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

Jiang, Yanfei yanfei.jiang at cfa.harvard.edu
Tue Apr 5 09:05:42 PDT 2016 

Hi Mike and Matt,

     The logarithmic grid in the code is actually very simple. In each
level, starting from the left edge, the grid space for the first cell is
dx, then the next cell is r dx, where r is a fixed ratio. In spherical
polar coordinate system, the logarithmic grid is only used in the radial
direction.

     If this kind of function can be implemented in yt, that will be great.

Thank you.

On Mon, Apr 4, 2016 at 1:38 PM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> I think that the main mapping functions that stellar people are thinking
> about are these:
>
> http://math.boisestate.edu/~calhoun/www_personal/papers/ca-he-le-2008.pdf
>
> On Mon, Apr 4, 2016 at 5:35 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
>
>> Hi Mike and Sam,
>>
>> That makes sense; one thing we need to be slightly careful about is if
>> the shape function needs to be modified considerably, or if it's
>> multi-variate.  Sam, I'm sorry I missed your message or didn't put
>> things together, but I think this is worth looking into further.  If
>> you'd like to correspond about this, yt-dev might be a better choice,
>> or we can chat offline and I'll send a summary.
>>
>> On Mon, Apr 4, 2016 at 4:31 PM, Michael Zingale
>> <michael.zingale at stonybrook.edu> wrote:
>> > This mapped grid capability is similar to what Sam Jones e-mailed the
>> list
>> > about a week or two ago.  Their grid is logically Cartesian, but a
>> mapping
>> > function transforms it to a different shape.
>> >
>> > On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk at gmail.com>
>> wrote:
>> >>
>> >> 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
>> >> >>>>>> yt-users at lists.spacepope.org
>> >> >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >>>>>
>> >> >>>>>
>> >> >>>>> _______________________________________________
>> >> >>>>> yt-users mailing list
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>> >> >>>>>
>> >> >>>>
>> >> >>>>
>> >> >>>> --
>> >> >>>> Yan-Fei Jiang
>> >> >>>>
>> >> >>>> Einstein Fellow
>> >> >>>> Harvard-Smithsonian Center for Astrophysics
>> >> >>>> 60 Garden Street, Cambridge MA USA 02138
>> >> >>>>
>> >> >>>> _______________________________________________
>> >> >>>> yt-users mailing list
>> >> >>>> yt-users at lists.spacepope.org
>> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >>>>
>> >> >>> _______________________________________________
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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
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > yt-users mailing list
>> >> > yt-users at lists.spacepope.org
>> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
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>> >> >
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>> >
>> >
>> >
>> >
>> > --
>> > 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
>> > web: http://www.astro.sunysb.edu/mzingale
>> > github: http://github.com/zingale
>> >
>> >
>> > _______________________________________________
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>> >
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>
>
>
> --
> 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
> *web*: http://www.astro.sunysb.edu/mzingale
> github: http://github.com/zingale
>
>
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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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