Mailman 3 September 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

8 14

trouble with callback on phase plot
by Christine Simpson Oct. 3, 2011

Oct. 3, 2011

Hi all, I'm having trouble adding text through a callback onto a phase plot. I tried this code: pc.add_phase_sphere(r200[j],'kpc',["Density","Temperature","CellMassMsun"],weight = None) pc.set_zlim(1.0e-2,1.0e5) pc.set_xlim(1.0e-30,5.0e-19) pc.set_ylim(10.0,1.0e7) pc.plots[-1].modify["text"]([0.92,0.92],redshift_string) pc.save("output_%(file_num)s_branch_%yt-users(a)lists.spacepope.org(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) And I get this error: Traceback (most recent call last): File "test_phase_plots.py", line 41, in <module> pc.save("output_%(file_num)s_branch_%(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 157, in save override=override, force_save=force_save)) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 108, in save_image self._redraw_image() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 903, in _redraw_image self._run_callbacks() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 800, in _run_callbacks cb(self) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 910, in __call__ y = plot.image._A.shape[1] * self.pos[1] IndexError: tuple index out of range The error arises in the save command, but the problem only happens when I add the modify["text"] command. Any ideas? Christine

2 5

log-linear phase plot
by Wolfram Schmidt Sept. 30, 2011

Sept. 30, 2011

Hi everyone, I defined two fields, say, FieldOne and FieldTwo, to make 2D phase plot. FieldOne is logarithmic by default, FieldTwo is linear (i.e., I set take_log=False in add_field). I want to produce a phase plot with logarithmic bins for FieldOne and linear bins for FieldTwo, where the range of FieldTwo is [-10,10] I thought that pc.add_phase_object(dd, ["FieldOne", "FieldTwo", "CellMass"], weight=None, x_bins=100,y_bins=100, \ x_bounds=[1e0,1e10], y_bounds=[-10,10]) might do the job, but yt returns the error message: Warning: invalid value encountered in log10 yt : [ERROR ] 2011-09-30 16:55:05,610 Your min/max values for x, y have given me a nan. yt : [ERROR ] 2011-09-30 16:55:05,610 Usually this means you are asking for log, with a zero bound. Traceback (most recent call last): File "stability.py", line 352, in <module> x_bounds=[1e0,1e10], y_bounds=[-10,10]) File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/visualization/plot_collection.py", line 1149, in add_phase_object lazy_reader) File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/data_objects/profiles.py", line 408, in __init__ raise ValueError ValueError It appears that add_phase_object treats FieldTwo logarithmically, although it is linear. So how can I do a log-linear phase plot? Best, Wolfram

3 2

who is interested in a yt workshop?
by Britton Smith Sept. 30, 2011

Sept. 30, 2011

Hi everyone, There has been some discussion on the developers list about holding a yt workshop within roughly the next six months. Ideally, this workshop would have two parts. The first part would focus on education for users, from basic intro to advanced usage, and perhaps spending time helping users craft specific analysis routines. The second part would focus on development, where we discuss new features we would like the code to have as well as existing parts that are in need of some work, and then we actually get down to working on these thing and coding. Since one of the main goals of yt is to blur the lines between user and developer, we would try to aim the end of the users portion at understanding yt internals and how best to work on the code. The goal here would be to make a natural transition between the two parts to maximize the number of people willing to stick around for the development section. As it's not yet clear what kind of external funding we can get, we would like to make this as accessible as possible. This probably means choosing a city that is a major airport hub, like Chicago, Detroit, etc. The timing would be sometime early next year, currently anywhere between late January and say March. Before any of this can move forward, we really would like to know how many people are actually interested in such a thing. If you are at all interested in participating in a yt users/developers workshop, please respond to this email in at least the following way: I am [am not] interested in coming to a users workshop. I am [am not] interested in coming to a developers workshop. Any and all other comments are also welcome, as to timing, location, content, etc. Personally, I think this could really be a great thing, but let's here what you think. Britton

27 31

IsBound and mpi4py
by Eve Lee Sept. 28, 2011

Sept. 28, 2011

Hello, I'm doing a simple analysis of looking for a gravitationally bound sphere centred at the most dense point in each level of clumps by iteratively increasing the radius from 0.5pc to 4pc until the derived quantity "IsBound" is True. I'm trying to use mpi4py as this iteration takes a very long time on serial but I'm getting an error very similar to the error I received when I tried mpi4py with clump finding routine: Traceback (most recent call last): bound = sp_cand.quantities["IsBound"](truncate=True, include_thermal_energy=False) File "/home/elee/accretion/analysis/codes/clump_excise_sph.py", line 71, in <module> File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 86, in __call__ self.func(e, *args, **kwargs) self.func(e, *args, **kwargs) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound self.func(e, *args, **kwargs) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound bound = sp_cand.quantities["IsBound"](truncate=True, include_thermal_energy=False) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 86, in __call__ bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' self.func(e, *args, **kwargs) AttributeError: 'FieldDetector' object has no attribute 'quantities' File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' It seems like parallelization loses the attribute "quantities" associated with data, which, if I understand correctly, should be the sphere object. Does this mean it somehow loses the sphere object that was passed in as an argument? Or is this somehow related to the parallel contouring algorithm that Britton has mentioned before? Thanks. Best Regards, Eve

4 6

change resolution of a slice
by Jean-Claude Passy Sept. 27, 2011

Sept. 27, 2011

Hi all, I have a pretty dumb question. I have data from which I would like to take a slice with a resolution of one cell per pixel. How can I do that ? Thanks a lot, JC

3 3

Kraken YT/SQLite3 Issues
by Brian Crosby Sept. 23, 2011

Sept. 23, 2011

Hi everyone, I was trying to use the YT installation on Kraken to create a merger tree and seem to have run into a problem with it being unable to import SQLite3. The error appears to stem from the following: P190 yt : [ERROR ] 2011-09-20 00:02:03,730 sqlite3 not imported! Digging around the YT installs, it appears that SQLite3 isn't there. Oddly, when I installed and built it in my home directory I still got the same error, so perhaps this is an issue with YT or Kraken rather than with the community install. Do anyone have an idea what might be going on? The output file is attached. Thanks, Brian

2 1

Yt version 2.2 on Nautilus and Kraken
by Harinarayan Krishnan Sept. 22, 2011

Sept. 22, 2011

Hi all, Nautilus and Kraken now have yt-2.2 installed. Please let me know if there are any issues. The yt module on Kraken is still using h5py 1.2.0. I will try to update it to 1.3.1 as soon as I can. Kraken: module swap PrgEnv-pgi PrgEnv-gnu module load yt/2.2 Nautilus: module load yt/2.2 If no major issues come up, I will make them "default." That is, "module load yt" will load version 2.2 Thanks, Hari

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Re: [yt-users] pc.save with old Enzo
by Elizabeth Tasker Sept. 22, 2011

Sept. 22, 2011

Sorry -- correction: this problem also occurs with a new data set from Enzo 2.0. It doesn't happen, however, with the older version of yt. The version it fails on is 9cb628620da6 (yt). Unfortunately, the version it works on gives an error linked with finding the mercurial libraries when I run yt instinfo, so I'm not sure which version it is. Elizabeth On Sep 22, 2011, at 6:50 PM, Elizabeth Tasker wrote: > Hi, > > I'm trying to analyse an older Enzo simulation which writes its output in hdf5 but with files that look like: > > GT_RotFrame_128AMR8_stars_0200.grid.cpu0029 > > the script runs fine until it reaches pc.save(fn), then I get: > > AttributeError Traceback (most recent call last) > > /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() > ----> 1 > 2 > 3 > 4 > 5 > > /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() > 55 > 56 > ---> 57 pc.save(fn) > 58 > 59 > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_collection.pyc in save(self, basename, format, override, force_save) > 155 for plot in self.plots: > 156 fn.append(plot.save_image(basename, format=format, > --> 157 override=override, force_save=force_save)) > 158 mylog.info("Saved %s", fn[-1]) > 159 if ytcfg.getboolean("yt", "__withinreason"): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in save_image(self, prefix, format, override, force_save, figure_canvas) > 106 prefix. > 107 """ > --> 108 self._redraw_image() > 109 if not override: > 110 self._generate_prefix(prefix) > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _redraw_image(self, *args) > 399 self.norm.autoscale(na.array((newmin,newmax), dtype='float64')) > 400 self._reset_image_parameters() > --> 401 self._run_callbacks() > 402 > 403 def _reset_image_parameters(self): > > /home/taskere/yt/src/yt-hg/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/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) > 83 yv = "%s-velocity" % (y_names[plot.data.axis]) > 84 qcb = QuiverCallback(xv, yv, self.factor, scale=self.scale, scale_units=self.scale_units) > ---> 85 return qcb(plot) > 86 > 87 class MagFieldCallback(PlotCallback): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) > 148 X = na.mgrid[0:plot.image._A.shape[0]-1:nx*1j]# + 0.5*factor > 149 Y = na.mgrid[0:plot.image._A.shape[1]-1:ny*1j]# + 0.5*factor > --> 150 plot._axes.quiver(X,Y, pixX, pixY, scale=self.scale, scale_units=self.scale_units) > 151 plot._axes.set_xlim(xx0,xx1) > 152 plot._axes.set_ylim(yy0,yy1) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/axes.pyc in quiver(self, *args, **kw) > 5873 def quiver(self, *args, **kw): > 5874 if not self._hold: self.cla() > -> 5875 q = mquiver.Quiver(self, *args, **kw) > 5876 self.add_collection(q, False) > 5877 self.update_datalim(q.XY) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/quiver.pyc in __init__(self, ax, *args, **kw) > 392 transOffset=ax.transData, > 393 closed=False, > --> 394 **kw) > 395 self.polykw = kw > 396 self.set_UVC(U, V, C) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, verts, sizes, closed, **kwargs) > 664 %(Collection)s > 665 """ > --> 666 Collection.__init__(self,**kwargs) > 667 self._sizes = sizes > 668 self.set_verts(verts, closed) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, edgecolors, facecolors, linewidths, linestyles, antialiaseds, offsets, transOffset, norm, cmap, pickradius, urls, **kwargs) > 106 > 107 self._pickradius = pickradius > --> 108 self.update(kwargs) > 109 > 110 > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/artist.pyc in update(self, props) > 624 func = getattr(self, 'set_'+k, None) > 625 if func is None or not callable(func): > --> 626 raise AttributeError('Unknown property %s'%k) > 627 func(v) > 628 changed = True > > AttributeError: Unknown property scale_units > > > > > > Is there an easy fix for this? If it helps, an example data set is at: > > http://www.physics.mcmaster.ca/~taskere/GT_RotFrame_128AMR8_stars_0200.tar.… > > (about 650 Mb) and the yt script: > > http://paste.yt-project.org/show/1816/ > > Elizabeth > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 2

pc.save with old Enzo
by Elizabeth Tasker Sept. 22, 2011

Sept. 22, 2011

Hi, I'm trying to analyse an older Enzo simulation which writes its output in hdf5 but with files that look like: GT_RotFrame_128AMR8_stars_0200.grid.cpu0029 the script runs fine until it reaches pc.save(fn), then I get: AttributeError Traceback (most recent call last) /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 2 3 4 5 /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() 55 56 ---> 57 pc.save(fn) 58 59 /home/taskere/yt/src/yt-hg/yt/visualization/plot_collection.pyc in save(self, basename, format, override, force_save) 155 for plot in self.plots: 156 fn.append(plot.save_image(basename, format=format, --> 157 override=override, force_save=force_save)) 158 mylog.info("Saved %s", fn[-1]) 159 if ytcfg.getboolean("yt", "__withinreason"): /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in save_image(self, prefix, format, override, force_save, figure_canvas) 106 prefix. 107 """ --> 108 self._redraw_image() 109 if not override: 110 self._generate_prefix(prefix) /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _redraw_image(self, *args) 399 self.norm.autoscale(na.array((newmin,newmax), dtype='float64')) 400 self._reset_image_parameters() --> 401 self._run_callbacks() 402 403 def _reset_image_parameters(self): /home/taskere/yt/src/yt-hg/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/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) 83 yv = "%s-velocity" % (y_names[plot.data.axis]) 84 qcb = QuiverCallback(xv, yv, self.factor, scale=self.scale, scale_units=self.scale_units) ---> 85 return qcb(plot) 86 87 class MagFieldCallback(PlotCallback): /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) 148 X = na.mgrid[0:plot.image._A.shape[0]-1:nx*1j]# + 0.5*factor 149 Y = na.mgrid[0:plot.image._A.shape[1]-1:ny*1j]# + 0.5*factor --> 150 plot._axes.quiver(X,Y, pixX, pixY, scale=self.scale, scale_units=self.scale_units) 151 plot._axes.set_xlim(xx0,xx1) 152 plot._axes.set_ylim(yy0,yy1) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/axes.pyc in quiver(self, *args, **kw) 5873 def quiver(self, *args, **kw): 5874 if not self._hold: self.cla() -> 5875 q = mquiver.Quiver(self, *args, **kw) 5876 self.add_collection(q, False) 5877 self.update_datalim(q.XY) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/quiver.pyc in __init__(self, ax, *args, **kw) 392 transOffset=ax.transData, 393 closed=False, --> 394 **kw) 395 self.polykw = kw 396 self.set_UVC(U, V, C) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, verts, sizes, closed, **kwargs) 664 %(Collection)s 665 """ --> 666 Collection.__init__(self,**kwargs) 667 self._sizes = sizes 668 self.set_verts(verts, closed) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, edgecolors, facecolors, linewidths, linestyles, antialiaseds, offsets, transOffset, norm, cmap, pickradius, urls, **kwargs) 106 107 self._pickradius = pickradius --> 108 self.update(kwargs) 109 110 /home/taskere/yt/lib/python2.6/site-packages/matplotlib/artist.pyc in update(self, props) 624 func = getattr(self, 'set_'+k, None) 625 if func is None or not callable(func): --> 626 raise AttributeError('Unknown property %s'%k) 627 func(v) 628 changed = True AttributeError: Unknown property scale_units Is there an easy fix for this? If it helps, an example data set is at: http://www.physics.mcmaster.ca/~taskere/GT_RotFrame_128AMR8_stars_0200.tar.… (about 650 Mb) and the yt script: http://paste.yt-project.org/show/1816/ Elizabeth

1 0

subregion halo find
by Geoffrey So Sept. 21, 2011

Sept. 21, 2011

Hi Stephen, I'm trying to do halo finding in a subregion of the box, but do the various halo finders know that the boundary conditions are no longer periodic? If periodic BC is on by default, is there a flag to switch off periodicity during the subregion halo find? From G.S.

2 2

Re: [yt-users] yt on Nautilus
by meecegre＠msu.edu Sept. 19, 2011

Sept. 19, 2011

Hi, I had this same problem on Kracken. Matplotlib tries to create a hidden directory in your home directory when it is loaded, but the compute nodes don't have write access to your home directory. Try adding a line to your job script changing MPLCONFIGDIR to the local directory and see if that fixesit. All credit to Britton who explained this to me! -- Greg ------Original Message------ From: Stephen Skory Sender: yt-users-bounces(a)lists.spacepope.org To: Discussion of the yt analysis package ReplyTo: Discussion of the yt analysis package Subject: Re: [yt-users] yt on Nautilus Sent: Sep 19, 2011 10:43 AM Carolyn, > RuntimeError: Could not write to MPLCONFIGDIR="/lustre/scratch/perutaca/.matplotlib/" The error that matters is this one, above. Does that directory exist? Is it writable? Is this your Kraken path and therefore not functional on Nautilus? -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org Sent from my Verizon Wireless BlackBerry

1 0

yt on Nautilus
by Carolyn Peruta Sept. 19, 2011

Sept. 19, 2011

When I load the yt module on Nautilus and try to use it I get the following error: File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/bin/yt", line 9, in <module> load_entry_point('yt==2.2dev', 'console_scripts', 'yt')() File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg/pkg_resources.py", line 305, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg/pkg_resources.py", line 2244, in load_entry_point return ep.load() File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/utilities/command_line.py", line 26, in <module> from yt.mods import * File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/mods.py", line 92, in <module> from yt.visualization.api import \ File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/visualization/api.py", line 31, in <module> from color_maps import \ File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/visualization/color_maps.py", line 26, in <module> import matplotlib File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/matplotlib/__init__.py", line 739, in <module> rcParams = rc_params() File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/matplotlib/__init__.py", line 657, in rc_params fname = matplotlib_fname() File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/matplotlib/__init__.py", line 595, in matplotlib_fname fname = os.path.join(get_configdir(), 'matplotlibrc') File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/matplotlib/__init__.py", line 248, in wrapper ret = func(*args, **kwargs) File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/matplotlib/__init__.py", line 460, in _get_configdir raise RuntimeError('Could not write to MPLCONFIGDIR="%s"'%configdir) RuntimeError: Could not write to MPLCONFIGDIR="/lustre/scratch/perutaca/.matplotlib/" Does the module need to be updated or is there something wrong with my setup? Best, Carolyn

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Nearest neighbours
by Elizabeth Tasker Sept. 14, 2011

Sept. 14, 2011

Hi, Is there a routine in yt for returning the nearest neighbours to a cell? I was looking at Sam's amr_kdtree and it mentions bricks.... what's a brick? Is a cell a brick? Is a brick a cell? Is that a deep question? If it's horribly complex, I can work on an extracted uniform mesh, I just thought it would be cool not to. Elizabeth

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generic computation of derivatives
by Wolfram Schmidt Sept. 12, 2011

Sept. 12, 2011

Hi everyone, how can I generically define the derivatives of fields in a yt script (or is there already something to do that in yt)? I want to define, say, second-order centered differences of a field without referring to data["particular field"] but with a place holder for just any field (like in a Fortran or C subroutine) so that I can use this single piece of code for several different fields. Thanks, Wolfram

2 1

load error
by Stephen Skory Sept. 9, 2011

Sept. 9, 2011

Hi all, I am getting the error below on an enzo dataset. I am using a completely fresh install of yt using the development branch. I've tried deleting .yt files and clearing out my ~/.yt directory. Nothing works. Does anyone have any ideas? Thanks! Traceback (most recent call last): File "projections.py", line 9, in <module> pf = load("DD%04d/data%04d" % (this,this)) File "/home/stsk4691/yt/src/yt-hg/yt/convenience.py", line 91, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/home/stsk4691/yt/src/yt-hg/yt/frontends/enzo/data_structures.py", line 660, in __init__ StaticOutput.__init__(self, filename, data_style, file_style=file_style) File "/home/stsk4691/yt/src/yt-hg/yt/data_objects/static_output.py", line 86, in __init__ self._parse_parameter_file() File "/home/stsk4691/yt/src/yt-hg/yt/frontends/enzo/data_structures.py", line 786, in _parse_parameter_file vals = pcast(vals[0]) ValueError: invalid literal for int() with base 10: 'inf' -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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Trouble projecting a derived field
by Nathan Goldbaum Sept. 8, 2011

Sept. 8, 2011

Hello all, Right now I'm trying to generate maps of the Toomre Q in an isolated galaxy simulation. To do so, I'm using yt to generate maps of the gas column density as well as density-weighted projections of the sound speed and orbital frequency, which I'm using as a proxy for the epicyclic frequency. Unfortunately, I'm having some trouble making projected maps of the orbital frequency. I've defined two new derived fields, CylinderRadius and AngularVelocity (http://paste.yt-project.org/show/1784/). When I try to project the AngularVelocity field, I get what looks like garbage: http://i.imgur.com/PkYhe.png However, slices work just fine: http://i.imgur.com/NnEbq.png I've written the derived fields in a coordinate-dependent way, since I'll always be doing projections down a fixed axis. Is that where my problem lies? My understanding of how yt does projections is too shallow to figure out exactly what's going wrong here, so I'm hoping the collective wisdom of the yt developers and user base can come to the rescue. Best regards, Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

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combining data objects
by Christine Simpson Sept. 6, 2011

Sept. 6, 2011

Hi all, Is there a simple way I can combine two data objects to create a new data object? For example, if I created two sphere objects, is there a way I can combine them to create an object that contains the data of both of them? Thanks Christine

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setting limits on phase plots
by Christine Simpson Sept. 2, 2011

Sept. 2, 2011

Hi all, I'm trying to make some phase plots and specify the x axis limits, the y axis limits and the color bar limits. I've tried this: pc.add_phase_sphere(r200[j],'kpc',["Density","Temperature","CellMassMsun"],weight=None) pc.set_zlim(1.0**-2,1.0**5) pc.set_xlim(1.0**-30,5.0**-19) pc.set_ylim(10.0,1.0**7) It sets the limits to some random values and I get an empty plot. I thought there was some 'redraw' callback that I could try and I tried 'pc.redraw()' and 'pc.redraw_image()', but I guess 'redraw' can only be used with interactive plot collections? Christine

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yt-2.2 Release Announcement
by Cameron Hummels Sept. 2, 2011

Sept. 2, 2011

Release Announcement (Please feel encouraged to forward this message to any other interested parties.) We are proud to announce the release of yt version 2.2. This release includes several new features, bug fixes, and numerous improvements to the code base and documentation. At the new yt homepage, http://yt-project.org/, an installation script, a cookbook, documentation and a guide to getting involved can be found. We are particularly proud of the new GUI, entitled "Reason," which allows real-time exploration of datasets, and which can be used (locally or remotely over SSH) with no dependencies other than a web browser. A basic demonstration of its usage can be found at 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, ART, and Maestro codes. It can be used to create many common types of data products such as: * Slices * Projections * Profiles * Arbitrary Data Selection * Cosmological Analysis * Halo finding * Parallel AMR Volume Rendering * Gravitationally Bound Objects Analysis There are a few major additions since yt-2.1 (Released April 8, 2011), including: * New web GUI "Reason," designed for efficient remote usage over SSH tunnels * Command-line submission to the yt Hub (http://hub.yt-project.org/) <about:blank> * Absorption line spectrum generator for cosmological simulations * Support for the Nyx code * An order of magnitude speed improvement in the RAMSES support * Experimental interoperability with ParaView * Quad-tree projections, speeding up the process of projecting by up to an order of magnitude and providing better load balancing * "mapserver" for in-browser, Google Maps-style slice and projection visualization * Many bug fixes and performance improvements With this release, we also unveil the yt Hub, an astrophysical simulation-specific location for sharing scripts, analysis and visualization tools, documents and repositories used to generated publications. The yt Hub has been designed to allow programmatic access from the command line, and we encourage you to browse the current offerings and contribute your own. The yt Hub can be found at http://hub.yt-project.org/. Documentation: http://yt-project.org/doc/ Installation:http://yt-project.org/doc/advanced/installing.html Cookbook: http://yt-project.org/doc/cookbook/recipes.html Get Involved:http://yt-project.org/doc/advanced/developing.html If you can't wait to get started, install with: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh <http://install_script.sh/> Development has been sponsored by the NSF, DOE, and University funding. We invite you to get involved with developing and using yt! Please forward this announcement to interested parties. Sincerely, The yt development team

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Trouble with FixedResolutionBuffer
by Nathan Goldbaum Sept. 2, 2011

Sept. 2, 2011

Hi all, I'm trying to use FixedResolutionBuffer to generate 2d projections following the example in the docs (http://yt-project.org/doc/analyzing/generating_processed_data.html) from yt.mods import * pf = load("DD0000/test_disk_0000") projden = pf.h.proj(0,'Density',data_source=pf.h.all_data(),center=[0.5,0.5,0.5]) frb = FixedResolutionBuffer(projden,(0,0,1,1),(512,512)) print frb['Density'] ------> print(frb['Density']) yt : [INFO ] 2011-09-02 00:03:10,273 Making a fixed resolution buffer of 512 by 512 [[ nan nan nan ..., nan nan nan] [ nan nan nan ..., nan nan nan] [ nan nan nan ..., nan nan nan] ..., [ nan nan nan ..., nan nan nan] [ nan nan nan ..., nan nan nan] [ nan nan nan ..., nan nan nan]] Is there a problem with how I'm creating the buffer? I'm pretty sure the way this is done in the docs on the page I linked is incorrect, since I get an error when I do when I try to say sl = pf.h.proj(0,0.5) Thanks for your help, Nathan

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Re: [yt-users] yt-2.2 Release Announcement
by Cameron Hummels Sept. 2, 2011

Sept. 2, 2011

Oops, the link to the yt GUI screencast got stripped out of the last email with that poor formatting. Here you go: http://vimeo.com/groups/ytgallery/videos/28506477 ----- Release Announcement (Please feel encouraged to forward this message to any other interested parties.) We are proud to announce the release of yt version 2.2. This release includes several new features, bug fixes, and numerous improvements to the code base and documentation. At the new yt homepage, http://yt-project.org/, an installation script, a cookbook, documentation and a guide to getting involved can be found. We are particularly proud of the new GUI, entitled “Reason,” which allows real-time exploration of datasets, and which can be used (locally or remotely over SSH) with no dependencies other than a web browser. A basic demonstration of its usage can be found at http://vimeo.com/groups/ytgallery/videos/28506477. 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, ART, and Maestro codes. It can be used to create many common types of data products such as: * Slices * Projections * Profiles * Arbitrary Data Selection * Cosmological Analysis * Halo finding * Parallel AMR Volume Rendering * Gravitationally Bound Objects Analysis There are a few major additions since yt-2.1 (Released April 8, 2011), including: * New web GUI “Reason,” designed for efficient remote usage over SSH tunnels * Command-line submission to the yt Hub (http://hub.yt-project.org/) * Absorption line spectrum generator for cosmological simulations * Support for the Nyx code * An order of magnitude speed improvement in the RAMSES support * Experimental interoperability with ParaView * Quad-tree projections, speeding up the process of projecting by up to an order of magnitude and providing better load balancing * “mapserver” for in-browser, Google Maps-style slice and projection visualization * Many bug fixes and performance improvements With this release, we also unveil the yt Hub, an astrophysical simulation-specific location for sharing scripts, analysis and visualization tools, documents and repositories used to generated publications. The yt Hub has been designed to allow programmatic access from the command line, and we encourage you to browse the current offerings and contribute your own. The yt Hub can be found at http://hub.yt-project.org/. Documentation: http://yt-project.org/doc/ Installation:http://yt-project.org/doc/advanced/installing.html Cookbook: http://yt-project.org/doc/cookbook/recipes.html Get Involved:http://yt-project.org/doc/advanced/developing.html If you can’t wait to get started, install with: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh Development has been sponsored by the NSF, DOE, and University funding. We invite you to get involved with developing and using yt! Please forward this announcement to interested parties. Sincerely, The yt development team

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yt Hub recap
by Britton Smith Sept. 1, 2011

Sept. 1, 2011

Hi everyone, It's been just over a week since we launched the yt Hub ( http://hub.yt-project.org/). In that time, the Hub has received 13 submissions, including all of the tools that were available on the old Enzotools Barn. The only hiccup so far has been that it seems the original announcement sent to this list did not arrive for anyone with a gmail address. So if you're hearing about this thing called the yt Hub for the first time, here's what you missed: http://blog.yt-project.org/introducing-the-yt-hub Thanks to everyone who has contributed so far. If you haven't yet, we hope to see you there soon. Once again, feel free to reply to this thread or send me an email if you have any ideas for making the yt Hub better. Britton

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Clear memory?
by Elizabeth Tasker Sept. 1, 2011

Sept. 1, 2011

Hi, Is there any way in yt to get a script to delete (or ignore) all the .yt and .harray files and clear its memory? I run into errors when I'm re-doing a plot or I've re-run the simulation and over-written the last data set I looked at with yt. I have to exit yt, delete the above files by hand and restart, which is a bit of a pain. Elizabeth

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