[yt-users] load structured mesh

Tue May 3 06:43:23 PDT 2016

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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