Mailman 3 June 2011 - yt-users

covering_grid question
by Elizabeth Tasker June 7, 2011

June 7, 2011

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 … [View More]

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Problem with ParallellAnalysisInterface._mpi_allsum
by Anthony Harness June 7, 2011

June 7, 2011

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 … [View More]

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Big speedup with projections
by Matthew Turk June 6, 2011

June 6, 2011

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 … [View More]

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Re: [yt-users] Colourbar tick labels
by Elizabeth Harper-Clark June 6, 2011

June 6, 2011

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 … [View More]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") [View Less]

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documentation site
by gso＠physics.ucsd.edu June 3, 2011

June 3, 2011

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 June 2, 2011

June 2, 2011

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 June 1, 2011

June 1, 2011

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 June 1, 2011

June 1, 2011

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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