[yt-users] load spherical polar coordinate data with mesh refinement in HDF5

[Jiang, Yanfei]

Hi Matt and Jonah,

    I think I can use load_hexahedral_mesh to load data from each mesh
block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the
whole mesh due to mesh refinement. I guess I can create a dict to collect
the data from each mesh block, as in load_amr_grids (but not the same). The
question is will such a data structure (a dict of hexahedral_mesh) be
recognized by yt?

On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <
jonah.maxwell.miller at gmail.com> wrote:

> Hi Yanfei,
>
> To add to Matt's comment. Here is the documentation for using
> load_hexahedral_mesh.
>
> http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data
>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html
>
> Best,
> Jonah
>
>
> On 16-03-30 05:15 PM, Matthew Turk wrote:
>
>> Hi Yanfei,
>>
>> This is possible -- but it will also slow some things down.  You can
>> use the load_hexahedral_mesh function, and there're examples of this.
>> This takes away some of the optimizations that regular grids can do,
>> but we're hoping to add them back in shortly.  Like the other
>> functions it too takes a geometry argument.
>>
>> -Matt
>>
>> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
>> <yanfei.jiang at cfa.harvard.edu> wrote:
>>
>>> Hi Jonah,
>>>
>>>     I am able to load the data to yt now using load_amr_grids(). I notice
>>> that it can also set geometry to spherical. This is great. But to make
>>> life
>>> more complicate. Is it possible to let yt know that the grid is
>>> logarithmic?
>>> Currently, load_amr_grids() just take left and right edges of each
>>> block. I
>>> guess yt assumes the grid is uniform between left and right edges. Is it
>>> possible to provide arrays of coordinate values for each cell in each
>>> block?
>>>
>>> Thanks.
>>>
>>> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
>>> <jonah.maxwell.miller at gmail.com> wrote:
>>>
>>>> Hi Yan-Feng,
>>>>
>>>> I haven't tried it, but I think there is functionality for this. You can
>>>> use the load_amr_grids() function which can load amr data in Cartesian,
>>>> spherical, or polar coordinates. Here's the documentation:
>>>>
>>>>
>>>>
>>>> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
>>>>
>>>>
>>>>
>>>> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
>>>>
>>>> Best,
>>>> Jonah
>>>>
>>>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>>>> yanfei.jiang at cfa.harvard.edu>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>           I have some data from a new version of Athena simulations.
>>>>> It is
>>>>> in spherical polar coordinate with mesh refinement written in HDF5.
>>>>> The data
>>>>> structure is similar to flash data but not the same. Does anyone have
>>>>> suggestions to load such data to yt directly?
>>>>>
>>>>> Thank you.
>>>>> --
>>>>> Yan-Fei Jiang
>>>>>
>>>>> Einstein Fellow
>>>>> Harvard-Smithsonian Center for Astrophysics
>>>>> 60 Garden Street, Cambridge MA USA 02138
>>>>> _______________________________________________
>>>>> yt-users mailing list
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>>>>>
>>>>
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>>>>
>>>
>>> --
>>> Yan-Fei Jiang
>>>
>>> Einstein Fellow
>>> Harvard-Smithsonian Center for Astrophysics
>>> 60 Garden Street, Cambridge MA USA 02138
>>>
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-- 
Yan-Fei Jiang

Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
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