I think a ValidatePeriodic field validation like what Matt suggested makes the most sense, as it would then error out if someone throws it a non-periodic dataset. Sam On Fri, Dec 21, 2012 at 3:19 PM, John ZuHone wrote:

Perhaps this should be a field parameter?

John ZuHone Laboratory for High-Energy Astrophysics NASA/Goddard Space Flight Center 8800 Greenbelt Rd., Code 662 Greenbelt, MD 20771 (w) 301-286-2531 (m) 773-758-0172 jzuhone@gmail.com john.zuhone@nasa.gov

On Dec 21, 2012, at 8:15 PM, Nathan Goldbaum wrote:

...

This is a discussion that began on yt-users but since I'm going to speculate about how to change the code, I'm replying over here on yt-dev.

I see now that it's difficult to check for periodic boundary conditions in a code-independent way in the middle of a field definition. There are a number of places where yt assumes periodic boundary conditions (mostly in plotting routines) but I don't see any places that programatically check the boundary conditions that the simulation was run with. Am I missing something somewhere?

I feel like this functionality should be there but I'm not sure what the best solution is.

Just spitballing: perhaps there be something like pf.periodic which is True or False? This would have to be defined in the individual code frontends by looking at runtime parameters. It's not obvious to me that this will be easy to do for codes that don't have self-describing data formats. Another issue is that a binary Periodic attribute won't be sufficient for simulations run with mixed boundary conditions.

Does anyone else have any thoughts on this? I don't want to cause a huge disruption but I'm strongly -1 on the way the Radius field is currently written since it quietly produces incorrect results on a large number of test problem-like datasets. It won't be a problem in cosmological simulations so I worry that inexperienced users will tend to get bit by it.

Cheers,

Nathan

...

I've seen and used something similar in my ellipsoids, where the domain width (DW) is used to calculate the shortest distance between two points due to periodic boundary condition. So if you do not have a periodic box

On 12/21/12 4:26 PM, Geoffrey So wrote: then that line (involving DW) should be changed. This is part of the reason why my ellipsoid container is limited to periodic box only.

...

I'm hoping to put in a flag to turn it off and on later, but if a flag

is put in to turn it off maybe I'll imitate it for the ellipsoids, too.

...

From G.S.

On Fri, Dec 21, 2012 at 4:18 PM, Nathan Goldbaum

nathan12343@gmail.com>> wrote:

...

Hi all,

I encountered a bit of odd code deep in the field definition code and I need some help to understand why it is the way it is.

The field I'm curious about is the Radius field (defined on line 796 of universal_fields.py):

def _Radius(field, data): center = data.get_field_parameter("center") DW = data.pf.domain_right_edge - data.pf.domain_left_edge radius = np.zeros(data["x"].shape, dtype='float64') for i, ax in enumerate('xyz'): r = np.abs(data[ax] - center[i]) radius += np.minimum(r, np.abs(DW[i]-r))**2.0 np.sqrt(radius, radius) return radius

In particular, I don't understand this line:

radius += np.minimum(r, np.abs(DW[i]-r))**2.0

Is this supposed to correct for some effect in periodic simulations?

The reason I bring this up is because it caused some very weird behavior in a 1D FLASH simulation. In this simulation, the domain went from x = -.01 pc to x = +500 pc. Since the middle of the domain wasn't lined up with the 'center' of the simulation at x = 0, the offending line in the radius calculation led to an incorrect calculation of the radius beyond x = 250 pc. In that case, I was able to fix it by changing the offending line to

radius += r**2.0

Before I issue a patch, I want to see why it's defined the way it is currently and see if we can come up with a workaround.

Cheers,

Nathan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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