Mailman 3 September 2008 - yt-users

No extrema in BinnedProfile3D
by rsoares 29 Sep '08

29 Sep '08

Hi, I have successful prof(sphere...) and prof2d(sphere...) objects plus the plots formatted with pylab, but prof3d(sphere...) gives "extrema" error: >>> prof3d = lagos.BinnedProfile3D(sphere, ... 8,"Density",extrema[0][0],extrema[0][1],True, ... 8,"Temperature",extrema[1][0],extrema[1][1],True, ... 8,"z-velocity",extrema[2][0],extrema[2][1],True, ... lazy_reader=True) *************************************** Traceback (most recent call last): File "<stdin>", line 2, in <module> NameError: name 'extrema' is not defined help(lagos.BinnedProfile3D) doesn't show any reference to "extrema" *************************************** my sphere object: >>> sphere = a.h.sphere([0.171875,0.21875,0.4453125],100/a["kpc"]) my prof, prof2d objects: >>> prof = lagos.BinnedProfile1D(sphere,8,"Radiuskpc",1.5,102.72,True,True) >>> prof.add_fields(["Density","Temperature"],weight="CellMassMsun") >>> prof2d = lagos.BinnedProfile2D(sphere,8,"Density",1e-10,1e-1,True,8,"Temperature",1e2,1e5,True,True) >>> prof2d.add_fields("CellVolume",weight="CellMassMsun") Thanks, -R.Soares

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No extrema in BinnedProfile3D
by rsoares 29 Sep '08

29 Sep '08

Hi, I have successful prof(sphere...) and prof2d(sphere...) objects plus the plots formatted with pylab, but prof3d(sphere...) gives "extrema" error: >>> prof3d = lagos.BinnedProfile3D(sphere, ... 8,"Density",extrema[0][0],extrema[0][1],True, ... 8,"Temperature",extrema[1][0],extrema[1][1],True, ... 8,"z-velocity",extrema[2][0],extrema[2][1],True, ... lazy_reader=True) *************************************** Traceback (most recent call last): File "<stdin>", line 2, in <module> NameError: name 'extrema' is not defined help(lagos.BinnedProfile3D) doesn't show any reference to "extrema" *************************************** my sphere object: >>> sphere = a.h.sphere([0.171875,0.21875,0.4453125],100/a["kpc"]) my prof, prof2d objects: >>> prof = lagos.BinnedProfile1D(sphere,8,"Radiuskpc",1.5,102.72,True,True) >>> prof.add_fields(["Density","Temperature"],weight="CellMassMsun") >>> prof2d = lagos.BinnedProfile2D(sphere,8,"Density",1e-10,1e-1,True,8,"Temperature",1e2,1e5,True,True) >>> prof2d.add_fields("CellVolume",weight="CellMassMsun") Thanks, -R.Soares

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Assertion Error in python2.5 yt
by rsoares 24 Sep '08

24 Sep '08

Hi, I don't know why I'm getting "AssertionError" and "KeyError: 'Density'" below. Anyone can explain? Thanks, R.Soares >>> import yt.lagos as lagos yt.lagos WARNING 2008-09-24 20:26:36,993 No HDF4 support >>> a = lagos.EnzoStaticOutput("RedshiftOutput0004") >>> v,c = a.h.find_max("Density") yt.lagos INFO 2008-09-24 20:27:38,292 Skipping serialization! yt.lagos INFO 2008-09-24 20:27:38,292 Caching hierarchy information yt.lagos INFO 2008-09-24 20:27:38,299 Gathering a field list (this may take a moment.) Warning: invalid value encountered in sqrt Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in sqrt yt.lagos INFO 2008-09-24 20:27:38,799 Max Value is 1.75364e-25 at 0.2890625000000000 0.2812500000000000 0.4843750000000000 in grid Grid_0001 at level 0 [36 35 61] >>> print v 1.75364112031e-25 >>> print c [ 0.2890625 0.28125 0.484375 ] >>> sphere = a.h.sphere([0.5,0.5,0.5],0.1/a["kpc"]) >>> prof = lagos.BinnedProfile1D(sphere,16,"Radiuskpc",0.0001,0.1,True,True) >>> prof.add_fields(["Density"]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/robyn/yt-pentiumD/lib/python2.5/site-packages/yt/lagos/Profiles.py", line 105, in add_fields self._lazy_add_fields(fields, weight, accumulation) File "/home/robyn/yt-pentiumD/lib/python2.5/site-packages/yt/lagos/Profiles.py", line 64, in _lazy_add_fields pbar = get_pbar('Binning grids', len(self._data_source._grids)) File "/home/robyn/yt-pentiumD/lib/python2.5/site-packages/yt/funcs.py", line 127, in get_pbar maxval=maxval).start() File "/home/robyn/yt-pentiumD/lib/python2.5/site-packages/yt/progressbar.py", line 213, in __init__ assert maxval > 0 AssertionError >>> print prof["Density"] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/robyn/yt-pentiumD/lib/python2.5/site-packages/yt/lagos/Profiles.py", line 115, in __getitem__ return self._data[key] KeyError: 'Density'

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Parallel yt
by Matthew Turk 17 Sep '08

17 Sep '08

Hi everyone, I've merged a bunch of changes from the parallel_profiles branch back into trunk. This means that projections and ("lazy") profiles are now transparently parallelized if you have mpi4py (mpi4py.scipy.org) installed. Un-lazy profiles are not, however, so that means you will need to (for now) know your min/max before you execute any profiles in parallel. To take advantage of the parallel projections and profiles you only need to install mpi4py. If you are running off trunk, the following command, if executed through mpirun, will be transparently parallel. (In fact, the plots will only be saved on the head node, as well.) -- from yt.mods import * pf = EnzoStaticOutput("galaxy1200.dir/galaxy1200") pc = PlotCollection(pf) pc.add_projection("Density", 0) pc.add_profile_sphere(0.1, '1', ["Density","Temperature"], lazy_reader=True, x_bounds=(1e-31,1e-24)) pc.add_phase_sphere(0.1, '1', ["Density","Temperature","VelocityMagnitude"], lazy_reader=True, x_bounds=(1e-31,1e-24), y_bounds=(1e1,1e8)) pc.save("par") -- Soon un-lazy profiles will be parallel as well, and then simpler commands like add_profile_sphere(width, unit, fields) will be parallelized by default. Let me know if you run into any problems. All of the unit tests pass, and I've tested in parallel and out of parallel and it all seems to work, but this change also touches a couple different places in the code so it could be a bit problematic for some corner cases. Another side effect of this change is that parallel data analysis now uses a much more efficient IO subsystem for the Packed HDF5 output. A single file open is executed on each CPU file, rather than one for every grid. -Matt

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Two new (undocumented) features: halo callback and periodic boundary conditions
by Matthew Turk 12 Sep '08

12 Sep '08

Hi guys, There are two new things I've found it necessary to add lately. These are only in trunk/ , so if you're on branches/yt-1.0 , you won't have them. (They might not be stable yet anyway!) The first is a hop circle callback. It accepts the output from Hop and adds on circles at the halo centers with the maximum particle radius as the radius of the circle. Here is a full example script, where it looks for halos in the *entire* dataset, then projects density and overplots the halo positions. You can also feed in a max_number argument to the HopCircleCallback, and it will only plot the first N halos, in order of decreasing mass. -- pf = EnzoStaticOutput("my_data0001.dir/my_data0001") hop = hop.HopList(pf.h.sphere([0.5]*3, 1.00)) pc = PlotCollection(pf,center=[0.5]*3) for ax in range(3): pc.add_projection("Density", ax) pc.plots[ax].add_callback(HopCircleCallback(hop, ax)) -- The other new addition is periodic plots. For this one, you can now do: -- pf = EnzoStaticOutput("my_data0001.dir/my_data0001") pc = PlotCollection(pf,center=[0.5, 0.8, 0.8]) pc.add_projection("Density", 0, periodic=True) -- note that the only difference is the keyword argument periodic=True. This will wrap your plot around based on its current center and the size of the domain. (It should respect axially-dependent DomainLeftEdge and DomainRightEdge.) Additionally -- for those of you that have read all the way to the bottom -- I started working on a profile to use inside IPython (ipython.scipy.org), which is just the most amazing Python shell in the world. Jeff Oishi is more of an IPython expert than I am, so he'll be adding to it and cleaning up my mistakes, but the end result is going to be that the operations of moving around, opening data, recursively finding data and examining data are all going to be simplified significantly. Much of the verbosity of the scripting interface is going to be hidden from the user and the guts will be more easily exposed. Have a good one! -Matt

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