being properly compared to existing answers. Source code repository: https://bitbucket.org/grackle/grackle Documentation: http://grackle.readthedocs.io/ Method paper: http://adsabs.harvard.edu/abs/2017MNRAS.466.2217S Since the Grackle 3.0 release, 25 pull requests have been accepted from 7 people, including one new contributor (in bold): *Christine Corbett* Andrew Emerick Nathan Goldbaum Cameron Hummels Hsi-Yu Schive Britton Smith John Wise We thank these people for their contributions. Development of Grackle happens in the open on Bitbucket: https://bitbucket.org/grackle/grackle. We welcome new contributors. -The Grackle development team

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Question on saving OffAxisSlicePlot as dataset and ploting
by Huanqing 03 Apr '18

03 Apr '18

Hi, I have a question on save OffAxisSlicePlot. My original dataset is very large so every time it takes a long time to make a slice. I wish to save it as dataset so I can quickly reload it to plot. However, after I reload it and use OffAxisSlicePlot, it says “received the following particle fields: (‘gas’,’density’). I had a look at the source code (http://yt-project.org/doc/_modules/yt/visualization/plot_window.html#OffAxi… <http://yt-project.org/doc/_modules/yt/visualization/plot_window.html#OffAxi…>) and it has a step to validate_mesh_fields, in which the comments says ytdata plot datasets load mesh data as a particle field. I wonder how to get rid of this error and plot the saved slice dataset? Thank you very much! Huanqing

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