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

Mon Apr 4 14:31:13 PDT 2016

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
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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
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> >>>>
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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
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