Mailman 3 October 2010 - yt-dev

NumPy Upgrade
by Matthew Turk Oct. 18, 2010

Oct. 18, 2010

Hi all, I just got an email that numpy versions less than 1.5 can't compile on PPC. Normally I would just upgrade the install script, but version 1.5 of NumPy also brings with it a change in the behavior of histogram. http://mail.scipy.org/pipermail/numpy-discussion/2010-August/052522.html The behavior is to change the bounds of the bins. I wanted to ping the list before I upgrade to 1.5 in the install script; if no one has any objections in the next, oh, 2 days or so, I'll go ahead and do so. Best, Matt

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yt 2.0
by Stephen Skory Oct. 4, 2010

Oct. 4, 2010

Hey all, I am trying to come up to speed on 2.0, and I'm getting this issue below. My question is, is this the way things are supposed to be? In particular, this is how it worked before, and how all of the docs & examples are written and posted on the website right now. Thanks! ------- $ iyt Welcome to yt! In [1]: pf = load("data0005") In [2]: h = parallelHF(pf) --------------------------------------------------------------------------- NameError Traceback (most recent call last) /home/sskory/yt/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/EGG-INFO/scripts/iyt in <module>() ----> 1 2 3 4 5 NameError: name 'parallelHF' is not defined _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Bug in PlotCollectionInteractive.add_phase_sphere and add_profile_sphere
by Andrew Myers Oct. 3, 2010

Oct. 3, 2010

Hi Folks, I wanted to bring them problem to your attention as well as show you an extremely hacky attempt at solving it. The add_profile_sphere and add_phase_sphere methods of PlotCollectionInteractive appear to have a bug in them. When I do: In [3]: p = pc.add_phase_sphere(0.015, 'pc', ["Density", "Temperature", "CellMassMsun"], weight = None) I get the following traceback: TypeError Traceback (most recent call last) /indirect/o/atmyers/yt/src/yt-trunk-svn/scripts/iyt in <module>() ----> 1 2 3 4 5 /indirect/o/atmyers/yt/src/yt-trunk-svn/yt/raven/plot_collection.py in pylabify(self, *args, **kwargs) 1440 kwargs['axes'] = self.pylab.gca() 1441 kwargs['figure'] = self.pylab.gcf() -> 1442 retval = func(self, *args, **kwargs) 1443 retval._redraw_image() 1444 retval._fig_num = new_fig.number /indirect/o/atmyers/yt/src/yt-trunk-svn/yt/raven/plot_collection.py in add_phase_sphere(self, radius, unit, fields, center, cmap, weight, accumulation, x_bins, x_log, x_bounds, y_bins, y_log, y_bounds, lazy_reader, id, axes, figure, fractional) 1128 x_bins, x_log, x_bounds, 1129 y_bins, y_log, y_bounds, -> 1130 lazy_reader, id, axes, figure, fractional) 1131 p["Width"] = radius 1132 p["Unit"] = unit /indirect/o/atmyers/yt/src/yt-trunk-svn/yt/raven/plot_collection.py in pylabify(self, *args, **kwargs) 1440 kwargs['axes'] = self.pylab.gca() 1441 kwargs['figure'] = self.pylab.gcf() -> 1442 retval = func(self, *args, **kwargs) 1443 retval._redraw_image() 1444 retval._fig_num = new_fig.number TypeError: add_phase_object() got multiple values for keyword argument 'axes' The same thing happens when I use pc.add_profile_sphere, but only with PlotCollectionInteractive. Using the same methods with PlotCollection works fine. The problem seems to be that the wrapper that "Interactifies" the PlotCollection methods assumes that you will not call them with "axes" or "figure" in the positional arguments. However, as currently coded, the add_phase_sphere and add_profile_sphere methods both call add_phase_object or add_profile_object, and when they do so they pass an axes and figure in the positional arguments. Probably the best way to fix this is to re-write the wrapper function to not assume that you don't have an axes or figure in *args, but in the meantime I've got mine to work just by changing add_profile_sphere and add_phase_sphere like so (docstring snipped) def add_phase_sphere(self, radius, unit, fields, center = None, cmap=None, weight="CellMassMsun", accumulation=False, x_bins=64, x_log=True, x_bounds=None, y_bins=64, y_log=True, y_bounds=None, lazy_reader=True, id=None, axes = None, figure = None, fractional=False): if center is None: center = self.c r = radius/self.pf[unit] data_source = self.pf.hierarchy.sphere(center, r) p = self.add_phase_object(data_source, fields, cmap, weight, accumulation, x_bins, x_log, x_bounds, y_bins, y_log, y_bounds, lazy_reader, id, axes = axes, figure = figure, fractional = fractional) p["Width"] = radius p["Unit"] = unit p["Axis"] = None return p So now the call to add_phase_object takes keyword arguments instead of positional ones for axes and figure. I made the same change to add_profile_sphere, and they work for me in interactive mode now. Thanks, Andrew M

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Announcement: Enzo-2.0
by Matthew Turk Oct. 1, 2010

Oct. 1, 2010

Dear Colleague, Please pass this email along to any researchers that you feel may be interested, and apologies if you receive multiple copies of this message. Announcing the availability of Enzo Version 2.0 =============================================== We are proud to announce the public release of Enzo version 2.0. Enzo is a parallel code for astrophysical and cosmological simulations utilizing adaptive mesh refinement. Enzo 2.0 features many new physics capabilities including ideal MHD, radiation transport (ray tracing and flux limited diffusion), star particle class, metallicity-dependent cooling, and several new hydro solvers. More importantly, we have introduced new software tools to make using and developing Enzo easier. We have adopted distributed version control using Mercurial which supports the growing Enzo developer community. The documentation has been made more accessible and is now distributed with the source code. We have more than doubled the number of test problems and example problems (as well as the number of developers!) In addition, we have added solution testing to the nightly regression tests. Enzo 2.0 is the product of developments made at UC San Diego, Stanford, Columbia, MSU, CU Boulder, CITA, McMaster, SMU, and UC Berkeley. Enzo 2.0 now lives at http://enzo.googlecode.com/ to reflect its multi-institutional provenance. Prospective users are also encouraged to view online lectures from the 2010 Enzo Users' Workshop at http://lca.ucsd.edu/workshops/enzo2010. Enzo development is supported by grants AST-0808184 and OCI-0832662 from the National Science Foundation. THE ENZO DEVELOPMENT TEAM

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