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

[Jonah Miller]

Hi Yan-Fei,

I don't think this will work out of the box. Matt may have more insight 
here.

Best,
Jonah

On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
> 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 
> <mailto: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
>         <mailto: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
>             <mailto: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
>                 <mailto: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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>
> -- 
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
>
>
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