Mailman 3 October 2017 - yt-users

About ProfilePlot
by ｔyuta 18 Oct '17

18 Oct '17

Dear yt-users, Hi, I have a question on ProfilePlot. I want to make profile plot of dark matter density, taking gas density as a bin field, weighted by dark matter mass in the cell.I could make the plot, but the plot looks strange (it looks like chopped in small pieces). Also, I tried other plot changing n_bins like 64,32,16,8,... but they still be "chopped", or sometimes there were no line at all. For comparison, I made a plot weighted by cell_mass (which I don't want), and this look OK. To my understanding, if and only if there is at least 1 cell which fall into each bin, there should be some nonzero value no matter what weight I use, so the range of density which has nonzero dark matter density doesn't depend on the choice of weight field. It seems there is a discrepancy between these two plots. Could you tell me what's wrong with me? I tried on yt example dataset, IsolatedGalaxy/galaxy0030/galaxy0030. I'm working with yt-3.4.0. this is my code: import yt from yt.data_objects.particle_filters import add_particle_filter def stars(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 2 return filter def DMparticles(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 1 return filter add_particle_filter("stars", function=stars, filtered_type='io', requires=["particle_type"]) add_particle_filter("DMparticles", function=DMparticles, filtered_type='io', requires=["particle_type"]) def only_DM(field, data): return data['deposit','DMparticles_density'] def DM_in_cell_mass(field, data): return (data['only_DM_Density']*data['cell_volume']) ds_all=yt.load("~/IsolatedGalaxy/galaxy0030/galaxy0030") ds_all.add_particle_filter('stars') ds_all.add_particle_filter('DMparticles') ds_all.add_field(("gas", "only_DM_Density"), units="g/cm**3", function=only_DM) ds_all.add_field(("gas", "DM_cell_mass"), units="g", function=DM_in_cell_mass) sp = ds_all.sphere([0.5, 0.5, 0.5], (10, "kpc")) lineplot_gas_DM_density_128 = yt.ProfilePlot(sp, "density", [ "only_DM_Density"], weight_field="DM_cell_mass", n_bins=128) lineplot_gas_DM_density_gasweighted_128 = yt.ProfilePlot(sp, "density", [ "only_DM_Density"], weight_field="cell_mass", n_bins=128) lineplot_gas_DM_density_gasweighted_128.save("128_gasweighted") lineplot_gas_DM_density_128.save("128_DMweighted") Sincerely, Y.T.

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Question on derived field
by ｔyuta 17 Oct '17

17 Oct '17

Dear yt users, Hi, I have a question on derived field. I want to define "Dark Matter cell mass", which can be defined by (Dark matter density) * (cell_volume). To check that "Dark Matter cell mass" defined well, I also tried to define "my_cell_mass", which should give the same value as the default 'cell_mass', but it gave me an error, and I don't have any idea what the problem is. Could you help me with the problem? I'm working on Enzo data. Here is my python code (I'm sorry that it's lengthy): import yt from yt.data_objects.particle_filters import add_particle_filter def stars(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 2 return filter def DMparticles(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 1 return filter add_particle_filter("stars", function=stars, filtered_type='io', requires=["particle_type"]) add_particle_filter("DMparticles", function=DMparticles, filtered_type='io', requires=["particle_type"]) def only_DM(field, data): return data['deposit','DMparticles_density'] def DM_in_cell_mass(field, data): return (data['only_DM_Density']*data['cell_volume']) def my_cell_mass(field, data): return (data['density']*data['cell_volume']) ds_all=yt.load("/.../redshift00??") ds_all.add_particle_filter('stars') ds_all.add_particle_filter('DMparticles') ds_all.add_field(("gas", "only_DM_Density"), units="g/cm**3", function=only_DM) ds_all.add_field(("gas", "DM_in_cell_mass"), units="g", function=DM_in_cell_mass) ds_all.add_field(("gas", "my_cell_mass"), units="g", function=my_cell_mass) sp = ds_all.sphere([centerx, centery, centerz], ((somevalue), "kpc")) sp['cell_volume'] YTArray([ 4.44089210e-16, 4.44089210e-16, 4.44089210e-16, ..., 6.93889390e-18, 6.93889390e-18, 6.93889390e-18]) code_length**3 sp[('gas', 'my_cell_mass')] YTFieldNotFound: Could not find field '('gas', 'my_cell_mass')' in redshift00??. Best, Y.T.

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particle filters
by ｔyuta 16 Oct '17

16 Oct '17

Dear yt users, Hi, I want to know about particle filters. I learned that I can specify some particle type by doing like this: def stars(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 2 return filter I learned that the filter for star is No.2 from this example. What about other particles like gas or dark matter ? (Nathan kindly told me that dark matter is 0, but fragmentary information I got from google search suggest that it's 1, so I'm confused...) Is there any good documentation for this? I'm working with Enzo data. Best, Y.T.

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Problem while installing YT with Rockstar
by Prateek Gupta 15 Oct '17

15 Oct '17

Hello everybody, I am trying to install yt with enabling ROCKSTAR with the attached install_script.sh. I got some OS related error of FIlename is too long: Building Rockstar ******************************************** FAILURE REPORT: ******************************************** config=config) File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/ lib/python3.6/site-packages/conda_build/build.py", line 1030, in build create_env(config.build_prefix, specs, config=config) File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/ lib/python3.6/site-packages/conda_build/build.py", line 736, in create_env os.makedirs(join(prefix, 'conda-meta')) File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/lib/python3.6/os.py", line 210, in makedirs makedirs(head, mode, exist_ok) File "/home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/lib/python3.6/os.py", line 220, in makedirs mkdir(name, mode) OSError: [Errno 36] File name too long: '/home/dumbo/Documents/PhD_ Simulation/YT_Halo/yt-conda/conda-bld/rockstar_1508075330148/_b_env_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_p' ******************************************** ******************************************** Failure. Check /home/dumbo/Documents/PhD_Simulation/YT_Halo/yt-conda/yt_install.log. The last 10 lines are above. Please provide me some solution so that I can successfully enable ROCKSTAR. Thanks With best regards, -Prateek

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Digital NEST - Data Visualization Project
by Frederick Bogert 15 Oct '17

15 Oct '17

Hello Everyone, I am a volunteer at Digital NEST, a non-profit high-tech training and collaboration space for young people. We have been exploring the idea of using yt as the main focus of a course that will introduce young students to data visualization, python programming and open source software. One of our ideas is to contribute to the open issues marked "new-contributor-friendly" on the yt github. However, we were hoping to find someone who has a visualization project in mind and would want to collaborate with us. Maybe you have a data set and want visualizations produced and don't have the time to create them. We are open to discuss other projects that are more in-depth and are still focused on data visualization. You can find out more about Digital NEST here : http://digitalnest.org/about / Thanks, Alex

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Re: [yt-users] comoving distance a_box
by Nick Gnedin 13 Oct '17

13 Oct '17

Britton, In the simulations with the non-zero DC mode there are two scale factors to consider, a_uni (global scale factor of the universe) and a_box (the scale factor of the simulated region). YT recognizes this when reading ART data, but appears to use a wrong scale factor in computing comoving units. n On 10/13/2017 2:44 PM, Britton Smith wrote: > Hi Huanqing, > > I am a bit unclear on what the problem is. I think it is correct that > the conversion between proper and comoving uses the expansion factor. > I'm not sure what abox is. Can you elaborate on that? > > Britton > > On Thu, Oct 12, 2017 at 4:27 PM, Huanqing <hqchen(a)oddjob.uchicago.edu > <mailto:hqchen@oddjob.uchicago.edu>> wrote: > > Hi all, > > I’m using yt to generate halo catalog. However, when I check the > halos created by HaloCatalog function, I found the corresponding > comoving unit uses the expansion factor of the universe rather than > a_box. > > For example, My boxsize is 20cMpc/h, but if I use > .in_units(‘Mpccm/h’), the halos are offset by some amount (see > attached). I wonder if this is a bug in converting physical unit to > comoving unit? > > Thanks, > Huanqing > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> > > > > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> > Virus-free. www.avg.com > <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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comoving distance a_box
by Huanqing 13 Oct '17

13 Oct '17

Hi all, I’m using yt to generate halo catalog. However, when I check the halos created by HaloCatalog function, I found the corresponding comoving unit uses the expansion factor of the universe rather than a_box. For example, My boxsize is 20cMpc/h, but if I use .in_units(‘Mpccm/h’), the halos are offset by some amount (see attached). I wonder if this is a bug in converting physical unit to comoving unit? Thanks, Huanqing

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Density / DMDensity
by ｔyuta 12 Oct '17

12 Oct '17

Dear yt-users, Hi, I'm a new user of yt. I have a question about the default 'Density' field and 'Dark_Matter_Density' field. Do they contain stellar mass? If so, how can I read and subtract stellar mass from the data? Sincerely, Y.T.

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Conversion of Arepo file into Enzo format?
by aschauer＠usm.lmu.de 11 Oct '17

11 Oct '17

Dear usergroup, we are currently thinking of mapping an output from an Arepo simulation (in the hdf5 file format) to Enzo. We are wondering if someone has done this before and could help us or if this even is somehow incorporated into yt. Thanks for your help! Best regards, Anna

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installing yt on Stampede2 machine
by tazkera haque 08 Oct '17

08 Oct '17

Hi yt community, I am trying to install yt on Stampede2. I did $ wget https://raw.githubusercontent.com/yt-project/yt/master/doc/install_script.sh I made the following changes: INST_YT_SOURCE=1, INST_PY3=0, INST_SCIPY=1, INST_ASTROPY=1 $ bash install_script.sh I am getting the following error: Installing setuptools ******************************************** FAILURE REPORT: ******************************************** File "/home1/03858/thaque56/yt-conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 702, in __call__ instance = super(EntityType, cls).__call__(*args, **kwargs) File "/home1/03858/thaque56/yt-conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 719, in __init__ setattr(self, key, kwargs[key]) File "/home1/03858/thaque56/yt-conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 424, in __set__ instance.__dict__[self.name] = self.validate(instance, self.box(instance, val)) File "/home1/03858/thaque56/yt-conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 465, in validate raise ValidationError(getattr(self, 'name', 'undefined name'), val) ValidationError: Invalid value 1507188548.94 for timestamp ******************************************** ******************************************** I have attached the yt_install.log file Thanks for your time. Best Tazkera

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