Mailman 3 January 2013 - 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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yt volume render/AMRKDtree help
by Renyue Cen Aug. 25, 2013

Aug. 25, 2013

Hi, I did some simple volume rendering with the following script: volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"], no_ghost=False, tree_type="domain", le=c-0.5*WW, re=c+0.5*WW) cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False, north_vector=L, steady_north=True) cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j)) I got rather strange results in that the pictures look symmetric, which I am pretty sure can not be true. I attach the obtained plot. Note that I am using KD tree and using 32 cores. Your help at your earliest convenience is appreciated. Best, Renyue

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eps_writer question
by Jun-Hwan Choi Feb. 8, 2013

Feb. 8, 2013

Hi yt user, This question mostly goes to John Wise (maybe not). I try to use eps_writer module in the yt to generate a high-quality .eps figure. I attempt to make four phase plot (rho-T) from four different times (i.e. four different data output) But, I got the following error message: File "Phase_eps.py", line 39, in <module> ep = eps.multiplot_yt(2,2,pc) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/eps_writer.py", line 1010, in multiplot_yt "x ncol(%d)." % (len(plot_col.plots), nrow, ncol) TypeError: not all arguments converted during string formatting It look that there is a problem when I over write PlotCollection object for four different data output (or maybe not). How can I solve the issue? I paste my script at http://paste.yt-project.org/show/3112/ . In addition, I would like to get more information/document about eps_writer. For example, I would like to write the time of four phase respectively. Where can I get the information about it? 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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errno.h
by Mark Kremenetsky Feb. 6, 2013

Feb. 6, 2013

Guys, I am using a script recommended on ENZO boot-camp page $ bash install_script.sh in order to set up all libraries needed for enzo compilation. Everything is going good and well until I got a following error: gcc -fPIC -c bzip2.c In file included from /usr/include/errno.h:36, from bzip2.c:55: /usr/include/bits/errno.h:25:26: error: linux/errno.h: No such file or directory make: *** [bzip2.o] Error 1 I checked and certainly I don't have such thing as /usr/include/linux/errno.h Any advice ? Thanks, Mark

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Improved support for isolated boundary conditions
by Nathan Goldbaum Feb. 1, 2013

Feb. 1, 2013

Hi all, As you may know, yt was originally written to handle outputs from cosmological simulations produced by the Enzo code. Due to this pedigree, yt assumes internally in a number of places that the simulation box has periodic boundary conditions. In the last couple of years, we've been working on improving support for both non-cosmological simulations and datasets produced by codes besides Enzo. This effort has come a long way, but until recently the nature of the boundary conditions has received relatively little development attention. However, as yt becomes commonly used by people outside of the enzo community, the lack of proper support for general periodic or non-periodic boundary conditions is starting to be felt. A particularly nasty case is the radius field, which in the current codebase assumes periodic boundary conditions, producing incorrect results when someone tries to profile a field versus radius in a simulation that assumed some sort of isolated boundary conditions. Recently, Matt Turk came up with a summary of our strategy for improving support general boundary conditions, summarized in YTEP-0006: https://bitbucket.org/yt_analysis/ytep/src/tip/source/YTEPs/YTEP-0006.rst The main take-away points are that each of the code frontends will need to define a periodicity attribute that hangs off of each of the StaticOutput class. This way, one can check the periodicity of a parameter file by doing something like: >>> pf = load(filename) >>> print pf.periodicity (True, True, True) Here, pf.periodicity is a tuple, from which one can read off that the simulation is periodic along all three directions. We intend to fully support simulations that have arbitrary mixed periodic and isolated boundary conditions. We will then use the new periodicity attribute to modify the places in the code where we need to worry about boundary conditions. I've gone ahead and added the periodicity attribute for most of the code frontends. I've also enhanced the Radius and ParticleRadius fields to properly handle the periodicity. These modifications are included in Pull Request #410: https://bitbucket.org/yt_analysis/yt/pull-request/410/first-pass-at-ytep-6-… At this point, the PR is more or less ready to go. However, since this is a somewhat invasive change that might temporarily break code frontends if there is a bug somewhere, it would be great if some of you would check to make sure that everything works correctly for your datasets. In particular, I need help figuring out how to set the periodicity for the orion, chombo (i.e. pluto and orion2), maestro, and nyx frontends. It would also be great to hear from users who commonly work with 1D or 2D data, as these sorts of datasets have caused trouble in the past. I'll also note that if you're interested in helping out with yt development, finishing up YTEP-0006 would be an excellent starter project. If you run into trouble, please send a message to the yt-users or yt-dev mailing lists or, if you're looking for low-latency discussion, stop by on our IRC channel (#yt on freenode, or use the web chat interface: http://yt-project.org/irc.html). Cheers, Nathan Goldbaum

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yt + x11 on a mac
by Mark Krumholz Jan. 27, 2013

Jan. 27, 2013

Hi yt Users, I'm trying to figure out how to get yt working using an x11-based backend on my mac, so that I can forward python windows. For my non-yt python install, which is handled via macports, the trick (gleaned from http://www.astrobetter.com/remote-display-in-python-ask-astrobetter/) was to use macports to recompile the tk package so that it uses x11 rather than quartz, via the command sudo port upgrade --enforce-variants tk -quartz +x11 This works fine. However, it is not clear to me how to force a similar change in the sandbox python install used by yt. Nor have I been able to get any other x11-based backend to work with yt's python install on my mac. The packages required for the gtk or wx backends refuse to install via pip install, and the Qt backend fails to load with the cryptic error "no module named sip". I'd appreciate any suggestions. -- Mark Krumholz

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need to plot a box with borders
by henry wasker Jan. 24, 2013

Jan. 24, 2013

Hello, I am new to yt and I am interesting in plotting a volume rendering with output file from enzo cosmology simulation. For the time being, I get to plot a box ; here's the result : http://imgur.com/dPwSQEh I would like now to plot borders of this box too like on this image : http://imgur.com/bJ25I0l Here's the yt script I use : ------------------------------------------------------------------------------------------------------------ from yt.mods import * from yt.utilities.amr_kdtree.api import AMRKDTree from time import time import matplotlib.colorbar as cb # Load up your dataset num='70' pf = load('RD00'+num+'/RedshiftOutput00'+num) c = [0.5]*3 # Center L = [1.0,1.0,1.0] # Viewpoint W = na.sqrt(3) # Width N = 768 # Pixels (512^2) up = [0.,0.,1.] # Get density min, max # These might take a long time, so I'd suggest hand-coding mi, ma so # that you don't have to find the maxima and minima each time you # test. Note that mi, ma, should be a log value since we are # rendering the log of density. mi, ma = pf.h.all_data().quantities['Extrema']('Density')[0] mi, ma = na.log10(mi), na.log10(ma) print mi, ma #mi, ma = -31.0, -26.0 # Construct transfer function, pad the TF space by a bit so that # gaussians sampling the data range don't hit the edge. tf = ColorTransferFunction((mi-10, ma+10), nbins=1024) # Sample transfer function with 20 gaussians. Use col_bounds keyword # to restrict color mapping to true data range. tf.add_layers(20, w=0.001, col_bounds=(mi,ma),colormap='jet') # Create the camera object cam = pf.h.camera(c, L, W, (N,N), transfer_function=tf, north_vector=up, no_ghost=True) cam.snapshot("volume_rendered%s.png" % num, clip_ratio=8.0) ------------------------------------------------------------------------------------------------------------ Is there an option for 'camera" or "snapshot" which allows to add the borders for this box ? Any help would be really appreciated.

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Define a field of spacial derivatives for FLASH4 2D cylindrical uniform grid
by Ji Suoqing Jan. 24, 2013

Jan. 24, 2013

Hi, I would like to compute some spacial derivatives for FLASH4 2D cylindrical uniform grid datafile with YT. For simplicity, I tried the example given in YT docs, although I know the derivative form is only valid for Cartesian, and this is just for code test purposes. My script are: @derived_field(name='DivV') # I do not use ValidateSpatial… ghost_zone… because the ghost cells are not stored in FLSAH check point file def DivV(field, data): sl_left = slice(None,-2) sl_right = slice(2,None) div_fac = 2.0 ds = div_fac * data['dx'].flat[0] f = data["velx"][sl_right,1:-1]/ds f -= data["vely"][sl_left ,1:-1]/ds ds = div_fac * data['dy'].flat[0] f += data["velx"][1:-1,sl_right]/ds f -= data["vely"][1:-1,sl_left]/ds new_field = na.zeros(data["velx"].shape, dtype='float64') new_field[1:-1,1:-1] = f return new_field Then, if I add: pf = load('relax_hdf5_chk_0001') pf.h.find_max('DivV') The script works, but if I use: dd = pf.h.all_data() print dd['DivV'].sum() and it will give error: yt : [INFO ] 2013-01-23 21:17:01,551 Getting field dx from 256 yt : [INFO ] 2013-01-23 21:17:01,625 Getting field velx from 256 Traceback (most recent call last): File "test.py", line 28, in <module> print dd['DivV'].sum() File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 330, in __getitem__ self.get_data(key) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 2607, in get_data if self._generate_field(field): File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 360, in _generate_field self[field] = self.pf.field_info[field](self) File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 378, in __call__ dd = self._function(self, data) File "test.py", line 11, in DivV f = data["velx"][sl_right,1:-1]/ds IndexError: too many indices Nor can I make slice plot for this field. I would appreciate your suggestions for this issue. Best wishes, Suoqing

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ProjectionTransferFunction()
by Michael Kuhlen Jan. 22, 2013

Jan. 22, 2013

Hi all I'm not having any success with off-axis projections using the pf.h.camera() with AMRKDTree and ProjectionTransferFunction(). cam.snapshot() returns an all-zeros array, even in situations where ColorTransferFunction() produces great images. This script (based on the first part of amrkdtree_downsampling.py) demonstrates the problem: http://paste.yt-project.org/show/3072/ Any ideas what's going wrong? Maybe something to do with preventing the log'ing of the field, which I attempted to do with "pf.field_info['Density'].take_log=False"? Thanks for you help! Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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new yt feature: yt update --all
by Britton Smith Jan. 22, 2013

Jan. 22, 2013

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 Jan. 22, 2013

Jan. 22, 2013

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 Jan. 21, 2013

Jan. 21, 2013

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 Jan. 18, 2013

Jan. 18, 2013

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 Jan. 16, 2013

Jan. 16, 2013

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 Jan. 15, 2013

Jan. 15, 2013

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 Jan. 13, 2013

Jan. 13, 2013

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 Jan. 11, 2013

Jan. 11, 2013

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 Jan. 11, 2013

Jan. 11, 2013

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 Jan. 9, 2013

Jan. 9, 2013

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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IOError in h5py
by Patrick Rieser Jan. 7, 2013

Jan. 7, 2013

I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback: File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored I'd be very thankful if somebody got any idea how to fix this! Best wishes, Patrick

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