Mailman 3 January 2013 - yt-users

new yt feature: yt update --all
by Britton Smith 22 Jan '13

22 Jan '13

Greetings everyone, I would like to announce a new feature that has been added to the development version of yt. For some time now, one could update their yt installation by issuing the command "yt update". However, updating yt's dependencies has required one to rerun the install script manually. Now you can simply do: yt update --all and yt will rerun the install script for you with the proper installation path. Additionally, when you type "yt instinfo", yt will print the last time the dependencies were updated. In order to have this feature, you will need to be using the development version of yt, and will have to first run "yt update" once. Note: only use this if you originally used the install script for your installation. Custom installations, such as those using the system python, should still be updated manually. We hope this will simplify the process of keeping one's installation up to date. As always, please let us know if you encounter any unexpected behavior with this. Team yt

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yt.utilities.amr_utils
by Renyue Cen 22 Jan '13

22 Jan '13

Hi, I am trying to compute gridded density of some subset of particles. So I tried to import some modules first in the python script as follows: from yt.data_objects.field_info_container import \ FieldInfoContainer, \ NullFunc, \ TranslationFunc, \ FieldInfo, \ ValidateParameter, \ ValidateDataField, \ ValidateProperty, \ ValidateSpatial, \ ValidateGridType import yt.data_objects.universal_fields from yt.utilities.physical_constants import mh from yt.funcs import * import yt.utilities.amr_utils as amr_utils But I got this error message: Traceback (most recent call last): File "SFR.py", line 28, in <module> import yt.utilities.amr_utils as amr_utils ImportError: No module named amr_utils Am I doing something wrong? Thanks, Renyue

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Error saving clumps to the data file
by Andrew Myers 21 Jan '13

21 Jan '13

Dear yt users, I've generated some clumps, and would like to save them to look at later. When I try pf.h.save_object(master_clump, 'Clumps') I get the following error, which looks like it's coming fron hdf5. Has anybody seen this before? Thanks, Andrew ---------------------------------------------------------------------------ValueError Traceback (most recent call last)<ipython-input-13-0bda0f3d0b42> in <module>()----> 1 pf.h.save_object(master_clump, 'Clumps') /indirect/o/atmyers/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.pyc in save_object(self, obj, name) 299 """ 300 s = cPickle.dumps(obj, protocol=-1)--> 301 self.save_data(s, "/Objects", name, force = True) 302 303 def load_object(self, name): /indirect/o/atmyers/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.pyc in _save_data(self, array, node, name, set_attr, force, passthrough) 274 for q in node.split('/'): 275 if q: myGroup = myGroup.require_group(q)--> 276 arr = myGroup.create_dataset(name,data=array) 277 if set_attr is not None: 278 for i, j in set_attr.items(): arr.attrs[i] = j /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/group.pyc in create_dataset(self, name, shape, dtype, data, **kwds) 69 """ 70 ---> 71 dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) 72 dset = dataset.Dataset(dsid) 73 if name is not None: /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue) 92 93 if data is not None:---> 94 dset_id.write(h5s.ALL, h5s.ALL, data) 95 96 return dset_id /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/h5d.so in h5py.h5d.DatasetID.write (h5py/h5d.c:2866)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_proxy.so in h5py._proxy.dset_rw (h5py/_proxy.c:1766)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/defs.so in h5py.defs.H5Tconvert (h5py/defs.c:18439)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_errors.so in h5py._errors.set_exception (h5py/_errors.c:711)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.str2vlen (h5py/_conv.c:3382)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.generic_converter (h5py/_conv.c:1302)() /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.conv_str2vlen (h5py/_conv.c:2158)() ValueError: VLEN strings do not support embedded NULLs

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yt SlicePlot questions
by Jun-Hwan Choi 18 Jan '13

18 Jan '13

Hi all, I have two questions on yt SlicePlot. First, when I make a new field and generate the SlicePlot of the simulation with a given field, I face on following error message: Traceback (most recent call last): File "Pot.py", line 16, in <module> pc = SlicePlot(pf, "x", "PotentialFieldCGS", width = (6.0, 'kpc'),center=den_center) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py", line 804, in __init__ PWViewerMPL.__init__(self, slc, bounds, origin=origin) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py", line 447, in __init__ if setup: self._setup_plots() File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py", line 617, in _setup_plots self.plots[f].image, cax = self.plots[f].cax) File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/figure.py", line 1104, in colorbar cb = cbar.Colorbar(cax, mappable, **kw) File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/colorbar.py", line 731, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/colorbar.py", line 246, in __init__ self.draw_all() File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/colorbar.py", line 260, in draw_all self._process_values() File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/colorbar.py", line 558, in _process_values b = self.norm.inverse(self._uniform_y(self.cmap.N+1)) File "/home/jhchoi/common/lib/python2.7/site-packages/matplotlib/colors.py", line 895, in inverse return vmin * ma.power((vmax/vmin), val) File "/home/jhchoi/common/lib/python2.7/site-packages/numpy/ma/core.py", line 6043, in power m |= invalid ValueError: invalid return array shape I suspect the reason is that Field value is negative and z value tends to be log scale (because I make it positive the yt work). Is there any way to make plot in negative with making linear z-value? Second, when I make a SlicePlot with small region, owing to resolution (certain grid cell size is not 1/10 of the Sire x-y size) the plot looks ugly. Is there any way to visually improve the low resolution SlicePlot? Thank you in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Problems with Scipy
by jutreras＠das.uchile.cl 16 Jan '13

16 Jan '13

Hi, I'm a Master student a new user of yt I have some troubles to use scipy and yt together. When I'm usin the yt environment yt works fine but i can't import scipy, but when I'm out of the environment i can use it. I really have no idea what's happening so if you could help me would be great Best regards Jose

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Announcing the 2013 yt developer conference - March 6-8, Santa Cruz California
by Nathan Goldbaum 15 Jan '13

15 Jan '13

Dear Colleagues, We are proud to officially announce the upcoming 2013 yt developer workshop. This three day event, to be held on the campus of the University of California, Santa Cruz on March 6th through 8th, will bring together a diverse group of students, researchers, and developers. yt is a community-developed analysis and visualization toolkit, primarily directed at astrophysical hydrodynamics simulations, offering full support for output from the Enzo, FLASH, Orion, and Nyx codes, with preliminary support for several others. It provides access to simulation data using an intuitive python interface, can quickly and easily perform many common visualization and analysis tasks, and offers a framework for conducting data reductions and analysis of simulation data. More details about yt, including download and installation instructions as well as full documentation are available on our website: http://yt-project.org. Up to this point, yt development has proceeded largely over the internet, leveraging e-mail lists, our online code repository (http://bitbucket.org/yt_analysis), and IRC to track, discuss, and evaluate changes to the code. Unfortunately, this model makes it difficult to jump in to development as a newcomer. This workshop will not only allow experienced developers to collaborate in person on new features, but will also be a means for new developers to learn what yt is about and begin contributing. The workshop will include several training sessions, constituting a primer in distributed version control, test-based development, and best practices for scientific programming. The workshop will also serve as a venue to plan and execute some of the major new features we are planning for the upcoming yt 3.0 release, including full support for outputs of Lagrangian codes like Gadget, Gasoline and AREPO, better support for oct-based codes like ART and RAMSES, initial conditions generation, the new Grid Data Format, a new way of handling units and unit conversion, non-cartesian geometries, and advanced graphical browser widgets inside the iPython notebook. More information and a registration form for the workshop are available on the workshop website: http://yt-project.org/workshop2013/. We have limited funding support for hotels and airfare. Funds will be preferentially distributed to students and the level of individual support will depend on demand. If you have questions or concerns about the workshop, please feel free to contact the organizers at workshop2013(a)yt-project.org. On behalf of the organizing committee, Nathan Goldbaum

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Installing yt on stampede
by Munier Azzam Salem 13 Jan '13

13 Jan '13

Hi yt, I've just tried installing yt on the new TACC Stampede system<https://www.xsede.org/web/guest/tacc-stampede>(just a basic build of the stable release). Things were going quite smoothly, until ... *Installing BZLIB* *Installing ZLIB* *Installing PNG* *Installing FreeType2* *Installing HDF5* *Installing SQLite3* *Installing Python. This may take a while, but don't worry. YT loves you.* *Setting YT_DIR=/home1/01686/msalem/yt-x86_64/src/yt-hg/* *Installing distribute* *Installing pip* *Installing numpy-1.6.1 (arguments: 'numpy-1.6.1')* *Installing matplotlib-1.1.0 (arguments: 'matplotlib-1.1.0')* *Installing ZeroMQ* ********************************************** * FAILURE REPORT:* ********************************************** * * *checking whether we are using Intel C++ compiler... no* *checking whether we are using Sun Studio C++ compiler... no* *checking whether we are using clang C++ compiler... no* *checking whether we are using gcc >= 4 C++ compiler... yes* *checking whether to enable debugging information... no* *checking whether to enable code coverage... no* *checking for pthread_create in -lpthread... yes* *checking for sem_init in -lrt... yes* *checking for uuid_generate in -luuid... no* *configure: error: cannot link with -luuid, install uuid-dev.* * * ********************************************** ********************************************** *Failure. Check /home1/01686/msalem/yt-x86_64/yt_install.log. The last 10 lines are above.* Does anyone know what's going wrong here? Thanks! best, Munier -- Munier A. Salem // 845.489.6450

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Profile/phase misalignment
by david collins 11 Jan '13

11 Jan '13

Hi, all-- We're trying to overplot a phase diagram and profile, and we're seeing a strange mis-alignment of the data. I've attached the plot, and the arguments used to create it are as follows: phase_therm_neg = \ pc.add_phase_object(dd, ["Pressure", "Lambda_therm_neg", "CellVolumeNorm"], weight=None, x_bins=xnbins, y_bins=ynbins, \ x_bounds=[xmin,xmax], y_bounds=[ymin,ymax], cmap = "PuBuGn") profile_therm_neg = pc.add_profile_object(dd, ["Pressure", "Lambda_therm_neg"], weight='CellVolumeNorm', \ x_bounds=[xmin,xmax], x_bins=xnbins) phase_therm_neg.modify["line"](profile_therm_neg.data["Pressure"], profile_therm_neg.data["Lambda_therm_neg"]) The fact that the line is below the peak of the color in the P=[10,10^4] range could be real, since the peak of the color distribution will trace the median, but the line is the average, though the effect is more pronounced than I would expect. But in 10^4-10^5, there simply aren't any points down there, which leads me to believe I'm doing something funny. Is there any obvious error in this script to anyone else? Or any funny statistical phenomenon that I might be missing? d. -- Sent from my computer.

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Line-of-sight density profile
by Jun-Hwan Choi 11 Jan '13

11 Jan '13

Hi all, I would like to estimate the gas density profile between two points in the simulation. Let say the tow points are (x0, y0, z0) and (x1, y1, z1), and make line between them. This line will intersect with the grid cell and I would like to make profile of the density as function of the distance from (x0, y0, z0). I think that I can use the ray object and make profile from this, but there is very limited information how to do so. Has anyone done this kind of analysis? Thank you, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Density profile issue
by Jun-Hwan Choi 09 Jan '13

09 Jan '13

Hi all, I have a gas disk simulation and try to compute gas density profile. I generate to make spherical average density profile by feeding a sphere object to the BinnedProfile1D and cylindrical average density profile by feeding a disk object to the BinnedProfile1D. Surprisingly, both density profile is almost the same. Does any one have idea why? FYI, I past my yt script at http://paste.yt-project.org/show/3046/ . Thank you in advance. Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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