[yt-users] Covering Grid Dimensions: multiple refinement levels

[Nathan Goldbaum]

What is dims*2**3? Depending on your data this might be a very large array
that won't fit in memory on your machine.

You will need to find a machine that has more RAM to do this or create a
covering grid that only covers a subset of the domain.

On Thursday, November 19, 2015, Carla Bernhardt <carla.j.bernhardt at gmail.com>
wrote:

> Thanks again for the help. Once I implemented that, I have a follow-up
> problem: Once I have this much larger grid covering, it seems possibly too
> large for yt/python to handle. When I run:
>
> cg=ds.smoothed_covering_grid(3,[0,0,0], dims*2**3)
> data=cg['density']
>
> (where before I had dims*2**1), the variable data does not load and gives a
> few errors <http://pastebin.com/JVhenc4z> which lead me to believe that
> python or yt will not let me use that much space. Can I force yt to let me
> use more space?
>
> Thanks,
> Carla
>
> 2015-11-19 16:11 GMT+01:00 Nathan Goldbaum <nathan12343 at gmail.com
> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>>:
>
>> Hi Carla,
>>
>> So it looks like ref_factors is only defined in the boxlib frontend,
>> which is why it doesn't work for your Enzo data. Boxlib needs a concept of
>> ref_factors because it allows AMR refinement jumps larger than a factor of
>> two on a single level (i.e. level 2 might be four times higher resolution
>> as level 1). Enzo and many other AMR codes do not allow this, instead only
>> allowing a factor of two increase in linear resolution per AMR level.
>>
>> The dimensions you want to use depend on what fraction of the full domain
>> you want to interpolate to uniform resolution. It looks like you want to
>> create a covering grid covering your full domain, so to create a covering
>> grid at the same resolution as AMR level 3 you would do:
>>
>> all_data_level_3 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0],
>>                                     dims=ds.domain_dimensions * 2**3)
>>
>> This is because each refinement level jump in an Enzo simulation
>> corresponds to a factor of two increase in spatial resolution.
>>
>> Hope that makes sense,
>>
>> Nathan
>>
>> On Thu, Nov 19, 2015 at 8:58 AM, Carla Bernhardt <
>> carla.j.bernhardt at gmail.com
>> <javascript:_e(%7B%7D,'cvml','carla.j.bernhardt at gmail.com');>> wrote:
>>
>>> Thank you for your quick response. However, when I used:
>>>
>>> ref = int(np.product(ds.ref_factors[0:3])),
>>>
>>> I got this error:
>>>
>>> AttributeError: 'EnzoDataset' object has no attribute 'ref_factors'
>>>
>>> Did I misunderstand your suggestion? Or do I need to import something?
>>>
>>> Thanks,
>>>
>>> Carla
>>>
>>> 2015-11-19 15:39 GMT+01:00 Michael Zingale <
>>> michael.zingale at stonybrook.edu
>>> <javascript:_e(%7B%7D,'cvml','michael.zingale at stonybrook.edu');>>:
>>>
>>>> I've done this in the past:
>>>>
>>>> ref = int(np.product(ds.ref_factors[0:max_level]))
>>>>
>>>>
>>>>
>>>> # allocate for our uniformly-gridded result
>>>>
>>>> dims = ds.domain_dimensions*ref
>>>>
>>>> this will work for a more general case when the jump between levels can
>>>> change as a function of level.
>>>>
>>>> On Thu, Nov 19, 2015 at 9:10 AM, Carla Bernhardt <
>>>> carla.j.bernhardt at gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','carla.j.bernhardt at gmail.com');>> wrote:
>>>>
>>>>> Dear YT Users,
>>>>>
>>>>> To better understand covering_grid (or smoothed_covering_grid), can
>>>>> someone explain what dimensions I should use when I have multiple levels of
>>>>> refinement? If I have 1 level of refinement from AMR data, the dimensions
>>>>> should be the same, I believe, but what if I have 2 or 3 levels of
>>>>> refinement? Should the fixed resolution region then have dimensions of
>>>>> dims*2^2 and dims*3^2 respectively?
>>>>>
>>>>> Here is one example from a tutorial
>>>>> <http://yt-project.org/doc/examining/low_level_inspection.html#examining-grid-data-in-a-fixed-resolution-array>
>>>>> if that helps isolate my question:
>>>>> all_data_level_2 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0],
>>>>>                                       dims=ds.domain_dimensions * 2**2)
>>>>>
>>>>> Thanks in advance,
>>>>> Carla
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Michael Zingale
>>>> Associate Professor
>>>>
>>>> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
>>>> 11794-3800
>>>> *phone*:  631-632-8225
>>>> *e-mail*: Michael.Zingale at stonybrook.edu
>>>> <javascript:_e(%7B%7D,'cvml','Michael.Zingale at stonybrook.edu');>
>>>> *web*: http://www.astro.sunysb.edu/mzingale
>>>> github: http://github.com/zingale
>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151119/9c2abb67/attachment.html>