Geometry debug function

[viktormai]

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

• Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
• Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
• Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

• Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
• Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
• Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

• I have performed a self-review of my own code
• I have run clang-format (version 18) on any C++ source files (if applicable)
• I have followed the style guidelines for Python source files (if applicable)
• I have made corresponding changes to the documentation (if applicable)
• I have added tests that prove my fix is effective or that my feature works (if applicable)

[paulromano]

Thanks for the initial shot at this! Here are my initial thoughts:

[viktormai]

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

[paulromano]

Thanks for the updates @viktormai! Here is another round of comments:

[paulromano]

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

[paulromano]

This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

[paulromano]

This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

[paulromano]

While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

[paulromano]

These are easily inspectable from the data itself and can be removed IMO