Mailman 3 September 2012 - yt-users

Slice plot error
by Ji Suoqing Sept. 17, 2012

Sept. 17, 2012

Hi all, Yesterday I've updated YT (af06f14fcd9e), but after that I found I got some error in slice plot for 2d FLASH data, in both cartesian and cylindrical cases. In cartesian, the error is: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ yt : [WARNING ] 2012-09-17 01:19:45,023 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [WARNING ] 2012-09-17 01:19:45,023 … [View More]integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: current_time = 1.01787779719e-09 yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_dimensions = [1280 64 1] yt : [INFO ] 2012-09-17 01:19:45,029 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: domain_right_edge = [ 256. 12.8 12.8] yt : [INFO ] 2012-09-17 01:19:45,030 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field enuc to list of fields yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ar36 to list of fields yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field c12 to list of fields yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field ca40 to list of fields yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field cr48 to list of fields yt : [INFO ] 2012-09-17 01:19:45,040 Adding unknown field fe52 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field he4 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field mg24 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ne20 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ni56 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field o16 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field s32 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field si28 to list of fields yt : [INFO ] 2012-09-17 01:19:45,041 Adding unknown field ti44 to list of fields yt : [INFO ] 2012-09-17 01:19:45,356 Max Value is 4.25001e+07 at 22.7500000000000000 0.8375000000000000 0.5000000000000000 in grid FLASHGrid_0001 ([64 64 1]) at level 0 (45, 33, 0) yt : [INFO ] 2012-09-17 01:19:45,401 Making a fixed resolution buffer of (dens) 800 by 800 Traceback (most recent call last): File "slice.py", line 14, in <module> p1 = SlicePlot(pf, "z", my_var, origin="left-domain") File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 949, in __init__ PWViewerMPL.__init__(self, slc, bounds, origin=origin) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 473, in __init__ if setup: self._setup_plots() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 725, in _setup_plots self.plots[f].image, cax = self.plots[f].cax) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.py", line 1196, in colorbar cb = cbar.Colorbar(cax, mappable, **kw) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 743, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 258, in __init__ self.draw_all() File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 272, in draw_all self._process_values() File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colorbar.py", line 570, in _process_values b = self.norm.inverse(self._uniform_y(self.cmap.N+1)) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/matplotlib/colors.py", line 948, in inverse return vmin * ma.power((vmax/vmin), val) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 3642, in __mul__ return multiply(self, other) File "/aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/numpy/ma/core.py", line 936, in __call__ if m: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ And in cylindrical case, the error is: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> from yt.mods import * >>> pf=load('relax_hdf5_chk_0000') yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: current_time = 0.0 yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_dimensions = [256 128 1] yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_left_edge = [ 0.00000000e+00 -6.55360000e+09 0.00000000e+00] yt : [INFO ] 2012-09-17 01:22:27,082 Parameters: domain_right_edge = [ 1.31072000e+10 6.55360000e+09 1.74532925e-02] yt : [INFO ] 2012-09-17 01:22:27,083 Parameters: cosmological_simulation = 0.0 >>> p1 = SlicePlot(pf, 'z', 'dens', origin="left-domain") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 948, in __init__ slc = pf.h.slice(axis, center[axis], fields=fields) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1045, in __init__ self._refresh_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data self.get_data() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 830, in get_data self._generate_coords() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1079, in _generate_coords for grid in self._get_grids(): File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 898, in _get_grids return ObjectIterator(self, attr='_grids') File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 102, in __init__ raise YTNoDataInObjectError(pobj) yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. It may lie on a grid face. Try offsetting slightly. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I would very appreciate it if you have any idea on solving these errors. Best wishes, Suoqing [View Less]

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Re: [yt-users] Problem when making a slice plot
by Markus Haider Sept. 16, 2012

Sept. 16, 2012

Hi Matthew, Thanks for the detailed answer. It is not a problem, I just wanted to know for sure that it is the visualization and not the data which is wrong, Cheers, Markus > Hi Markus, > > On Sat, Sep 15, 2012 at 7:18 AM, Markus Haider <markus.haider(a)uibk.ac.at> wrote: >> Hi everyone, >> >> I am experiencing a strange problem when making a slice plot of a flash >> snapshot. From the first snapshot (which should be the initial condition) I >> … [View More]plotted the temperature, which should just be the same value all over the >> simulation box. >> >> However, when I make a slice through the middle of the volume, this is how >> the result looks like, when yt automatically determines limits of the >> colorbar: >> http://ubuntuone.com/4I63O6KY7LDELHa0ZWvjem > Ah, yes. This is a familiar problem -- the colorbar limits are so > tight as to not be visible on the colorbar itself! What you're seeing > is actually the roundoff error in the antialiasing that yt applies, > which preferentially builds up at cell boundaries and in higher > refined areas. I think the (relative) scatter should be on the order > of 1e-14 or so. Since it's so small, it only shows up when *all* the > values are the same. For reference, here's the source code: > > https://bitbucket.org/yt_analysis/yt/src/tip/yt/visualization/_MPL.c#cl-143 > > The problem comes in during the calculation of the overlap factors, > which are meant as a simple means of anti-aliasing. Please note, this > code is overdue for touching up; it's not only terse but a bit > obscure. The overlap lines: > > overlap2 = ((min(rypx, ysp+dysp) - max(lypx, (ysp-dysp)))*ipx_dy); > overlap1 = ((min(rxpx, xsp+dxsp) - max(lxpx, (xsp-dxsp)))*ipx_dx); > and then the value deposited is: (dsp*overlap1)*overlap2; > > This is taking the overlap of a pixel with a cell in the y, then in > the x, and multiplying the two. When there are multiply cells > overlapping a pixel, this becomes off by just a tiny bit. > > You can disable this behavior by turning off antialiasing in the FRBs. > Perhaps we should simply do this by default, although I think it will > lead to slightly less attractive plots in most cases. This can be > done on a slice plot like: > > slice_plot = SlicePlot( ... ) > slice_plot.antialias = False > slice_plot._recreate_frb() > >> If I specify the color-bar limits on my own, it looks like as it should be: >> http://ubuntuone.com/7E1YmEgKoV9XmR77Ddplhs >> >> Does someone know what is going wrong here? > Yup, in short -- the values are all correct to extremely tight > precision, but matplotlib will happily expose that tight precision > when it autosets colorbar limits. I think one possibility we could > explore is actually having the SlicePlot / ProjectionPlot do a better > job of auto-calculating limits, and not letting matplotlib do it, when > values are quite tightly clustered. One could imagine ensuring that > we get a bit of room on both sides, or perhaps not logging plots that > have < 1 OOM in spread. > > Hope that helps -- let us know! > > Matt > > PS I just saw you had asked this in IRC -- hope to see you again soon! > >> Here is the script I used to make the plot: >> http://ubuntuone.com/7icVc1nNDBaQfRRZBRTXEt >> >> And in case you want to reproduce the error, here is the snapshot file: >> http://ubuntuone.com/6wq4c6HALXdqyktHjWTtaB >> >> Thanks for your help, >> Markus >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 55, Issue 19 > **************************************** > [View Less]

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cell volume for 2d cylindrical FLASH data
by Ji Suoqing Sept. 15, 2012

Sept. 15, 2012

Hi all, I've just found something confusing when dealing with 2d cylindrical data: the CellVolume is defined as cartesian form instead of cylindrical form. In FLASH, the cell volume for 2d cylindrical is defined as: r * dr * dz * 2pi While in YT, all the cell volumes have the same value. Although it's not difficult to define our own cell volume by ourselves, I just wonder this might lead to problems when calculating other quantities, such as any summation of volume-average quantities. Best wishes, Suoqing

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Problem when making a slice plot
by Markus Haider Sept. 15, 2012

Sept. 15, 2012

Hi everyone, I am experiencing a strange problem when making a slice plot of a flash snapshot. From the first snapshot (which should be the initial condition) I plotted the temperature, which should just be the same value all over the simulation box. However, when I make a slice through the middle of the volume, this is how the result looks like, when yt automatically determines limits of the colorbar: http://ubuntuone.com/4I63O6KY7LDELHa0ZWvjem If I specify the color-bar limits on my … [View More]

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Fwd: [FLASH-USERS] FLASH 4.0 released
by Nathan Goldbaum Sept. 14, 2012

Sept. 14, 2012

This may be of interest to some of the subscribers to this list. Begin forwarded message: > From: Klaus Weide <klaus(a)flash.uchicago.edu> > Date: September 14, 2012 3:28:24 PM PDT > To: flash-users(a)flash.uchicago.edu > Subject: [FLASH-USERS] FLASH 4.0 released > > The Flash Center is pleased to announce the release of the new version of > the FLASH code, version 4.0. FLASH4 closely follows the architecture of > FLASH3. The most important changes from FLASH3 … [View More]are several new > capabilities in both physics solvers and infrastructure. A major part of > the new physics capabilities were introduced to support simulations of > high-energy-density physics (HEDP). FLASH4 also includes four significant > capabilities contributed by our external users. > > > The major new capabilities in FLASH4 that were not included in FLASH3 > are (marked with ** are the external contributions, please see the > User's Guide for references and appropriate credits): > > * 3T capabilities in the split and unsplit Hydro solvers. > There is support for non-Cartesian geometry, and > the unsplit solver also supports stationary rigid bodies. > > * Upwind biased constrained transport (CT) scheme in the unsplit > staggered mesh MHD solver. > > * Full corner transport upwind (CTU) algorithm in the unsplit > hydro/MHD solver. > > * Cylindrical geometry support in the unsplit > staggered mesh MHD solver on UG and AMR. A couple of MHD > simulation setups using cylindrical geometry. > > * Radiation diffusion. > > * Conduction. > > * Heat exchange. > > * Multi-Temperature Multi-Material Multi-Table Eos. > > * Opacities, ability to use hot and cold opacities. > > * EnergyDeposition unit with laser ray tracing, with threading > for performance. > > * A new multipole solver. > > * Ability to replicate mesh for multigroup diffusion or other > similar applications. > > * OpenMP threading of several important solvers at both > coarse-grain (one block per thread) and fine-grain > (threads within a block) levels. > > * Ability to add particles during evolution. > > * Limited support for Chombo as an alternative AMR mesh package. > > * Several new HEDP simulation setups. > > * Hybrid PIC. ** > > * Barnes-Hut-Tree based gravity solver. ** > > * Primordial chemistry. ** > > * Sink particles. ** > > > The release also includes several new features and resolves a number > of bugs found in previous releases up to 4-beta. > > > Please see the attachment for a more detailed summary, > and for download instructions. > > > Development of the FLASH Code was funded by the DOE-supported > ASC/Alliance Center for Astrophysical Thermonuclear Flashes, > and continues to be funded by DOE NNSA and NSF. > We acknowledge support received from Lawrence Livermore National > Laboratory and the University of Chicago. > > All publications resulting from the use of the FLASH Code must > acknowledge the Flash Center for Computational Science. > Addition of the following text to the paper acknowledgments > will be sufficient. > > "The software used in this work was in part developed by the > DOE- and NSF-supported Flash Center for Computational Science > at the University of Chicago." [View Less]

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Flush to file
by david collins Sept. 14, 2012

Sept. 14, 2012

Hi, all-- Is there a way to write a derived quantity directly to the original data files? d. -- Sent from my computer.

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Announcement: NYC yt bootcamp
by Matthew Turk Sept. 13, 2012

Sept. 13, 2012

Dear Colleagues, On Friday, October 19th at Columbia University there will be a one-day yt bootcamp, designed to get you up and running with applying yt ( http://yt-project.org/ ) to analyze and visualize simulation data from fluid-based astrophysical simulation data. Starting with a basic facility with Python, attendees should expect to: * Learn how to use yt for basic visualization * Use yt for detailed quantitative analysis * Create and use derived fields and bulk fluid quantities * … [View More]

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Volume_rendering
by Craig Stephen Lage Sept. 13, 2012

Sept. 13, 2012

Greetings, I have been using the volume_rendering function in yt version 2.2. I recently downloaded the latest version(2.4 I think), and note that this function has disappeared. I have three questions: (1) Was there a problem with the old volume_rendering function, or is the new implementation just more efficient? (2) Is there an easy way to migrate from the old volume_rendering function? I had spent a fair amount of time confirming that the old function did projections in the way that I … [View More]

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Enzo compile under Debian 6.04 or Ubuntu 12.04 via YT script
by CCAC South Sept. 13, 2012

Sept. 13, 2012

Hi all, I am new to YT and Enzo. Currently I am trying to get Enzo to compiled to run the test simulations and analyze with YT. I was able to get YT installed and working and go thru some of the analysis examples. The Enzo package that downloaded with YT requires several dependencies. Is there anyone that is currently running Debian 6.04 or Ubuntu 12.04 that can provide some help in listing the compiler dependencies? My current compiler output is below. gmake Updating DEPEND gmake: [… [View More]

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yt on 'astronomy computing today'
by Peter Teuben Sept. 13, 2012

Sept. 13, 2012

I'm sure some of you have seen Berriman's blog on yt. http://astrocompute.wordpress.com/2012/09/07/yt-an-integrated-science-envir… so I certainly got energized and decided to install yt again. I hope this mailing list is ok to go over an installation problem, since I got stuck on something pretty silly now: the "yt serve" command comes back and tells me i need to install missing Reason support files. It gives an example what to do (has a minor typo) cd /home/teuben/yt/yt-… [View More]

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