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

Matthew Turk matthewturk at gmail.com
Mon Apr 4 14:13:26 PDT 2016


Hi Yan-Fei,

I've thought about this a bunch.  I *think* that it's feasible, with
only very minor modifications to the existing system, as long as
there's a mapping we can construct for the spacing, and that mapping
is unique across the grids at fixed levels.

What I mean by that is, if we can have a function that operates such
that it's given a set of integer values (integer coordinate [xyz],
resolution level) and it can return a position and a width (in linear
space), we can implement this without too much trouble.  I can see
some tricky things relating to how to switch between log/lin
visualization, but they should be surmountable. (And presumably, if
you have a log spaced dataset, you won't want linear viz terribly
frequently anyway.)  Generating the integer coordinate might be the
funniest part; in linear space it's just
(pos-domain_left_edge)/local_dx, but I don't know the specifics of
your data format.

-Matt

On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller
<jonah.maxwell.miller at gmail.com> wrote:
> 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> 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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