Mailman 3 August 2013 - yt-users

Re: [yt-users] convering_grid question
by Mark Subbarao Aug. 14, 2013

Aug. 14, 2013

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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line annotations, center and zooming
by David Collins Aug. 12, 2013

Aug. 12, 2013

Hi, everybody-- I'm having trouble getting plot_window coordinages and annotate_image_line coordinates to agree. I have a small region that I'm trying to annotate with lines, and zoom in on. I'm having trouble getting my coordinates working together. If I do proj = oober.pf.h.proj(ax,'Density',source=source) pw = proj.to_pw(center=proj_center,origin='domain' ) pw.zoom( 1/size) I have the object centered on the plot and zoomed appropriately. If I do proj = oober.pf.h.proj(ax,'Density',… [View More]

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Re: [yt-users] line annotations, center and zooming
by Mark Subbarao Aug. 12, 2013

Aug. 12, 2013

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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In temperature plot unable to plot in normal scale
by Reju Sam John Aug. 10, 2013

Aug. 10, 2013

Dear All, I am trying to plot a multi plot of temperatures at different red-shifts with following script. from yt.mods import * # set up our namespace import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 1, colorbar='vertical', bw = 4) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" list = [11,13,22] m=0 #for kk in range(20,37): for kk in list: fn_i=str(kk) fn=file1+fn_i+file2+fn_i # parameter file to load print … [View More]

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Re: [yt-users] yt-3.0 error on update, now yt doesn't work (Kyle Stewart)
by Kyle Stewart Aug. 9, 2013

Aug. 9, 2013

Ah, that was the problem. After updating all, including updating Cython, it works fine. Thanks! -Kyle -- Kyle Stewart, Ph.D. Assistant Professor of Physics Department of Natural and Mathematical Sciences California Baptist University 8432 Magnolia Avenue Riverside, CA 92504 On 8/9/13 10:55 AM, "yt-users-request(a)lists.spacepope.org" <yt-users-request(a)lists.spacepope.org> wrote: >Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > >To … [View More]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. yt-3.0 error on update, now yt doesn't work (Kyle Stewart) > 2. Re: yt-3.0 error on update, now yt doesn't work (Kacper Kowalik) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 9 Aug 2013 16:06:26 +0000 >From: Kyle Stewart <kstewart(a)calbaptist.edu> >To: "yt-users(a)lists.spacepope.org" <yt-users(a)lists.spacepope.org> >Subject: [yt-users] yt-3.0 error on update, now yt doesn't work >Message-ID: <CE2A61BA.2EB2%kstewart(a)calbaptist.edu> >Content-Type: text/plain; charset="us-ascii" > >After updating yt (3.0) to the latest version with a simple "yt update" >command, I got the following error in the update log: > >Error compiling Cython file: >------------------------------------------------------------ >... > cdef void *tree_root > cdef int num_root > cdef int max_root > >cdef extern from "search.h" nogil: > void *tsearch(const void *key, void **rootp, > ^ >------------------------------------------------------------ > >yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' > >error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with >Cython > > > >Now yt won't work at all. If I try to call it I get the error: >"ImportError: No module named particle_oct_container" > >Does anyone know what's going on here? >Thanks! > >-Kyle > >-- >Kyle Stewart, Ph.D. >Assistant Professor of Physics >Department of Natural and Mathematical Sciences >California Baptist University >8432 Magnolia Avenue >Riverside, CA 92504 > > [View Less]

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yt-3.0 error on update, now yt doesn't work
by Kyle Stewart Aug. 9, 2013

Aug. 9, 2013

After updating yt (3.0) to the latest version with a simple "yt update" command, I got the following error in the update log: Error compiling Cython file: ------------------------------------------------------------ ... cdef void *tree_root cdef int num_root cdef int max_root cdef extern from "search.h" nogil: void *tsearch(const void *key, void **rootp, ^ ------------------------------------------------------------ yt/geometry/oct_container.pxd:81:… [View More]

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Problem with multi plot
by Reju Sam John Aug. 7, 2013

Aug. 7, 2013

Dear all, I am trying to create a muti plot of density's at different red-shift with the following code. from yt.mods import * import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 3, colorbar='vertical', bw = 3) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" L = [11,15,18,20,22,25,30,35,40] #for i in range (0, 8): for kk in L: fn_i=str(kk) fn=file1+fn_i+file2+fn_i print fn pf = load(fn) pc = … [View More]PlotCollection(pf, center=[0.5, 0.5, 0.5]) for i in range (0,3): for j in range (0, 3): p = pc.add_slice("Density", 2, axes = axes[i][j],figure = fig, use_colorbar=False) p.set_log_field(True) p.set_zlim(1e-31,5e-26) p.set_cmap("jet") p.modify["contour"]("Density", ncont=10, plot_args = {'colors':'w'},clim=(2e-28,2e-26)) p.modify["contour"]("Temperature", ncont=10, plot_args = {'colors':'k'},clim=(3e7,1e8)) #pc.set_width(3.0, 'mpc') #break # i = i+1 for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("multi_plot_3_3" % pf) But I am getting a wrong result. It is printing same figure in all panels. I think my logic(algorithm) is wrong. We have to reverse first two for loop. But that also making problem. Please help me. And also if I include the following line in the code. (in my code I commented it out) pc.set_width(3.0, 'mpc') it is showing following error. *Traceback (most recent call last):* * File "multi_plot_loop.py", line 24, in <module>* * pc.set_width(3.0, 'mpc') * * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 292, in set_width* * plot.set_width(width, unit)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 458, in set_width* * self._refresh_display_width()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 476, in _refresh_display_width* * self._redraw_image()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 423, in _redraw_image* * self._run_callbacks()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 263, in _run_callbacks* * cb(self)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 312, in __call__* * self.ncont = np.linspace(self.clim[0], self.clim[1], self.ncont)* * File "/data1/pdf/csurajit/yt-x86_64/lib/python2.7/site-packages/numpy/core/function_base.py", line 74, in linspace* * num = int(num)* *TypeError: only length-1 arrays can be converted to Python scalars* Please suggest me the most efficient way to achieve my goal (create a muti plot of density's at different red-shift). -- Reju Sam John [View Less]

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problem with covering_grid for Nyx data sets
by Wolfram Schmidt Aug. 6, 2013

Aug. 6, 2013

Hi, I have got problem that concerns Nyx users and/or yt developers. I want to read the root-grid level from AMR data sets with the following piece of code: num_ghost_zones=2 left=na.amin(pf.h.grid_left_edge,axis=0) right=na.amax(pf.h.grid_right_edge,axis=0) resolution = (right-left)/pf.h.grids[0]['dx']+2*num_ghost_zones cg = pf.h.covering_grid(0,left,resolution,num_ghost_zones=num_ghost_zones) This works for Enzo data sets, but it fails for Nyx data sets. The error message is … [View More]

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Making slices of Athena SMR data
by Eve Lee Aug. 6, 2013

Aug. 6, 2013

Hello, I'm trying to make a slice plot of Athena MPI SMR data using TimeSeriesData, and I find that the code only make slices out of the base level and blanks out deeper level regions. Following is how I read in the Athena vtk files: ts = TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True) my_storage={} for sto,pf in ts.piter(storage=my_storage): slc = SlicePlot(pf, 'z', 'Density') slc.set_zlim('Density', 0.0, 3.0) num = (pf.h.hierarchy_filename).split('.')[1] … [View More]

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Problem with Rockstar in yt
by Brian O'Shea Aug. 5, 2013

Aug. 5, 2013

Dear yt-users, I'm trying to use the Rockstar halo finder within yt, and am encountering some odd problems. I'm using the main development tree ( https://bitbucket.org/yt_analysis/yt) with changeset f936432ed45d, and attempting to use Rockstar to find halos on a small server running Ubuntu 12.04. When I call this script: ---- file test_rockstar.py ---- from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder pf = load("DD0057/data0057") rh = … [View More]

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