Mailman 3 June 2011 - yt-users

covering_grid question
by Elizabeth Tasker 07 Jun '11

07 Jun '11

Hi all, When I extract a patch of my simulation as a uniform mesh using covering_grid, what happens if the arguments are incompatible? For example: cubit = pf.h.covering_grid(4, left_edge=extract_leftedge, right_edge=extract_rightedge, dims=extract_dims, fields=["PotentialField"]) If I specify both the left and right edge, then the dimensions of the extracted region and the required level of the extraction are not independent. So I could ask for dimensions that are larger or smaller than a grid of that size at that level; does the code extract to the desired level and then interpolate, or does it ignore one of the settings? Also, am I good to assume that left and right edge do not need to be exactly on a grid boundary, but yt will shift them slightly so they fit? Thank you! Elizabeth

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Problem with ParallellAnalysisInterface._mpi_allsum
by Anthony Harness 07 Jun '11

07 Jun '11

Hello, I am trying to add a profile object to a Plot Collection (via pc.add_profile_object(data,fields) ) while running in parallel on Kraken. I get the following error: "TypeError: message: expecting a list or tuple" which ultimately comes from mpi4py.MPI.Comm.Allreduce which is called by ParallelAnalysisInterface._mpi_allsum(). In ._mpi_allsum() there is the following comment: "# We use old-school pickling here on the assumption the arrays are relatively small ( < 1e7 elements )". The dataset I am working with is larger than 1e7 elements, so is _mpi_allsum not able to pass such a large array to Comm.Allreduce? Thanks, Anthony Here is the traceback: File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 146, in add_fields self._lazy_add_fields(fields, weight, accumulation) File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 94, in _lazy_add_fields for gi,grid in enumerate(self._get_grids(fields)): File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 134, in __iter__ if not self.just_list: self.pobj._finalize_parallel() File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/data_objects/profiles.py", line 122, in _finalize_parallel self.__data[key] = self._mpi_allsum(self.__data[key]) File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 185, in passage return func(self, data) File "/yt-2.1stable-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 1124, in _mpi_allsum MPI.COMM_WORLD.Allreduce(data, tr, op=MPI.SUM) File "Comm.pyx", line 530, in mpi4py.MPI.Comm.Allreduce (src/mpi4py_MPI.c:43646) File "message.pxi", line 426, in mpi4py.MPI._p_msg_cco.for_allreduce (src/mpi4py_MPI.c:14446) File "message.pxi", line 33, in mpi4py.MPI.message_simple (src/mpi4py_MPI.c:11108) TypeError: message: expecting a list or tuple

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Big speedup with projections
by Matthew Turk 06 Jun '11

06 Jun '11

Hi all, In the development repository I have just swapped out the old-style projections, which were based on geometric overlap at the *grid* level, to a quadtree projection method that operates at the *cell* level. This operation should scale better, should provide much faster runtimes, and is able to operate inline with simulation codes (I have tested this.) All your projections should now be much, much faster -- on the yt-dev list, speedups of 2-10x were reported before this change was made. If you choose to upgrade and run into any issues, please let me know or file a bug report. "yt bugreport" can help with this, or see http://hg.enzotools.org/yt/issues/new . Best, Matt

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Re: [yt-users] Colourbar tick labels
by Elizabeth Harper-Clark 06 Jun '11

06 Jun '11

ps, here is my script: import matplotlib matplotlib.use("Agg") from yt.mods import * import pylab import sys import numpy as na def _MyRadius(field, data): center = data.get_field_parameter("center") dx = data["x"] - center[0] dy = data["y"] - center[1] dz = data["z"] - center[2] return na.sqrt(dx*dx + dy*dy + dz*dz) add_field("Radius", function=_MyRadius, take_log=False, units='') def _ConvertAccel(data): return data.convert("Length") / (data.convert("Time"))**2.0 def _RadiationAccelerationMagnitude(field, data): return ( (data["RadAccel1"])**2.0 + \ (data["RadAccel2"])**2.0 + \ (data["RadAccel3"])**2.0 )**(1.0/2.0) #return ( (data["Density"])*0.0+1.e-28) add_field("RadiationAccelerationMagnitude", function=_RadiationAccelerationMagnitude, take_log=False,convert_function=_ConvertAccel, units=r"\rm{cm}/\rm{s}^{2}") def _RadiationForceMagnitude(field, data): return ( data["RadiationAccelerationMagnitude"] * data["Density"] * data["CellVolume"]) add_field("RadiationForceMagnitude", function=_RadiationForceMagnitude, take_log=False, units=r"\rm{dynes}") def _RadiationForce1(field, data): return ( (data["RadAccel1"] * data["Density"] * data["CellVolume"])) add_field("RadiationForce1", function=_RadiationForce1, take_log=False, units=r"\rm{dynes}") def _RadiationForce2(field, data): return (( data["RadAccel2"] * data["Density"] * data["CellVolume"])) add_field("RadiationForce2", function=_RadiationForce2, take_log=False, units=r"\rm{dynes}") def _RadiationForce3(field, data): return (( data["RadAccel3"] * data["Density"] * data["CellVolume"])) add_field("RadiationForce3", function=_RadiationForce3, take_log=False, units=r"\rm{dynes}") xc = 0.5 yc = 0.5 zc = 0.5 width = 179.2 frame_template = "aaSN/%s/RadPresProj_%s_%s" folder = sys.argv[1] starti = int(sys.argv[2]) endi = int(sys.argv[3]) Q = 1.e47 RPSF = 2.0 nu = 21.62 * 1.6022e-12 # in ergs print "Q:",Q print "RPScaleFactor:", RPSF print "nu:",nu rho_min = 1.e24 rho_max = 5.e27 for i in range(starti, endi ,1): print "a, i=",i pf = load("SciNet/%s/DD%04i/data%04i" % (folder, i, i)) if pf is None: continue sp = pf.h.sphere([xc,yc,zc], 1.0) v, c = pf.h.find_max("Density") print i, c print v,c pc = PlotCollection(pf, center=(xc,yc,zc)) total = 0 print "Initial time, code units =", pf["InitialTime"] for ax in range(0,1): p = pc.add_projection("RadiationForceMagnitude", ax, weight_field="Density") p.set_log_field(True) p.set_cmap('Blues') p.set_zlim(1e24, 1e28) p.set_width(width,"pc") sp= pf.h.all_data() v1 = "RadiationForce2" v2 = "RadiationForce3" p.modify["quiver"](v1, v2, 12) if na.any(pf.h.grid_particle_count): colours = sp["ParticleMassMsun"] p.modify["particles"](1.0, p_size=10.0, col='r', minimum_mass= 6e0) print " XXXXX Particles present XXXXX" Timemyr = pf["InitialTime"]*pf["years"]/1.e6 p.modify["text"]((0.006,0.899),"%6.1f Myr" % (Timemyr), text_args = {'color':'w','fontsize':'30'}) p.modify["text"]((0.005,0.9),"%6.1f Myr" % (Timemyr), text_args = {'color':'b','fontsize':'30' }) pc.save(frame_template % (sys.argv[1],ax,i), override=True, format="eps")

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documentation site
by gso＠physics.ucsd.edu 03 Jun '11

03 Jun '11

I seem to be having trouble accessing the YT doc on the website, wondering if anyone else is having the same trouble. From G.S.

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Trestles module
by Matthew Turk 02 Jun '11

02 Jun '11

Hi all, Adam Jundt at SDSC just let me know that there's now a yt module on Trestles. If you're running there you should be able to load yt with "module load yt". We now have modules at Trestles, Nautilus, Kraken and I'm also told on Odyssey and SciNet. Having modules created for community usage is a strategy we're going to try to keep pursuing, so let me know if there are modules elsewhere; this will soon be on a central wiki or document of "maintained installations." Best, Matt

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Visualize 2D Clump Finder
by Nicholas Earl 01 Jun '11

01 Jun '11

Hey all, I've been trying to do a clump finding on some 2D data, however I'm having difficulties visualizing it. I had sifted through the yt mailing list and came across Dave Collin's clump_tools, but when I use it and attempt to overlay the clump results on a slice of density, it seems as though they don't want to overlap. Here is the script, and the image is attached. http://paste.enzotools.org/show/1678/ Thanks! Nick

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Support for cylindrical coordinates?
by Pan, Kuo-Chuan 01 Jun '11

01 Jun '11

Hi, Does yt support FLASH data with 2D cylindrical coordinates? If yes, how to enable it? If not, is it easy to implement it? I couldn't find info about it in the website. Thank you very much. Sincerely yours, Kuo-Chuan

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