[yt-dev] data on different AMR levels

[Elizabeth Tasker]

Hi Matt and Mike,

Just a finishing note to say that all the below techniques (covering_grid, grid_collection and Mike's loop) work well, but unfortunately my 190GB machine runs out of memory when I try and create a covering grid / duplicate the array elements to the size of the finest level! 

So for the moment, I've abandoned that final step and just created a grid collection:

gc = pf.h.grid_collection([25e3, 25e3, 25e3], pf.h.select_grids(level)]

and written it to file. 

Delightfully short; thank you!

Out of curiosity, why does grid_collection take the box centre as an argument? AMRGridCollectionBase doesn't seem to use it in its source? 

Elizabeth

On Jan 17, 2013, at 12:01 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> On Wed, Jan 16, 2013 at 9:52 PM, Elizabeth Tasker
> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>> Hi Mike and Matt,
>> 
>> Thank you! Both those solutions look great.
>> 
>> I like Mike's a lot for its transparency, but possibly Matt's might end up making slightly neater code.
>> 
>> One question, Matt:
>> 
>>> Okay, sorry for being dense.  But basically what I'm getting is that
>>> you want the functionality of covering grids, but you want to be able
>>> to restrict the grids from going above some level L, right?
>> 
>> Or below. I just want cells on one level only.
> 
> Okay, the grid collection might work, but I still think the covering
> grid is the best, with the masking I describe below.
> 
> gc = pf.h.grid_collection([0.5, 0.5, 0.5], pf.h.select_grids(L))
> 
> gc["Density"]
> gc["dx"]
> gc["x"]
> 
> etc.  You'll have to manually manipulate the dx stuff, cell mass, etc.
> 
>> 
>>> 
>>> And for the Level 1 case you mention above, do you want contributions
>>> from Level 0?  (That's not so hard to do.)
>> 
>> No. So I want an array that contains only cells from level 1, with no contributions from 0 or 2.
> 
> Okay, then mask or use the grid collection.  :)
> 
>> 
>>> To do this with a covering grid you could pre-allocate:
>>> 
>>> Li = 0
>>> Lo = 3
>>> 
>>> cg = pf.h.covering_grid(Li, [0, 0, 0], pf.domain_dimensions * pf.refine_by**Li)
>>> output = np.empty(pf.domain_dimensions * pf.refine_by**Lo)
>>> nd = pf.refine_by**(Lo-li)
>>> for i in range(nd):
>>>   for j in range(nd):
>>>       for k in range(nd):
>>>           output[i::nd,j::nd,k::nd] = cg[field]
>> 
>> 
>> Ah ok! So this is the same as Mike's method in that a covering_grid is created at the resolution of the cell size on the specified level, and then the array values are multiplied to give the correct number for a higher resolution? (Which works fine for the basic quantities; density, energy and velocity but won't for cell mass -- which is totally fine).
> 
> Cell mass is converted correctly, I believe.  This is accomplished
> through a validator, NeedsGridType, which is specified if a field
> *needs* to be calculated in the original grid (i.e., Level) but
> otherwise fields are generated in the CG.  I've verified that
> specifically for CellMassMsun this is correctly done:
> 
> In [12]: ms = []
> 
> In [13]: for L in range(4):
>    cg = pf.h.covering_grid(L, [0,0,0], pf.domain_dimensions * pf.refine_by**L)
>    ms.append(cg["CellMassMsun"].sum())
>   ....:
> yt : [DEBUG    ] 2013-01-16 22:00:26,392 Appending object to
> galaxy0030 (type: <class 'yt.data_objects.hierarchy.AMRCoveringGrid'>)
> yt : [DEBUG    ] 2013-01-16 22:00:26,436 Getting fields ['Density']
> from 1 possible grids
> yt : [DEBUG    ] 2013-01-16 22:00:26,439 Appending object to
> galaxy0030 (type: <class 'yt.data_objects.hierarchy.AMRCoveringGrid'>)
> yt : [DEBUG    ] 2013-01-16 22:00:26,442 Getting fields ['Density']
> from 9 possible grids
> yt : [DEBUG    ] 2013-01-16 22:00:26,465 Appending object to
> galaxy0030 (type: <class 'yt.data_objects.hierarchy.AMRCoveringGrid'>)
> yt : [DEBUG    ] 2013-01-16 22:00:26,518 Getting fields ['Density']
> from 17 possible grids
> yt : [DEBUG    ] 2013-01-16 22:00:26,703 Appending object to
> galaxy0030 (type: <class 'yt.data_objects.hierarchy.AMRCoveringGrid'>)
> yt : [DEBUG    ] 2013-01-16 22:00:27,320 Getting fields ['Density']
> from 25 possible grids
> 
> In [14]: ms
> Out[14]:
> [18524964522.745506,
> 18524964453.698158,
> 18524964476.255985,
> 18524964484.909931]
> 
>> 
>> My only question is:
>> 
>> If I do this for level (e.g.) 2 and level 2 doesn't cover the whole domain -- what does the covering grid do when there are no level 2 cells over a region of space?
> 
> Fills 'em with level 1 or level 0, depending.  You can just mask these
> out, though, which might be the best solution if the covering grid
> (3D, handles the mass issue, etc) is the better solution:
> 
> bag_ind = cg["GridLevels"] != 2
> cg[field][bad_ind] = -1.0 # or something
> 
> That should do it, and that would go somewhere inside the loop above.
> 
> -Matt
> 
>> 
>> Thanks again!
>> 
>> Elizabeth
>> _______________________________________________
>> yt-dev mailing list
>> yt-dev at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
> _______________________________________________
> yt-dev mailing list
> yt-dev at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org