Mailman 3 June 2014 - yt-users

About Volume-Rendering segmentation fault
by 吳佳鴻 June 6, 2014

June 6, 2014

Dear all, I want to bring up a problem that whether volume-rendering is data size dependent? Every time l loaded in data of size over about 4 GB, YT would pop out with segmentation fault message. However, most of the time my simulation data are much larger than 4GB, sometimes even larger than 50GB. Could anyone help me with this? Now I’m using the stable 2.6 version of YT. Is there any suggestion about this problem? Thank you in advance. Jia-Hung Wu

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syntax error when defining a new field
by Mike Butler June 6, 2014

June 6, 2014

Hello, I am using the latest version of yt-3.0 and am having some problems defining a new field. Here is an example of a field that produces an error: def _Sigm(field,data): return data["Density"] add_field("Sigma",function=_Sigm,units=r"\rm{g}/\rm{cm}^{2}",display_name=r"\Sigma") and this is the error I get when I try to do a projection of it: File "<string>", line 1 \Symbol ('rm' ,positive =True ){Symbol ('g' ,positive =True )}/\Symbol ('rm' ,positive =True ){Symbol ('cm' ,positive =True )}^{Integer (2 )} ^ SyntaxError: unexpected character after line continuation character It works fine on the stable and dev versions of yt. Has something changed for defining fields in 3.0? Thanks, Mike

2 1

Particles on projections
by Jeremy Ritter June 6, 2014

June 6, 2014

Hello YT, When using annotate_particles() on a ProjectionPlot, it does not seem to respect the width field. I get a very thin slab when plotting a 2kpc x 2kpc image. The cookbook implies that a width of 1.0 would correspond to the entire 2kpc line-of-sight domain (e.g. http://yt-project.org/docs/2.6/cookbook/complex_plots.html#plotting-particl… ). It is definitately only a thin slab (about 10pc wide) regardless of whether I use width=1.0 or width=2000.0. The slab thickness seems to be the same as in a slice plot. What would be the correct way to plot the entire 2kpc cube of particles in projection? Here are some comparison plots from YT (metallicity projection and slice) and VisIt (metallicity slice). YT Projection (Width 2kpc): http://grapenut.org/code/yt/paper/project/project_particles_175300_Projecti… YT Slice: http://grapenut.org/code/yt/paper/slice/slice_particles_175300_Slice_z_Meta… Visit (10pc slab on 2kpc x 2kpc slice): http://grapenut.org/code/yt/paper/particle_slab_0000.png YT example source: plot = ProjectionPlot(pf, 'z', nfield, center=star_center, width=star_width, axes_unit=axunit, weight_field='Density', fontsize=32) plot.annotate_particles(1.0, ptype=1.0, col='white') Cheers, -Jeremy

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yt with system python
by Geoffrey So June 5, 2014

June 5, 2014

Hi all, Is there a easy way to use the install script but use system python and system mpi4py from a supercomputer? Or what's the best way to go about installing yt manually with system python? From G.S.

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FLASH Spherical/Cylindrical Geometry
by Ismael D. Boureima June 5, 2014

June 5, 2014

Hello YT, I am trying to analyze some simulation results produced with FLASH. I have simulations in Cylindrical geometry and other in Spherical geometry. I read that the 3.0 version of YT supports curvilinear coordinates, but I can find any references explaining the 'How to'. I was wondering if there is anyone that can help me with that or direct me to some tutorial or anything like that. Best, Ismael

2 1

Angular momentum with a general axis
by Junhwan Choi (최준환) June 5, 2014

June 5, 2014

Hi yt users, I wrote basic yt script to make Jz profile of my simulation as follow: ====== import matplotlib as matplotlib matplotlib.use('Agg') from yt.mods import * import matplotlib.pyplot as plt Nbin = 75 rmax = 1200 # in pc index = 60 pf = load("../DD%04d/DD%04d" % (index,index)) rmin = [1e-4,2.0*pf.h.get_smallest_dx()*pf.units['pc']] sphere = pf.h.sphere(center, (rmax, 'pc')) bulk_velocity = sphere.quantities['BulkVelocity']() sphere.set_field_parameter('bulk_velocity', bulk_velocity) profile = BinnedProfile1D(sphere, Nbin, "Radiuspc", max(rmin), rmax, log_space=True, lazy_reader=True, end_collect=False) profile.add_fields('AngularMomentumZ',weight=None) profile.add_fields('Radius',weight=None) plt.loglog(profile['Radiuspc'], profile['AngularMomentumZ'],label='t=%4.2fMyr' % (pf.current_time*7.26), linestyle="-",color='b') plt.xlabel('r [pc]') plt.ylabel(r'j ($\rm{cm}^2/\rm{s}$)',fontsize=17) plt.xlim(1e-4,1000) plt.legend(loc=4, prop={'size':10}) plt.savefig('jprof2K_%04d' % index) ========= Now I would like to compute the AngularMomentum not according to x, y,and z but according to a general axis (i.e. angular momentum axis). Is there any simple way in yt to compute the AngularMomentum according to the general axis? Thank you in advance, Junhwan

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PerspectiveCamera question
by Michael Zingale June 4, 2014

June 4, 2014

I'd like to try using the PerspectiveCamera instead of the normal orthographic Camera. My script renders fine with Camera(), but I thought that I should be able to just change Camera() to PerspectiveCamera() and it should render with the perspective. Instead, I get an empty rendering -- is there something else one needs to do to use the PerspectiveCamera rather than just changing the class name but otherwise keeping the argument list the same? Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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Intro to yt-3.0 presentation
by Nathan Goldbaum June 3, 2014

June 3, 2014

Hi all, Today I gave a short presentation to Enrico Ramirez-Ruiz's research group as an introduction to yt and yt-3.0 in particular. The slides are available here as a reveal.js presentation: http://ngoldbaum.net/CASH_presentation.slides.html#/ And as a notebook via nbviewer: http://nbviewer.ipython.org/gist/ngoldbaum/a2cea8a9db17cb962fc4 Let me know if you have any questions or concerns about the slides :) -Nathan

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derived fields up to virial radius
by Reju Sam John June 2, 2014

June 2, 2014

Dear All, >>> vr = halos[0].virial_radius() will give the virial radius of the halo. >>> vm = halos[0].virial_mass() will give the virial mass of the halo in Msun, using only the particles in the halo. Like this, is it possible for me to create a *new function for a derived field* which can be calculated only up to virial radius. If possible, How can I do this? Thank You. -- Reju Sam John

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