Mailman 3 August 2015 - yt-users

Arch Linux Packages
by Stuart Mumford Aug. 25, 2015

Aug. 25, 2015

Hello, I have uploaded new Arch Linux AUR yt packages for both Python 2 and Python 3. https://aur.archlinux.org/packages/python-yt/ https://aur.archlinux.org/packages/python2-yt/ For the Python 2 package I have appended a '2' to all the executable scripts so you can have both Python 2 and Python 3 versions installed along side one another. Any feedback and bug reports are welcome. Sorry it took a while after the 3.2 release, blame my impending release of Thesis 0.1. Stuart

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Re: [yt-users] [FLASH-USERS] ANN: yt-3.2 released
by Alexander Heger Aug. 25, 2015

Aug. 25, 2015

Dear John, I just tried the new version of yt. Installation worked! But going through the demo notebooks, already "3)_Simple_Visualization" fails on the first plot. Error trace below. I ma not really sure why the first error occurs as the font is installed, but the second error is a bug with trying to decode a string (you can decode bytes type and encode strings in python3), the last one seems strange why it would look for a font in the current directory. I also note that the notebook is still python 2 - so all the print statements don't work. I am happy to share my notebooks with these fixed if I can get them to run. -Alexander --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 706 try: --> 707 result = self._font[texname] 708 except KeyError: KeyError: 'cmsy10' During handling of the above exception, another exception occurred: AttributeError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2484 bbox_inches_restore=_bbox_inches_restore) -> 2485 self.figure.draw(renderer) 2486 renderer.finalize() /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/figure.py in draw(self, renderer) 1084 for zorder, a, func, args in dsu: -> 1085 func(*args) 1086 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axes/_base.py in draw(self, renderer, inframe) 2109 for zorder, a in dsu: -> 2110 a.draw(renderer) 2111 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer, *args, **kwargs) 1118 for tick in ticks_to_draw: -> 1119 tick.draw(renderer) 1120 /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in draw(self, renderer) 248 if self.label1On: --> 249 self.label1.draw(renderer) 250 if self.label2On: /home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs) 58 before(artist, renderer) ---> 59 draw(artist, renderer, *args, **kwargs) 60 after(artist, renderer) /home/alex/Python/lib/python3.4/site-packages/matplotlib/text.py in draw(self, renderer) 637 renderer.draw_tex(gc, x, y, clean_line, --> 638 self._fontproperties, angle, mtext=mtext) 639 else: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext) 1823 if dvifont.texname not in self.file.dviFontInfo: -> 1824 psfont = self.tex_font_mapping(dvifont.texname) 1825 self.file.dviFontInfo[dvifont.texname] = Bunch( /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in tex_font_mapping(self, texfont) 1530 dviread.PsfontsMap(dviread.find_tex_file('pdftex.map')) -> 1531 return self.tex_font_map[texfont] 1532 /home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py in __getitem__(self, texname) 708 except KeyError: --> 709 result = self._font[texname.decode('ascii')] 710 fn, enc = result.filename, result.encoding AttributeError: 'str' object has no attribute 'decode' During handling of the above exception, another exception occurred: FileNotFoundError Traceback (most recent call last) /home/alex/Python/lib/python3.4/site-packages/IPython/core/formatters.py in __call__(self, obj) 339 method = _safe_get_formatter_method(obj, self.print_method) 340 if method is not None: --> 341 return method() 342 return None 343 else: /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in newfunc(*args, **kwargs) 75 if hasattr(args[0], 'run_callbacks'): 76 args[0].run_callbacks() ---> 77 rv = f(*args, **kwargs) 78 return rv 79 return newfunc /home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py in _repr_html_(self) 642 ret = '' 643 for field in self.plots: --> 644 img = base64.b64encode(self.plots[field]._repr_png_()).decode() 645 ret += r'<img style="max-width:100%%;max-height:100%%;" ' \ 646 r'src="data:image/png;base64,{0}"><br>'.format(img) /home/alex/Python/lib/python3.4/site-packages/yt/visualization/base_plot_types.py in _repr_png_(self) 165 canvas = FigureCanvasAgg(self.figure) 166 f = BytesIO() --> 167 canvas.print_figure(f) 168 f.seek(0) 169 return f.read() /home/alex/Python/lib/python3.4/site-packages/matplotlib/backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs) 2209 orientation=orientation, 2210 bbox_inches_restore=_bbox_inches_restore, -> 2211 **kwargs) 2212 finally: 2213 if bbox_inches and restore_bbox: /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in print_pdf(self, filename, **kwargs) 2489 file.endStream() 2490 else: # we opened the file above; now finish it off -> 2491 file.close() 2492 2493 /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in close(self) 523 self.endStream() 524 # Write out the various deferred objects --> 525 self.writeFonts() 526 self.writeObject(self.alphaStateObject, 527 dict([(val[0], val[1]) /home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py in writeFonts(self) 623 # a normal TrueType font 624 matplotlib.verbose.report('Writing TrueType font', 'debug') --> 625 realpath, stat_key = get_realpath_and_stat(filename) 626 chars = self.used_characters.get(stat_key) 627 if chars is not None and len(chars[1]): /home/alex/Python/lib/python3.4/site-packages/matplotlib/cbook.py in __call__(self, path) 1020 stat_key = realpath 1021 else: -> 1022 stat = os.stat(realpath) 1023 stat_key = (stat.st_ino, stat.st_dev) 1024 result = realpath, stat_key FileNotFoundError: [Errno 2] No such file or directory: '/home/alex/yt/doc/source/quickstart/cmsy10' <yt.visualization.plot_window.ProjectionPlot at 0x7fb8225470b8> On 25 July 2015 at 05:48, John ZuHone <jzuhone(a)space.mit.edu> wrote: > We are proud to announce the release of yt 3.2! > > yt (http://yt-project.org) is an open source, community-developed toolkit > for analysis and visualization of volumetric data of all types, with a > particular emphasis on astrophysical simulations and nuclear engineering > simulations. > > Major enhancements > > Particle-Only Plots - a series of new plotting functions for visualizing > particle data. See here for more information. > Late-stage beta support for Python 3 - unit tests and answer tests pass for > all the major frontends under python 3.4, and yt should now be mostly if not > fully usable. Because many of the yt developers are still on Python 2 at > this point, this should be considered a “late stage beta” as there may be > remaining issues yet to be identified or worked out. > Now supporting Gadget Friend-of-Friends/Subfind catalogs - see here to learn > how to load halo catalogs as regular yt datasets. > Custom colormaps can now be easily defined and added - see here to learn > how! > Now supporting Fargo3D data > Performance improvements throughout the code base for memory and speed > > > Minor enhancements > > Various updates to the following frontends: ART, Athena, Castro, Chombo, > Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF, Tipsy > Numerous documentation updates > Generic hexahedral mesh pixelizer > Adding annotate_ray() callback for plots > AbsorptionSpectrum returned to full functionality and now using faster SciPy > Voigt profile > Add a color_field argument to annotate_streamline > Smoothing lengths auto-calculated for Tipsy Datasets > Adding SimulationTimeSeries support for Gadget and OWLS. > Generalizing derived quantity outputs to all be YTArrays or lists of > YTArrays as appropriate > Star analysis returned to full functionality > FITS image writing refactor > Adding gradient fields on the fly > Adding support for Gadget Nx4 metallicity fields > Updating value of solar metal mass fraction to be consistent with Cloudy. > Gadget raw binary snapshot handling & non-cosmological simulation units > Adding support for LightRay class to work with Gadget+Tipsy > Add support for subclasses of frontends > Dependencies updated > Serialization for projections using minimal representation > Adding Grid visitors in Cython > Improved semantics for derived field units > Add a yaw() method for the PerspectiveCamera + switch back to LHS > Adding annotate_clear() function to remove previous callbacks from a plot > Added documentation for hexahedral mesh on website > Speed up nearest neighbor evaluation > Add a convenience method to create deposited particle fields > UI and docs updates for 3D streamlines > Ensure particle fields are tested in the field unit tests > Allow a suffix to be specified to save() > Add profiling using airspeed velocity > Various plotting enhancements and bugfixes > Use hglib to update > Various minor updates to halo_analysis toolkit > Docker-based tests for install_script.sh > Adding support for single and non-cosmological datasets to LightRay > Adding the Pascal unit > Add weight_field to PPVCube > FITS reader: allow HDU in auxiliary > Fixing electromagnetic units > Specific Angular Momentum [xyz] computed relative to a normal vector > > > Bugfixes > > Adding ability to create union fields from alias fields > Small fix to allow enzo AP datasets to load in parallel when no APs present > Use proper cell dimension in gradient function. > Minor memory optimization for smoothed particle fields > Fix thermal_energy for Enzo HydroMethod==6 > Make sure annotate_particles handles unitful widths properly > Improvements for add_particle_filter and particle_filter > Specify registry in off_axis_projection's image finalization > Apply fix for particle momentum units to the boxlib frontend > Avoid traceback in "yt version" when python-hglib is not installed > Expose no_ghost from export_sketchfab down to _extract_isocontours_from_grid > Fix broken magnetic_unit attribute > Fixing an off-by-one error in the set x/y lim methods for profile plots > Providing better error messages to PlotWindow callbacks > Updating annotate_timestamp to avoid auto-override > Updating callbacks to consistently define coordinate system > Fixing species fields for OWLS and tipsy > Fix extrapolation for vertex-centered data > Fix periodicity check in FRBs > Rewrote project_to_plane() in PerspectiveCamera for draw_domain() > Fix intermittent failure in test_add_deposited_particle_field > Improve minorticks for a symlog plot with one-sided data > Fix smoothed covering grid cell computation > Absorption spectrum generator now 3.0 compliant > Fix off-by-one-or-more in particle smallest dx > Fix dimensionality mismatch error in covering grid > Fix curvature term in cosmology calculator > Fix geographic axes and pixelization > Ensure axes aspect ratios respect the user-selected plot aspect ratio > Avoid clobbering field_map when calling profile.add_fields > Fixing the arbitrary grid deposit code > Fix spherical plotting centering > Make the behavior of to_frb consistent with the docstring > Ensure projected units are initialized when there are no chunks. > Removing "field already exists" warnings from the Owls and Gadget frontends > Various photon simulator bugs > Fixed use of LaTeX math mode > Fix upload_image > Enforce plot width in CSS when displayed in a notebook > Fix cStringIO.StringIO -> cStringIO in png_writer > Add some input sanitizing and error checking to covering_grid initializer > Fix for geographic plotting > Use the correct filename template for single-file OWLS datasets. > Fix Enzo IO performance for 32 bit datasets > Adding a number density field for Enzo MultiSpecies=0 datasets. > Fix RAMSES block ordering > Fix ART star particle masses to correctly reflect current and initial mass > Updating ragged array tests for NumPy 1.9.1 > Force returning lists for HDF5FileHandler > > > Coming Soon! > > The next major release of yt will be version 3.3, which is slated to include > an overhaul of the volume rendering system and support for analyzing and > visualizing unstructured mesh data. > > Standard Installation Methods > > As with previous releases, you can install yt from source using one of the > following methods. > > 1) From the install script (http://yt-project.org/#getyt ): > > Note, many of the dependencies have been updated since version 3.1. If you > previously installed yt from the install script, it is advised that you > re-install yt from scratch. > > # Installation > > $ wget http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh > $ bash install_script.sh > > # Update > > $ yt update > > 2) From pip (source or binary wheel, see below for more details): > > # Installation > > $ pip install yt > > # Update > > $ pip install -U yt > > 3) From the Anaconda Python Distribution > (https://store.continuum.io/cshop/anaconda/): > > # Installation > > $ conda install yt > > # Update > > $ conda update yt > > Note that it might take a day or two for the conda package to be updated. > > If you are on the “stable” branch, updating will bring you from yt 3.1 to > 3.2, incorporating all > changes since 3.1, whereas if you are on the “dev” or “yt” branch, only the > changes since > your last update should be incorporated. > > Installing Binary Packages via pip > > New to this release is the ability to install binary packages (“wheels”) > using pip on Windows and Mac OS X (64-bit only for both). This has the > advantage of not needing to install yt from source using a proper compiler > setup, which has caused occasional problems on both of these platforms and > prevented us from installing yt easily on other Python distributions. > > We have so far been able to install and run the binary distribution via pip > on the following platforms and Python stacks: > > Note that it might take a day or two for the pip wheels to be updated. > > Windows x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > WinPython (http://winpython.sourceforge.net/) > > > Mac OS X x86_64: > > Enthought Canopy Python (https://www.enthought.com/products/canopy/) > Homebrew Python (http://brew.sh/) > Python.org Python > Mac OS X’s system Python > MacPorts Python (https://www.macports.org/) > > > This is somewhat experimental, so other distributions may work (or not), > please submit bug reports or successes to the mailing list or to the > Bitbucket issues page (http://bitbucket.org/yt_analysis/yt/issues). > > All distributions are recommended to be Python v. 2.7, although with yt 3.2 > there is late-stage beta support for Python 3.4. The requirements for > installing yt via this method are the same as from source: > > NumPy > h5py > HDF5 > SymPy > Matplotlib > IPython (not required, but strongly recommended) > > > To install a new version of yt on one of these platforms, simply do > > $ pip install yt > > and you should get the binary distribution automatically. Also, if your > python installation is system-wide (e.g., the Mac system Python) you might > need to run pip with administrator privileges. > > For more information, including more installation instructions, links to > community resources, and information on contributing to yt’s development, > please see the yt homepage at http://yt-project.org and the documentation > for yt-3.2 at http://yt-project.org/docs/3.2. > > yt is the product of a large community of developers and users and we are > extraordinarily grateful for and proud of their contributions. Please > forward this announcement on to any interested parties. > > As always, if you have any questions, concerns, or run into any trouble > updating please don't hesitate to send a message to the mailing list or stop > by our IRC channel. > > All the best, > The yt development team

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Derived Field Mass Unit Errors
by Madison Fitzgerald Aug. 25, 2015

Aug. 25, 2015

Hello, I’ve been working on a project where I created derived fields to represent inflowing and outflowing gas in the galaxy. In doing so, I’ve run into a strange issue where yt wants my derived field for inflowing/outflowing mass (cell mass) to be dimensionless, but it will scale graphs as though the units are grams (original script found here: http://paste.yt-project.org/show/5829/ <http://paste.yt-project.org/show/5829/>). However, this makes it difficult to work with the data, so I’ve tried to give units in the derived field function (g and Msun), but I receive errors similar to this (http://paste.yt-project.org/show/5830/ <http://paste.yt-project.org/show/5830/>). If I try to change the specified unit within the mass function in the script to g or Msun, I receive this error when I try to plot instead (http://paste.yt-project.org/show/5831/ <http://paste.yt-project.org/show/5831/>). I’m working with yt through miniconda, so I have yt version 3.2, no changeset, on a Mac with OS X 10.10.4. Any suggestions? Thank you, Madison Fitzgerald Astrophysics | Lyman Briggs College Women’s & Gender Studies | College of Arts & Letters LGBTQ and Sexuality Studies Specialization Women in Science, President Undergraduate Teaching Assistant Undergraduate Research Assistant Department of Physics and Astronomy Honors College Michigan State University

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Vorticity field with FLASH
by Markus Haider Aug. 21, 2015

Aug. 21, 2015

Hi, I was trying to calculate the vorticity for a flash dataset. I selected a region using center = (ad.quantities.min_location('gpot')[2],ad.quantities.min_location('gpot')[3],ad.quantities.min_location('gpot')[4]) LE = center-width.in_units('code_length')/2. CN = int(width/dx) Roi = ds.covering_grid(level=level_max,left_edge=LE, dims=[CN,CN,CN]) Then, for this region I wanted to compute the vorticity using Roi["gas","vorticity_x"] This resulted in the following error: http://paste.yt-project.org/show/5824/ Thanks for your help, Cheers, Markus

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ProfilePlot error: weakly-referenced object no longer exists
by Mateusz Ruszkowski Aug. 21, 2015

Aug. 21, 2015

Hi, I am trying to plot two profiles on one plot and adjust xlim. I am getting the following error message: Traceback (most recent call last): File "test.py", line 17, in <module> plot.set_xlim([0.1, 1.0]) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 62, in newfunc rv = f(*args, **kwargs) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.py", line 547, in set_xlim extrema=extrema, units=units) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 1436, in create_profile bin_fields = data_source._determine_fields(bin_fields) File "/home/mateuszr/my_yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 552, in _determine_fields finfo = self.ds._get_field_info(ftype, fname) ReferenceError: weakly-referenced object no longer exists --------------------------------------------------- I am using the following script: import yt profiles = [] labels = [] for i in range(0,2,1): print i ds=yt.load("./sedov_hdf5_chk_%04i"%i) my_data = ds.sphere(ds.domain_center, 1.0) sim_time = ds.current_time profiles.append(yt.create_profile(my_data, "radius", fields=["density"], weight_field="cell_volume", n_bins=32)) labels.append("t= %.0f" % sim_time) plot = yt.ProfilePlot.from_profiles(profiles, labels=labels) plot.set_xlim([0.1, 1.0]) plot.save() ------------------------------------------------------ I am using the following yt version: Version = 3.3-dev Changeset = 603eab147248 (yt) tip ------------------------------------------------------- Data = standard Flash Sedov test. Any idea what I may be doing wrong? Thanks, Mateusz

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Absorption Spectrum from Gadget snapshot problem
by Jared Coughlin Aug. 20, 2015

Aug. 20, 2015

Hello! I have a custom gadget snapshot distributed onto four files, and I'm trying to make an absorption spectrum from a LOS through the middle of the box parallel to the x-axis. To this end, I have done: lr = LightRay(fname, load_kwargs={'unit_base' : my_unit_base, 'field_spec' : my_field_def}) lr.make_light_ray(start_position=[0.0, 25000.0, 25000.0], end_position=[50000.0, 25000.0, 25000.0], solution_filename='lrsol.txt', data_filename='lr.h5', fields=['temperature', 'density'], get_los_velocity=True) sp = AbsorptionSpectrum(4862.4, 4949.04, 3000) my_label = 'HI Lya' field = 'H_number_density' wavelength = 1215.67 f_value = 4.164E-01 gamma = 6.265E+08 mass = 1.00794 sp.add_line(my_label, field, wavelength, f_value, gamma, mass, label_threshold=1e10) wl, flux = sp.make_spectrum('lr.h5', output_file='spectrum.txt', line_list_file='lines.txt', use_peculiar_velocity=True) And I get the error: KeyError: "Unable to open object (Object 'h_number_density' doesn't exist)" I didn't post the traceback because it's kind of long. I have two questions. First: When calling make_light_ray and passing it fields, do I need to pass it H_number_density? Second: Does yt read in those fields from the gadget snapshot, or does it calculate them from the data in the snapshot (for example, a standard gadget snapshot does not write the temperature, but rather the internal energy)? Thanks! -Jared

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convert arbitrary particle based quantities to cloud-in-cell mesh
by Brendan Griffen Aug. 19, 2015

Aug. 19, 2015

Hi, I'm looking to convert particle based quantities into a uniform grid based quantity (arepo data is input). So say I have a collection of gas elements with some density rho and x,y,z positions. I want to construct an 256^3 mesh representing the cells in a mesh. x,y,z,rho --> cic mesh where the values at i,j,k is the smoothed density are created by the cic algorithm Now, generalising this more, can I have rho to be any quantity? So now say I have star particles which similarly have x,y,z but I want to distribute their luminosity. Again, I want to do it for say the gas velocity field as well. Is there any general functionality for converting particle quantities to mesh quantites in yt with the deposit all_cic functionality? I have a basic code for just x,y,z particle data and distributing that based on density to a cic (see below) ad = pf.all_data() level = int(math.log(ndim,2)) cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim]) arr = cg['deposit', 'all_cic'], but I'm not sure what to do for the other variables. Any help is appreciated in advance. Thanks. Brendan

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Gadget snapshot read Problem
by Jared Coughlin Aug. 19, 2015

Aug. 19, 2015

Hello! I have two questions: the first is related to saving new field specs, and the second is related to reading in the file itself. I was following along with the documentation that describes saving new field specs, and I defined a new field spec as (it should be noted that my extra columns are for both gas and star particles, and I was unsure as to how to tell yt that it applied for both types, so I made a best guess): my_field_def = ("Coordinates", "Velocities", "ParticleIDs", "Mass", ("InternalEnergy", "Gas"), ("Density", "Gas"), ("SmoothingLength", "Gas"), ("RII", "Stars"), ("RIa", "Stars"), ("StellarAge", "Stars"), ("C", "Gas", "Stars"), ("O", "Gas", "Stars"), ("Ca", "Gas", "Stars"), ("Cr", "Gas", "Stars"), ("Mn", "Gas", "Stars"), ("Fe", "Gas", "Stars"), ) And a unit base: unit_base = {'UnitLength_in_cm' : 3.085678e+21, 'UnitMass_in_g' : 1.989e+43, 'UnitVelocity_in_cm_per_s' : 1.0e+5} Firstly, when I tried to add my custom field definition to the gadget_field_specs by doing: from yt.frontends.sph.definitions import gadget_field_specs I get the error: Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named definitions Just wondering what I was doing wrong? Also, when I try to load in the snapshot, I am doing: fname = 'snapshot_000.0' ds = yt.GadgetDataset(fname, unit_base=unit_base, field_spec=my_field_def) ds.index ad = ds.all_data() pz = yt.ProjectionPlot(ds, 'z', ('gas', 'density')) pz.show() The output is: yt : [INFO ] 2015-08-18 17:24:45,103 Calculating time from 2.500e-01 to be 6.950e+16 seconds yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: current_time = 6.95032608578e+16 s yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2015-08-18 17:24:45,144 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: domain_right_edge = [ 50000. 50000. 50000.] yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: cosmological_simulation = 1 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: current_redshift = 3.00000005201 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: omega_lambda = 0.726 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: omega_matter = 0.274 yt : [INFO ] 2015-08-18 17:24:45,145 Parameters: hubble_constant = 0.702 yt : [INFO ] 2015-08-18 17:24:45,146 Allocating for 4.194e+06 particles yt : [INFO ] 2015-08-18 17:24:45,664 Identified 3.077e+05 octs Traceback (most recent call last): File "yt_test_script.py", line 72, in <module> ds.index File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 321, in index self, dataset_type=self.dataset_type) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py", line 53, in __init__ super(ParticleIndex, self).__init__(ds, dataset_type) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 65, in __init__ self._detect_output_fields() File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py", line 125, in _detect_output_fields fl, _units = self.io._identify_fields(dom) File "/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/frontends/gadget/io.py", line 208, in _identify_fields field, req = field ValueError: too many values to unpack The snapshot I'm trying to load is a 128^3 50Mpc snapshot distributed onto 4 files and the error occurs on a call to ds.index, if that helps. Thank you! -Jared

4 9

Camera Annotation
by John Regan Aug. 19, 2015

Aug. 19, 2015

Hi All, Just wondering if there is a way to annotate a volume render with scale lines, text etc? From (quickly) looking at the source it looks like the annotate function only adds a colorbar and doesn't have the flexibility to add other labels? Cheers, John

2 1

How to take log of a user defined field ?
by Reju Sam John Aug. 18, 2015

Aug. 18, 2015

Hi, I have a user defined field with the following definition. def _epsilon(field, data): return (4.0/3.0)*(data['vShock']/data["VelocityMagnitude"]) add_field("epsilon", function=_epsilon, take_log=False, units=r" " ) Now I would like take ln(1 + data["epsilon"]). I am trying with the following definition. Is this the correct way of doing this ? def _lnepsilon(field, data): return 1 + data["epsilon"] add_field("lnepsilon", function=_lnepsilon, *take_log=True*, units=r" " ) Thank you -- Reju Sam John

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