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@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@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@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@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@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@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@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@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@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@lists.spacepope.org
>> >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
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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
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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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>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
> 11794-3800
> phone:  631-632-8225
> e-mail: Michael.Zingale@stonybrook.edu
> web: http://www.astro.sunysb.edu/mzingale
> github: http://github.com/zingale
>
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Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800
phone:  631-632-8225


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Yan-Fei Jiang

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60 Garden Street, Cambridge MA USA 02138