Mailman 3 June 2009 - yt-dev

Packer
by Matthew Turk 30 Jun '09

30 Jun '09

Hi guys, Did any of you write a packing script to go from unpacked HDF5 -> Packed HDF5 for Enzo data? -Matt

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Gas_Energy
by david collins 26 Jun '09

26 Jun '09

Hi-- I ran into a recursion limit in trying to access Gas_Energy-- I believe it has something to do with the workaround for the underscore in GasEnergy. I'm using code that worked at some time before April, but has since stopped, I believe that the 'working' code didn't have the "Gas_?Energy" update. I've overloaded GasEnergy in my plugins.py to return isothermal gas energy, since I don't have a GasEnergy field (or a TotalEnergy, for that matter) in my simulations. However, when I now go to access it, I get stuck in the ping pong between "GasEnergy" and "Gas_Energy" in EnzoFields.py: def _GasEnergy(field, data): return data["Gas_Energy"] / _convertEnergy(data) add_field("GasEnergy", function=_GasEnergy, units=r"\rm{ergs}/\rm{g}", convert_function=_convertEnergy) def _Gas_Energy(field, data): return data["GasEnergy"] / _convertEnergy(data) add_field("Gas_Energy", function=_Gas_Energy, units=r"\rm{ergs}/\rm{g}", convert_function=_convertEnergy) instead of using my own field. Why doesn't it take mine first, before looking in EnzoFields.py? Is there a way to force this behavior? Thanks, d.

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Software Carpentry
by Matthew Turk 25 Jun '09

25 Jun '09

Hi guys, I'd seen this before, but it just hit reddit again and I thought some of you might be interested. http://ivory.idyll.org/articles/advanced-swc/ There are some really good parts in this, particularly about naming functions and methods (http://ivory.idyll.org/articles/advanced-swc/#a-short-digression-naming-and… ) and a very clear introduction to generators and iterators ( http://ivory.idyll.org/articles/advanced-swc/#iterators and http://ivory.idyll.org/articles/advanced-swc/#generators ). It's totally worth reading/skimming. -Matt

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code review
by Matthew Turk 23 Jun '09

23 Jun '09

Hi guys, I've set up a reviewboard server: review.enzotools.org Right now it's not that nice to look at, but next version of the software will have theme support. I've also added a 'yt review' command to the trunk: $ yt review will submit a subversion diff of your entire current directory to the server; you can also specify which files you want it to submit diffs for, and you can update existing diffs, etc etc. I might have committed some errors, but the primary function of the script works, so it should be useful for us. I'm still working on getting the emails to send out. I'd like major changes, as well as changes to deep and relatively wide-reaching machinery, to go through here before they get committed. Let me know if there are any problems -- and there might very well be, because I'm still new to the review board software. :) -Matt

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HaloFinding stars/dm
by Stephen Skory 22 Jun '09

22 Jun '09

Yo, now that I've been playing around with stars and creation_time, I've noticed a bug in HaloFinding. The total_mass line below will include stars regardless of dm_only: # do it once with no padding so the total_mass is correct (no duplicated particles) self.padding = 0.0 padded, LE, RE, data_source = self._partition_hierarchy_3d(padding=self.padding) # For scaling the threshold, note that it's a passthrough total_mass = self._mpi_allsum(data_source["ParticleMassMsun"].sum()) Is there a better way to fix it than this? # do it once with no padding so the total_mass is correct (no duplicated particles) self.padding = 0.0 padded, LE, RE, data_source = self._partition_hierarchy_3d(padding=self.padding) # For scaling the threshold, note that it's a passthrough if dm_only: select = data_source["creation_time"] > 0 total_mass = self._mpi_allsum(data_source["ParticleMassMsun"][select].sum()) else: total_mass = self._mpi_allsum(data_source["ParticleMassMsun"].sum()) _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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EnzoCosmology
by Stephen Skory 20 Jun '09

20 Jun '09

Hi guys, may I propose standardizing convention of HubbleConstantNow in EnzoCosmology? In that file, HubbleConstantNow is in km/s/Mpc, but elsewhere in yt, it's in 100 km/s/Mpc: >>> pf['CosmologyHubbleConstantNow'] 0.65000000000000002 Hopefully this will prevent 10^2 problems in the future... like what I've been seeing until I discovered this discrepancy. _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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kdTree
by Stephen Skory 17 Jun '09

17 Jun '09

Hi guys, I want to add a couple routines to the HaloFinder having to do with halo nearest neighbor stuff. In particular, I'd like to add something like: halo_list.nearest_neighbor_3D(haloID,N) where it finds the Nth nearest neighbor to halo 'haloID' in three dimensions. halo_list.nearest_neighbor_2D(haloID,N,[x,y,z]) where it finds the Nth nearest neighbor in two dimensions, projected along vector [x,y,z]. The obvious way to go about this is a kdTree. I know this is something that Matt has put a lot of thought into. I've been playing around with this one <http://sites.google.com/site/mikescoderama/Home/kd-tree-knn> simply because it's in pure Python, not for any other reason. scipy comes with the spatial package, but it appears that some recent changes have caused its install to become tied to the rabbit hole that is the scipy package. Ideally, the scipy spatial would be better because it's surely faster, but scipy is a hassle. Before I put time into this, what thoughts do people have? The python kdTree works, and it can probably be included in yt. A kdTree will probably have uses elsewhere in yt, so if I write routines that use it, I'd like the kdTree I use to be useful elsewhere. Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Image list for documentation and image gallery
by Matthew Turk 10 Jun '09

10 Jun '09

Hi guys, Brian and I have been talking about an image gallery slash cookbook. RIght now the cookbook in the docs is a bit small, but in newer versions it is getting bigger, and what I'd like to do is to have an image gallery with corresponding scripts. I'll handle the presentation & collection of these, but what I'm thinking about is a set of "How to make fun images" scripts and, well, output images. Here's my initial list: * Slice * Slice with grid boundaries * Slice with temperature contour * Slice with velocity vectors * Projection * Projection with HOP circles * Weighted projection with clump-found overlay * Cutting plane * Cutting plane with velocity * 1D Profile * Time series of 1D Profile * 2D Profile * 2D Profile with overplotted 1D profile * 3D Profile (s2plot) * 3D volume rendering (s2plot) What else *should* be added? Specifically, what do you all think about multiplot examples? I will get these together this afternoon and evening and prepare the gallery to send out -- I am thinking having them in a source location in the doc repo, then generate both the output for the docs and for a nice image gallery. -Matt

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Padding
by Matthew Turk 10 Jun '09

10 Jun '09

Hi guys, HOP padding is set to 0.2 for parallel. Is this right? I thought it was supposed to be 0.02. Maybe this is part of why we have been having problems with parallel HOP and memory usage lately ... ? -Matt

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yt attempts to create a data file for serialization even when h5py is not present
by j s oishi 09 Jun '09

09 Jun '09

Hi, I don't have h5py installed. However, lagos now has some code that attempts to create a serialization data file regardless of whether or not h5py is present. I think maybe this is a bug and that the code should simply bypass all serialization methods if h5py isn't present. I filed a ticket: http://yt.enzotools.org/ticket/223 thanks, j -- ---------------- i am dot org: www.jsoishi.org

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