Mailman 3 July 2014 - yt-users

region_strict
by Markus Haider 15 Jul '14

15 Jul '14

Hi, As before, I am trying to get a script working in yt-3.0, and have the following problem: I use the following command In [6]: dregion = ff.h.region_strict(c_coords, c_coords-width/2.,c_coords+width/2.) and get /home/markus/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py in __getattr__(self, name) 94 pdb.set_trace() 95 return getattr(self.ds.index, name) ---> 96 raise AttributeError 97 98 def requires_index(attr_name): AttributeError: what could be the problem? Also, what would be the best way to debug this? I tried inserting a print statement and a pdb.set_trace() at said line, but this does not affect the behaviour. Cheers, Markus

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Flash Units
by Markus Haider 15 Jul '14

15 Jul '14

Hi, I'm moving some of my plotting scripts to yt 3.0, and I think some things about the units might have changed. There is one thing which puzzles me about the units using the Flash frontend. My Flash simulation is a 60 Mpccm/h volume. If I do In [32]: ff.domain_width I get Out[32]: YTArray([ 2.75876444e+26, 2.75876444e+26, 2.75876444e+26]) code_length which is the size of my 60 Mpccm/h in cm (I used h 0.6711). However, if I do In [40]: ff.domain_width.units it says Out[40]: code_length but code_length has the following properties Unit name: code_length CGS conversion: 0.664629553446 Dimensions: (length) so I think the CGS conversion should be 1. The factor 0.6646 is close to my value of h, but not exactly h. Where could things go wrong? Cheers, Markus

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Cache of projections
by David Collins 14 Jul '14

14 Jul '14

Hi, Everybody-- A while back the default behavior of projections was changed to stop writing projections to disk. How do I turn that back on? I've poked around the docs and my email, but don't see anything useful. Thanks! d. -- -- Sent from a computer.

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Area of Surface Cell
by Melinda Soares-Furtado 13 Jul '14

13 Jul '14

I created a surface using *surf = p1.h.surface(sp,"Radius",cluster_radius)* and then gathered the density values for the cells in this surface with *dens = surf['Density'], *which I can export as a textfile. I now need to get the area of each cell, but I'm having trouble doing this. Any advice?

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slice of a part of domain
by Chang-Goo Kim 11 Jul '14

11 Jul '14

Hi all, I have recently run a part of sphere by assuming mirror symmetry. So, the simulated domain only spans from 0 to L/2 in every direction, which should be -L/2 ~ L/2 for full domain. I then tried to make frb using slice and to_frb function. What I get is a slice in -L/4 ~L/4 domain with periodicity. How can I get correct slice? Here's a relevant part of script. for iax in range(3): slc = pf.slice(iax,0.0,center=(0.0,0.0,0.0)) slc_frb = slc.to_frb(pf.domain_width[0],512) frb.append(slc_frb) for i,field in enumerate(fields): ax = grid[iax*nrow+i] data=np.array(slc_frb[field]) im = ax.imshow(data, origin='lower', norm=LogNorm()) im.set_extent(np.array(slc_frb.bounds)) Thanks, Chang-Goo

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Cell Volume in regions
by Daniel 10 Jul '14

10 Jul '14

Hi there, I am extracting a region from a Gadget dataset using the sphere function and then attempting to access the "cell_volume" field. For some reason the number of elements in the cell volume field is not equal to the number of particles in the region. For example I have 4341760 particles but only 4228930 cell volume elements. I have extracted a sphere which encompassed all the particles and the number of cell volume elements is then equal. Any ideas or advice would be greatly appreciated. Kind Regards, Daniel

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FLASH 1D Data Radial Profiles
by Melinda Soares-Furtado 09 Jul '14

09 Jul '14

Is there a simple way to create density/temp/velocity profiles using 1D FLASH data? I've done this in the past for 3-dimensional data, which is very user friendly. Is the best method of attack is dumping the data to np arrays and then plotting from these arrays? Regards, Melinda Soares-Furtado msoares(a)princeton.edu http://cargo.ucsc.edu/msoares 415-860-0438

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memory error
by Juan Camilo Ibanez Mejia 08 Jul '14

08 Jul '14

Hi yt users, lately I’ve been running yt using the remote yt notebook. Sometimes the network crashes or the script crashes and the active yt session running remotely does not die, apparently holding the memory designated for IO. This has happened quite a number of times and now I can not run yt on the remote computer, and instead I obtain the following error “IOError: [Errno 28] No space left on device”. more about the error attached in the file:

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Using yt to build simulation initial conditions
by Stuart Mumford 08 Jul '14

08 Jul '14

Hello, I have a use case for yt that I do not know if anyone else has encountered (though somehow I think they might have done!). I need to build background conditions for my code, this for me entails complex stratified density and magnetic field geometry see this: http://labs.adsabs.harvard.edu/adsabs/abs/2013MNRAS.435..689G/ to get an idea of the problem. The yt derived field and other abstractions would make doing this much easier, however I don't know if there is a framework for creating base fields in yt in memory and then computing derived fields based on those and then saving a mix of input fields and derived fields to disk? To make this more complex I have some weird save out requirements, so being able to change array order and do mpi decomposition at save time would be very useful. Any suggestions or people telling me that this is obvious are welcome :) Thanks Stuart

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1000 pull requests
by Nathan Goldbaum 07 Jul '14

07 Jul '14

Hi all, Sometime in the next day or two, pull request #1000 in the yt_analysis/yt repository will be created. I want to congratulate everyone who has contributed to that goal. If you are a yt user and have noticed something that you want to fix, please feel free to send us patches. We love patches! More information about contributing to yt here: http://yt-project.org/docs/dev-3.0/developing/index.html Here's to PR #10000! -Nathan

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