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

_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

--
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

_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

--

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