Add periodic bond wrapping support in plotting functions#149
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eyjafjallac wants to merge 5 commits into
Closed
Add periodic bond wrapping support in plotting functions#149eyjafjallac wants to merge 5 commits into
eyjafjallac wants to merge 5 commits into
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- Introduced `show_periodic_wrap_bonds` parameter in both `plot_structure_mpl` and `plot_structure` functions to control the visualization of bonds that cross periodic boundaries. - Updated `compute_bonds` function to handle periodic boundary conditions more effectively, allowing for accurate bond representation in periodic lattices. - Enhanced documentation and tests to cover the new functionality and ensure correct behavior in various scenarios.
…eadability - Reformatted the assignment of `boundary_basis` in the `compute_bonds` function to enhance code clarity by breaking it into multiple lines. - This change aims to maintain consistency in code style and improve maintainability.
2 tasks
- Introduced `show_periodic_wrap_bonds` and `periodic_image_opacity` parameters in `plot_structure_mpl` and `plot_structure` functions to enhance visualization of bonds in periodic lattices. - Updated the `compute_bonds` function to improve handling of periodic boundary conditions, ensuring accurate bond representation. - Enhanced documentation to reflect these new features and their usage.
- Added notes for `show_periodic_wrap_bonds` and `periodic_image_opacity` parameters in the documentation to clarify their effects on bond connectivity and periodic-image visibility in plotting functions. - Enhanced the clarity of the documentation to ensure users understand the usage of these new features.
…ions - Introduced `bond_mode` parameter in `plot_structure_mpl` and `plot_structure` functions to allow users to specify bond-neighbor selection modes: `auto`, `nearest`, or `periodic`. - Updated the `compute_bonds` function to validate the `bond_mode` and ensure proper handling of periodic boundary conditions. - Enhanced documentation to clarify the usage of the new `bond_mode` parameter and its implications for bond visualization. - Added tests to verify the correct behavior of the new functionality and to ensure that invalid bond modes are properly rejected.
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Summary
compute_bondsinext/plots/src/qten_plots/_utils.pyto make periodic bond selection more robust and deterministic._plotly_impl.py,_mpl_impl.py) to pass lattice/offset metadata into bond computation.show_periodic_wrap_bonds(defaultFalse) to structure plotting so users can hide wrap-around seam bonds for cleaner finite-cell visuals, while still allowing torus-style wrap bonds when needed.Why
TODO
kagome.plot("structure")shows clean nearest-neighbor bonds without seam-wrap artifacts.kagome.plot("structure")no longer shows spurious extra-looking bonds in default mode.backend="plotly"backend="matplotlib"shape=(12, 12)honeycombandkagomeremains acceptable.