Hi Jonah, That's right -- the volume rendering won't work, but slices will. The VR should be working relatively soon, though. -Matt On Sun, May 24, 2015 at 8:47 PM, Jonah Miller wrote:

Oh, I should add that I don't think 3D visualization is possible with hexahedral meshes at the moment. The pixelizer doesn't support them yet... At least that's my understanding. If you really need a 3D visualization, you might want to try transforming your data into a regularly spaced grid (using another tool) and then loading uniformly spaced data as in this example: http://yt-project.org/docs/dev/examining/spherical_data.html

Best, Jonah

On 15-05-24 09:41 PM, Jonah Miller wrote:

Hi Katharina, Andrew,

There is a convenience function to create the coordinates and connectivity arguments: hexahedral_connectivity. This function takes three 1D arrays, which are the projections of your grid points onto your coordinate axes, here called x,y, and z. The function then returns the connectivity and coordinates arrays.

Here's an example: http://yt-project.org/docs/dev/examining/loading_data.html#semi-structured-g...

Best, Jonah

On 15-05-24 09:35 PM, Andrew Myers wrote:

Hi Katharina,

I don't have an example handy, but the "coordinates" and "connectivity" arguments are arrays you construct that describe the vertices and zones of the hexahedral mesh you want. The "coordinates" argument is supposed to be a (N_vertices, 3) - shaped array of floats that has the x, y, and z positions of all the vertices in the hexahedral mesh. The "connectivity" argument is a (N_zone, 8) - shaped array of ints that gives, for each zone, the indices of the 8 vertices that surround it. So for example, if connectivity[0][2] is '12', then coordinates[12] would give the position coordinate of the third vertex surrounding the first zone, if that makes sense.

Once you've constructed those arrays from the information in your dataset and fed them into "load_hexadral_mesh", yt shouldn't care whether the data came from an HDF5 file or not.

-Andrew

On Sun, May 24, 2015 at 11:46 AM, Katharina Wollenberg wrote:

...

Hello together,

for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has ratioed zones. For that I want to use the command yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, ...) . However, since I am new to yt, I am a little bit stuck right now… I am not quite sure what is meant in detail by the arguments connectivity and coordinates and how to formulate them in the load_hexahedral_mesh command.

Furthermore, do I need to pay particular attention on some commands because of using HDF5 data?

If anyone has an example for me, that’d be very helpful!

Thanks a lot!

Katharina Wollenberg

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