Mailman 3 January 2016 - yt-users

POLL: A New Default Colormap
by Matthew Turk 29 Jan '16

29 Jan '16

Hi folks, The current default colormap that yt uses is called "Algae," and it's been with us for a while. Recently some of us on the yt-dev mailing list (which is open to join!) have begun to look at alternate colormaps that have better characteristics, particularly from an accessibility perspective. If you have the time, it would be really, *really* helpful if you could take this anonymous, two question (only one of which is mandatory!) poll about which of the four candidates we've come up with you like the best. http://goo.gl/forms/D4qQqkPIMq Thanks very much! The poll will be open at least a week, and I'll report back the results here sometime after that. -Matt

2 1

particle angular momentum profile error and accumulation profile
by Junhwan Choi (최준환) 27 Jan '16

27 Jan '16

Hi yt users, I try to make a particle angular momentum profile using the following script: ================================ import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") index = 45 Nbin= 100 rmax = 3000 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] rmin = max([1.0e-3,2.0*ds.index.get_smallest_dx().in_units('pc')]) sphere = ds.sphere(center, rmax*units.pc) bulk_velocity = sphere.quantities['BulkVelocity']() sphere.set_field_parameter('bulk_velocity', bulk_velocity) profile = yt.Profile1D(sphere, 'radiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field=None) profile.add_fields(('all', 'particle_angular_momentum_x')) profile.add_fields(('all', 'particle_angular_momentum_y')) profile.add_fields(('all', 'particle_angular_momentum_z')) PartAngularMomentum = np.sqrt(profile[('all', 'particle_angular_momentum_x')]**2 + profile[('all', 'particle_angular_momentum_y')]**2 + profile[('all', 'particle_angular_momentum_z')]**2) plt.plot(profile.x, PartAngularMomentum, label='Total',linestyle="-",color='r') plt.xlabel('r [pc]') plt.ylabel('pang') ====================================== And I got the following error: ……….. Traceback (most recent call last): File "pang.py", line 26, in <module> profile.add_fields(('all', 'particle_angular_momentum_x')) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 112, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 425, in _bin_chunk rv = self._get_data(chunk, fields) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 240, in _get_data arr[:,i] = chunk[field][filter].in_units(units) File "/home/jhchoi/common/src/yt/yt/units/yt_array.py", line 1123, in __getitem__ ret = super(YTArray, self).__getitem__(item) IndexError: index 1322 is out of bounds for axis 1 with size 1322 I do not understand what the problem is? One more question: Is there any way to make accumulation density profile with yt.Profile1D(……)? Thank you in advance, Junhwan

2 7

unnecessary margin between multi panels with eps_writer
by Junhwan Choi (최준환) 26 Jan '16

26 Jan '16

Hi yt user, I try to make a multi panels plot with eps_writer modules. I use following script and it works with one unpleasant shortcoming. ================================================== import matplotlib as matplotlib matplotlib.use('Agg') import numpy as np import matplotlib.pylab as pylab import yt import yt.units as units import yt.visualization.eps_writer as eps import pyx index = 60 ds = yt.load('../DD%04d/DD%04d' % (index,index)) ds.add_particle_filter('sink') ad = ds.all_data() center = ds.find_max(('gas', 'density'))[1] # scale and limit LBox = [4000, 4] plot_list = [] for nrow in range(0,2): for norm in 'zxy': pc =yt.SlicePlot(ds, norm, ('gas', 'density'), center=center) pc.set_width(LBox[nrow],"pc") plot_list.append(pc) ep = eps.multiplot(ncol=3, nrow=2, yt_plots=plot_list, bare_axes = True) ep.title_box("xy", loc=(0.1,1.95)) ep.title_box("yz", loc=(1.1,1.95)) ep.title_box("xz", loc=(2.1,1.95)) ep.scale_line(label="%6.0f kpc" % (LBox[0]/4000.0), size=0.25, linewidth=pyx.style.linewidth.Thick, loc=(0.05,1.08)) ep.scale_line(label="%6.0f pc" % (LBox[1]/4.0) , size=0.25, linewidth=pyx.style.linewidth.Thick, loc=(0.05,0.08)) ep.save_fig("multi_plot") ================================================== Here, I attach the resulting plot. Everything is fine except there are white spacing/margin between panels. Is there any way to remove the white spacing/margin? Thanks in advance, Junhwan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

4 5

Magnetic quiver plots
by Sushilkumar 26 Jan '16

26 Jan '16

Dear yt: I am trying to use magnetic quiver plot from the following link http://yt-project.org/doc/visualizing/callbacks.html. As per the example, are we using annotate_magnetic_field() callback without passing any arguments in the parenthesis (like velocity_x,velocity_y for regular quiver plots)? On Sat, Jan 23, 2016 at 1:09 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: issue with saving a 1d profile as a dataset (Devin Silvia) > 2. Re: issue with saving a 1d profile as a dataset (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 22 Jan 2016 19:03:02 +0000 > From: Devin Silvia <devin.silvia(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] issue with saving a 1d profile as a dataset > Message-ID: > <CAFP_SCJmPNBhacaC= > 56yeB_TdJj7tcsEDjEtAiRT8gjeuvBxZw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I followed up with Britton on this off-list and it ended up being an issue > with my outdated version of Numpy. Updating to Numpy 1.10 fixed the > problem. > > -Devin > > On Tue, Jan 19, 2016 at 6:03 AM Britton Smith <brittonsmith(a)gmail.com> > wrote: > > > Hi Devin, > > > > I'm not able to reproduce this on test data using some other fields, so > > I'm guessing there's something strange with the profile. Can you print > out > > prof.x? If that doesn't show anything, can you upload the image that > this > > script makes? > > > > Britton > > On Mon, Jan 18, 2016 at 9:01 PM, Devin Silvia <devin.silvia(a)gmail.com> > > wrote: > > > >> Hi all, > >> > >> I'm currently trying to save a 1d profiles that I've generated using > >> ProfilePlot, using the "save_as_dataset" function. My code looks like: > >> > >> http://paste.yt-project.org/show/6169/ > >> > >> But I get the following error/traceback: > >> > >> http://paste.yt-project.org/show/6170/ > >> > >> Without knowing more about the internal machinery, I'm not sure what the > >> fix is for this. > >> > >> Thanks is advance to anyone who has time to look into this! > >> > >> Cheers, > >> Devin > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Fri, 22 Jan 2016 13:13:18 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] issue with saving a 1d profile as a dataset > Message-ID: > <CAJXewOnknL4FqS1TdJQaQh-= > w1Wwopkbw24o8fqsqoyPAskZ_Q(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Just out of curiosity - which version were you on? I think we should > at least be trying to support 1.8 or newer, although testing is always > a concern. > > On Fri, Jan 22, 2016 at 1:03 PM, Devin Silvia <devin.silvia(a)gmail.com> > wrote: > > Hi all, > > > > I followed up with Britton on this off-list and it ended up being an > issue > > with my outdated version of Numpy. Updating to Numpy 1.10 fixed the > > problem. > > > > -Devin > > > > > > On Tue, Jan 19, 2016 at 6:03 AM Britton Smith <brittonsmith(a)gmail.com> > > wrote: > >> > >> Hi Devin, > >> > >> I'm not able to reproduce this on test data using some other fields, so > >> I'm guessing there's something strange with the profile. Can you print > out > >> prof.x? If that doesn't show anything, can you upload the image that > this > >> script makes? > >> > >> Britton > >> On Mon, Jan 18, 2016 at 9:01 PM, Devin Silvia <devin.silvia(a)gmail.com> > >> wrote: > >>> > >>> Hi all, > >>> > >>> I'm currently trying to save a 1d profiles that I've generated using > >>> ProfilePlot, using the "save_as_dataset" function. My code looks like: > >>> > >>> http://paste.yt-project.org/show/6169/ > >>> > >>> But I get the following error/traceback: > >>> > >>> http://paste.yt-project.org/show/6170/ > >>> > >>> Without knowing more about the internal machinery, I'm not sure what > the > >>> fix is for this. > >>> > >>> Thanks is advance to anyone who has time to look into this! > >>> > >>> Cheers, > >>> Devin > >>> > >>> _______________________________________________ > >>> yt-users mailing list > >>> yt-users(a)lists.spacepope.org > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 95, Issue 35 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

2 1

issue with saving a 1d profile as a dataset
by Devin Silvia 22 Jan '16

22 Jan '16

Hi all, I'm currently trying to save a 1d profiles that I've generated using ProfilePlot, using the "save_as_dataset" function. My code looks like: http://paste.yt-project.org/show/6169/ But I get the following error/traceback: http://paste.yt-project.org/show/6170/ Without knowing more about the internal machinery, I'm not sure what the fix is for this. Thanks is advance to anyone who has time to look into this! Cheers, Devin _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 3

yt-3.2.2 Installation probelm
by 최호승 21 Jan '16

21 Jan '16

Hello all, I'm trying to install yt-3.2.2 using all-in-one installation script. (It's downloaded two days ago) Using the same script, I could install yt successfully on my desktop and laptop (ubuntu 14.04 & 15.10). But it fails on a server (Ubuntu 15.04) installation log tells that Cython import was not successful. failed to import Cython: /home/hopung/.local/lib/python3.4/site-packages/Cython/Compiler/ Code.cpython-34m.so : undefined symbol: PyFPE_jbuf error: Cython does not appear to be installed But I can import and run Cython modules on the same machine, both with Python2 and Python3. The Code.cpytohn-34m.so source file is there. I tried to exclude packages in install_script.sh - for example, not installing zlib, ftype, and/or pyx. No change in install_script.sh seems to make a difference. I get the same error when I try yt-dev version. I've installed many versions of yt on many machines, but this error is new to me. Does anyone have seen this error? Cheers, Hoseung _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

YT biggest data
by Nicolas Gillet 19 Jan '16

19 Jan '16

Hello, I just begin with yt, I run some of the exemple with small ramses simulations. I would like to know what are the limits of YT ? What is the biggest simulation that it can handle ? Currently yt is not really happy with my 1024**3 simulations, it seems very long to make a snap.all_data(). Is there some way do anyway the analysis with yt, or do I have to go back to my lower analysis functions ? An other completelly different question, I am trying to install rockstar. I see that rock star work well on full simulation dataset, but it is possible to run it on only one snap ? (of course losing the time information) Thank you for help, Nicolas _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

2D Axisymmetric BoxLib Dataset Issue
by Max Katz 19 Jan '16

19 Jan '16

Hi all, I'm trying to use yt for analysis of a 2D axisymmetric (R-z) dataset using the BoxLib frontend. After I load the dataset I am trying to make a covering grid with the following commands: ds = yt.load(pltfile) problo = ds.domain_left_edge.v probhi = ds.domain_right_edge.v dim = ds.domain_dimensions grid = ds.covering_grid(level=0, left_edge = problo, dims = dim) That leads to the following output at the terminal: yt : [INFO ] 2016-01-18 01:35:47,516 Parameters: current_time = 0.0 yt : [INFO ] 2016-01-18 01:35:47,516 Parameters: domain_dimensions = [1024 2048] yt : [INFO ] 2016-01-18 01:35:47,517 Parameters: domain_left_edge = [ 0.00000000e+00 -5.12000000e+09 0.00000000e+00] yt : [INFO ] 2016-01-18 01:35:47,517 Parameters: domain_right_edge = [ 5.12000000e+09 5.12000000e+09 6.28318531e+00] Traceback (most recent call last): File "analyze.py", line 78, in <module> wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile) File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 615, in rho_T_scatterplot grid = ds.covering_grid(level=0, left_edge = problo, dims = dim) File "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 503, in __init__ self.ActiveDimensions = self._sanitize_dims(dims) File "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 552, in _sanitize_dims "Length of dims must match the dimensionality of the dataset") RuntimeError: Length of dims must match the dimensionality of the dataset Thoughts? It seems like the code has some inconsistency in what the dimensionality of the dataset is. The Castro plot file in question doesn't provide that third angular dimension of size 2*pi. Max Katz Ph.D. Candidate, Department of Physics and Astronomy Stony Brook University http://astro.sunysb.edu/mkatz/ _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

4 10

FRB of OffAxisProjectionPlot data?
by Marc Schartmann 19 Jan '16

19 Jan '16

Dear all, can I create a fixed resolution buffer from an OffAxisProjectionPlot? Or is there another way to extract the data in form of a numpy array? I only managed to do this for projections along coordinate axes. Thanks a lot. Best wishes, Marc _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

yt for RAMSES
by Nicolas Gillet 18 Jan '16

18 Jan '16

Hello, I am Nicolas, I am a new YT user. I am working on RAMSES simulations. - First I have noted a "bug" (or misunderstand) in the yt.load of RAMSES data. It takes all the times of the output as 'code_units' times, which is not the case. The output times are negative and I think it needs a FLRW integration to be converted in conventional time. Using directly the 'code_units_time' to convert in cgs time is wrong. So all the times are false in the loaded yt data, simulation time, particles ages .... - My second question is link to the first point. With ramses there is a tool (getstarlist.f90) that extract only the stars in a .txt file, with the ages in Myr with the proper conversion. My idea is to load those new data in yt, and creat a new field for particles, with this correct ages. With the example I creat a filter to isolate the stars from 'all' particles, and it apear in the derived_field_list. But I do not find a way to creat a new field for this filtered particles and even for the 'all' particles. I would like to have the possibility to have a field ad['star', 'my_own_ages'] or ad['all', 'my_own_ages']. What I have done: ### isolate star particles def _star(pfilter, data): filter = data['all', 'particle_age'] < 0 return filter add_particle_filter('star', function=_star, filtered_type='all', requires=['particle_age','particle_identifier']) ds.add_particle_filter('star') ### stars are correctly created ok ### create a global star_age field, not linked to 'all' or 'star' def _star_age(field, data): T = data['particle_age'].in_units('Myr') * 0. selec_stars = np.where(data['particle_age'] < 0)[0] T[selec_stars] = Stars[5,:] * yt.units.Myr return T ds.add_field('star_age', function=_star_age, units='Myr') What I try: def _star_age2(field, data): T = data['all','particle_age'].in_units('Myr') * 0. selec_stars = np.where(data['all','particle_age'] < 0) [0] T[selec_stars] = Stars[5,:] * yt.units.Myr return T ds.add_field(('all','star_age2'), function=_star_age2, units='Myr') ### ('all','star_age2') appear in the derived_field_list but ad['all','star_age2'] => YTFieldTypeNotFound: Could not find field 'all' Thank you for your help, Nicolas _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

5 8