Mailman 3 December 2011 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins April 11, 2020

April 11, 2020

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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fig_size problem
by Stephen Skory Jan. 9, 2012

Jan. 9, 2012

Hi all, I am finding a bug when I try to use the 'fig_size' argument with add_projection: http://paste.yt-project.org/show/1998/ could this be related to the recent fields refactoring? I'm using the current tip rev c21592d52977. Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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Yt 2.3 installed on Kraken and Nautilus
by Harinarayan Krishnan Dec. 29, 2011

Dec. 29, 2011

Hi all, I just wanted to let any interested parties know that Yt 2.3 is now available on Nautilus and Kraken. Best regards and I hope everyone has a happy New Year, Hari

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sphere object without periodicity?
by j s oishi Dec. 26, 2011

Dec. 26, 2011

Hi All, I want to define a sphere with a center that sits on one face of my domain, [0., 0.5, 0.5] in unitary coordinates. However, the boundary conditions in this case are not periodic, and so I don't want periodicity. I did some preliminary testing, and it appears that periodicity is being enforced--if I make a sphere of radius 0.25 and set it at [0., 0.5,0.5] it returns the same number of cells as when it is at [0.5, 0.5, 0.5]--which is completely enclosed within the domain. I would expect the sphere to have half as many cells in the former case if periodicity is not being enforced, as only one hemisphere is in the domain then. I should point out that this is a non-AMR simulation. I perused the source, but I didn't see anything that obviously turned off (or on!) periodicity. Any suggestions would be most appreciated. thanks, JS

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yt 2.3 Release Announcement
by Stephen Skory Dec. 15, 2011

Dec. 15, 2011

(We encourage you to forward this message to any other interested parties.) Hello, Just in time for the New Year, we’re happy to announce the release of yt version 2.3! ( http://yt-project.org/ ) The new version includes many new modules and enhancements, and the usual set of bug fixes over the last point release. We encourage all users to upgrade to take advantage of the changes. yt is a community-developed analysis and visualization toolkit for astrophysical simulation data. yt provides full support for Enzo, Orion, Nyx, and FLASH codes, with preliminary support for the RAMSES code (and a handful of others.) It can be used to create many common types of data products, as well as serving as a library for developing your own data reductions and processes. Below is a non-comprehensive list of new features and enhancements: * Improved and expanded documentation located at http://yt-project.org/doc/.* Boolean logic data containers (joins, intersections and nots) to select arbitrary data regions.* Multi-level parallelism for subgroups of MPI tasks.* Extensive answer tests.* Isocontouring and flux-over-surface calculations, with WebGL interface.* A reorganized field system.* Adaptive resolution HEALpix-based all-sky volume rendering.* Radial column density calculations.* Memory usage, performance enhancements and bug fixes throughout the code. Everything, from installation, to development, to a cookbook, can be found on the homepage: http://yt-project.org/ We have updated the libraries installed with the install script; for more information, see the “Dependencies” section of the yt docs at http://yt-project.org/doc/advanced/installing.html. Development has been sponsored by the NSF, DOE, and various University funding. We invite you to get involved with developing and using yt! We’re also holding the FIRST YT WORKSHOP from January 24-26 at the FLASH center in Chicago. See the workshop homepage for more information! http://yt-project.org/workshop2012/ Please forward this announcement to interested parties. Sincerely, The yt development team

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error in setting width of slices
by Elizabeth Tasker Dec. 15, 2011

Dec. 15, 2011

Hi, Sometimes when I try and set the width of an image, yt throws an error and stops: /home/tasker/yt-test/scripts/iyt in <module>() 609 if (ncloudcells_final > 0): 610 p.modify["contour"]("Clouds", ncont=1, factor=1) --> 611 p.set_width(400, 'pc') 612 pc.save("%s_lowresgridpot_core%d" % (fn, c)) 613 /home/tasker/yt-test/yt/visualization/plot_types.pyc in set_width(self, width, unit) 438 unit = self.data.pf[str(unit)] 439 self.width = width / unit --> 440 self._refresh_display_width() 441 442 def _refresh_display_width(self, width=None): /home/tasker/yt-test/yt/visualization/plot_types.pyc in _refresh_display_width(self, width) 456 self.set_xlim(max(l_edge_x,self.xmin), min(r_edge_x,self.xmax)) 457 self.set_ylim(max(l_edge_y,self.ymin), min(r_edge_y,self.ymax)) --> 458 self._redraw_image() 459 460 def autoscale(self): /home/tasker/yt-test/yt/visualization/plot_types.pyc in _redraw_image(self, *args) 403 self.norm.autoscale(na.array((newmin,newmax), dtype='float64')) 404 self._reset_image_parameters() --> 405 self._run_callbacks() 406 407 def _reset_image_parameters(self): /home/tasker/yt-test/yt/visualization/plot_types.pyc in _run_callbacks(self) 256 self._axes.texts = [] 257 for cb in self._callbacks: --> 258 cb(self) 259 260 def set_label(self, label): /home/tasker/yt-test/yt/visualization/plot_modifications.pyc in __call__(self, plot) 238 print z.min(), z.max(), na.nanmin(z), na.nanmax(z) 239 print zi.min(), zi.max(), na.nanmin(zi), na.nanmax(zi) --> 240 plot._axes.contour(xi,yi,zi,self.ncont, **self.plot_args) 241 plot._axes.set_xlim(xx0,xx1) 242 plot._axes.set_ylim(yy0,yy1) /home/tasker/yt/lib/python2.7/site-packages/matplotlib/axes.pyc in contour(self, *args, **kwargs) 7314 if not self._hold: self.cla() 7315 kwargs['filled'] = False -> 7316 return mcontour.QuadContourSet(self, *args, **kwargs) 7317 contour.__doc__ = mcontour.QuadContourSet.contour_doc 7318 /home/tasker/yt/lib/python2.7/site-packages/matplotlib/contour.pyc in __init__(self, ax, *args, **kwargs) 1104 are described in QuadContourSet.contour_doc. 1105 """ -> 1106 ContourSet.__init__(self, ax, *args, **kwargs) 1107 1108 def _process_args(self, *args, **kwargs): /home/tasker/yt/lib/python2.7/site-packages/matplotlib/contour.pyc in __init__(self, ax, *args, **kwargs) 699 700 self._process_args(*args, **kwargs) --> 701 self._process_levels() 702 703 if self.colors is not None: /home/tasker/yt/lib/python2.7/site-packages/matplotlib/contour.pyc in _process_levels(self) 910 self._levels.append(max(self.levels[-1],self.zmax) + 1) 911 self._levels = np.asarray(self._levels) --> 912 self.vmin = np.amin(self.levels) # alternative would be self.layers 913 self.vmax = np.amax(self.levels) 914 if self.extend in ('both', 'min'): /home/tasker/yt/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in amin(a, axis, out) 1893 except AttributeError: 1894 return _wrapit(a, 'min', axis, out) -> 1895 return amin(axis, out) 1896 1897 ValueError: zero-size array to minimum.reduce without identity WARNING: Failure executing file: <findcloudsbypotential_lowresgrid.py> I think this happens when the contour modification is zero : p.modify["contour"]("Clouds", ncont=1, factor=1) Is there a way of telling it just not to plot the contour if there are no cells in the current slice that have a value and thereby avoid the crash? Elizabeth

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2012 yt workshop: registration closing soon
by Matthew Turk Dec. 14, 2011

Dec. 14, 2011

Hi all, As you may know, we're holding a yt workshop in late January in Chicago. We're capping attendees, and approaching that limit, so if you were putting off registering please go ahead and fill out the form: http://yt-project.org/workshop2012/ NOTE: if you filled out the survey of interest a couple months ago, that does not count as a "binding" registration that secures your spot. If you're not sure, email me directly and I'll confirm your registration status; the registration form asks a few questions the survey didn't, like "Which code do you use?" and "What's your experience level with Python?" We're planning on putting all the talks and materials online, so even if you can't make it you can still participate. -Matt

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Clearing a derived field from all grids
by Elizabeth Tasker Dec. 13, 2011

Dec. 13, 2011

Hi, Is there a way of deleting a single derived field from all grids? I seem to be having a problem with my derived field not being re-calculated for every element in a loop (it needs to be). Therefore, if I run the complete loop, I get an incorrect result for some of the elements which are totally fine if I tell the code to just calculate that element in a single sweep. I've tried deleting the individual elements that use that variable, but it doesn't seem to be enough, e.g. ng, nc = kd.locate_neighbors_from_position(nposn) . . . del ng Elizabeth

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Clump Finder Crashing
by Nicholas Earl Dec. 12, 2011

Dec. 12, 2011

Hey yt users, I am getting some weird exiting happening with the clump finder and Ranger, and I was wondering if anyone else has experienced the issue, or know what I might be doing wrong? I see that it gets to a point where the min and max densities are the same, but I didn't think it would cause the script to crash... Here is what I'm getting: Finding clumps: min: 1.000000e-22, max: 1.000000e-21, step: 10.000000 > Wiping out existing children clumps. > Joining... > Finished joining in 1.06e+00 seconds > Investigating 2 children. > Finding clumps: min: 1.000000e-21, max: 1.000000e-21, step: 10.000000 > Traceback (most recent call last): > File > "/scratch/01198/earln/run_files/clump_analysis/find_clumps_plot.py", line > 69, in <module> > amods.level_sets.find_clumps(master_clump, c_min, c_max, step) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", > line 179, in find_clumps > find_clumps(clump, min_val*d_clump, max_val, d_clump) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", > line 188, in find_clumps > elif (child._isValid()): > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py", > line 143, in _isValid > self.function_value = eval(self.function) > File "<string>", line 1, in <module> > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/derived_quantities.py", > line 93, in __call__ > return self._call_func_unlazy(args, kwargs) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/derived_quantities.py", > line 116, in _call_func_unlazy > retval = self.func(self._data_source, *args, **kwargs) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/derived_quantities.py", > line 320, in _IsBound > thermal = (data["ThermalEnergy"] * data["CellMass"]).sum() > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 286, in __getitem__ > self.get_data(key) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 2277, in get_data > if self._generate_field(field): > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 2347, in _generate_field > self[field] = self.pf.field_info[field](self) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/field_info_container.py", > line 309, in __call__ > dd = self._function(self, data) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/frontends/enzo/fields.py", > line 131, in _ThermalEnergy > return data["GasEnergy"] > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 286, in __getitem__ > self.get_data(key) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 2277, in get_data > if self._generate_field(field): > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/data_containers.py", > line 2347, in _generate_field > self[field] = self.pf.field_info[field](self) > File > "/share/home/00688/tg458377/local/src/yt-hg/yt/data_objects/field_info_container.py", > line 310, in __call__ > dd *= self._convert_function(data) > TypeError: unsupported operand type(s) for *=: 'NoneType' and 'float' > TACC: Cleaning up after job: 2259004 > TACC: Done. I've also attempted lowering the step size to 5.0, but with the same result. It also seems to be the case that I do not get this behavior when I use function=True parameter, but I kept keeping jobs that would never end, they would just be outputting Getting field Density from 1 the entire time. So I've had to rerun the clump finder a few times, putting in some minimum conditions, and still it'd happen. Any ideas? Thanks! Nick

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