[yt-users] load structured mesh

Tue May 3 06:52:55 PDT 2016

Whoops!  I meant load_hexahedral_mesh, but that link still works.  :)

On Tue, May 3, 2016 at 8:43 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Andrea,
>
> I *think* you could use load_semistructured_mesh for this; it can accept
> different coordinate systems, too.  There's an example here:
>
>
> http://yt-project.org/docs/dev/examining/loading_data.html#semi-structured-grid-data
>
> -Matt
>
> On Tue, May 3, 2016 at 3:01 AM, Andrea Negri <negri.andre at gmail.com>
> wrote:
>
>> Hi John,
>>
>> unfortunately I have a cell spacing varying inside a grid. A viable
>> way would be to interpolate my data on a regular grid, and then load
>> it.
>> The interpolation part is not so computationally demanding (I have
>> already tested it), it is just the plotting which is slow process (I'm
>> talking of plotting a slice).
>> Maybe this can be improved by building a set of grid with lower and
>> lower resolution. Is there any documentation on how t he grid in the
>> grid data format should be?
>>
>>
>> Andrea
>>
>> On 3 May 2016 at 01:37, John ZuHone <jzuhone at gmail.com> wrote:
>> > If by "non-uniform" you mean that you have grids of differing
>> resolutions
>> > then yt and grid data format support that, but if you have cell spacing
>> > varying _inside_ a grid then yt does not yet support this. We're
>> working on
>> > it, but it will probably take some time before it is operational.
>> >
>> >
>> > =================================
>> > John ZuHone, Chandra/ACIS operations
>> > Harvard-Smithsonian Center for Astrophysics
>> >
>> > 60 Garden St., MS-67       (w) 617-496-1816
>> > Cambridge, MA 02138.     (m) 781-708-5004
>> >
>> > john.zuhone at cfa.harvard.edu
>> > http://hea-www.cfa.harvard.edu/~jzuhone
>> > =================================
>> >
>> > On May 2, 2016, at 7:18 PM, Andrea Negri <negri.andre at gmail.com> wrote:
>> >
>> > Dear John,
>> >
>> > thanks for the suggestions. Do you know if the grid data format is
>> > compatible with a non uniform mesh? I was thinking of porting my
>> > outputs in this format.
>> >
>> >
>> > Cheers,
>> > Andrea
>> >
>> > On 2 May 2016 at 18:52, John Zuhone <jzuhone at gmail.com> wrote:
>> >
>> > Hi Andrea,
>> >
>> >
>> > yt has some support for axisymmetric grids in 2D, so you won’t need to
>> > convert to a 3D array.
>> >
>> >
>> > The bigger issue is the logarithmic grid spacing. This is currently
>> being
>> > worked on, but is in a very early state. Currently what it does is use
>> > “logr” as the coordinate instead of r, which may not be very ideal for
>> every
>> > situation. A lot of yt functionality is probably not compatible with
>> this
>> > way of doing things.
>> >
>> >
>> > Nevertheless, if you would like to explore it further, let us know.
>> >
>> >
>> > Best,
>> >
>> >
>> > John Z
>> >
>> >
>> > On May 2, 2016, at 10:53 AM, Andrea Negri <negri.andre at gmail.com>
>> wrote:
>> >
>> >
>> > Of course. I have a 2.5D simulation in spherical coordinates. It is
>> >
>> > axial symmetric, so the actual grid is 2D, r and theta. The grid is
>> >
>> > structured, the grid spacing in theta is constant, while the spacing
>> >
>> > in r follows a geometrical progression, i.e. dr[i+1] = dr[i] * factor,
>> >
>> > where factor is a constant.
>> >
>> >
>> > I don't know if yt supports axisymmetric grids, but I can bypass this
>> >
>> > issue by duplicating the 2D array into a 3D one. Sure, it is not
>> >
>> > efficient...
>> >
>> >
>> > My ultimate goal is to produce projections, off axis projections and
>> >
>> > mock X-ray observations.
>> >
>> >
>> >
>> > Thanks,
>> >
>> > Andrea
>> >
>> >
>> > On 2 May 2016 at 16:43, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>> >
>> > Can you share a little bit more detail about your grid structure? I know
>> >
>> > that support for log-radial bins is being worked on right now, for
>> example.
>> >
>> >
>> > On Mon, May 2, 2016 at 3:18 AM, Andrea Negri <negri.andre at gmail.com>
>> wrote:
>> >
>> >
>> > Hi all,
>> >
>> >
>> > I'm trying to read ZEUS-MP 2 data, and I'm building my programs step
>> >
>> > by step. I was able to load data regularly spaced in spherical
>> >
>> > coordinates. However, I actually have a non-uniform radial grid.
>> >
>> >
>> > I tried with the script in attachment, but I have got odd errors...
>> >
>> >
>> > Also, I have found this page, is it relevant for my case (just because
>> >
>> > my code is mentioned, the answer would be yes :) )?
>> >
>> > https://bitbucket.org/yt_analysis/grid_data_format
>> >
>> >
>> >
>> > Thanks,
>> >
>> > Andrea
>> >
>> >
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