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

Jonah Miller jonah.maxwell.miller at gmail.com
Wed Mar 30 15:01:04 PDT 2016


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
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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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