| # Restore continuous periodic trajectories in changing cells |
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| You are repairing a scientific trajectory-analysis workflow in the supplied |
| MDAnalysis source snapshot. The workflow is used to remove artificial jumps |
| caused by periodic boundary wrapping before quantities such as mean-square |
| displacement and diffusion are calculated. |
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| The current implementation behaves inconsistently for valid constant-pressure |
| molecular-dynamics trajectories whose periodic cell changes with time. In |
| particular, a trajectory can contain a physically continuous path but the |
| transformed result can retain a box-length jump. The same physical type of |
| motion can produce different results under different valid frame schedules, |
| even though the numerical motion obeys the method assumptions. |
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| Inspect the complete source snapshot and run |
| `python reproduce.py`. Repair the implementation so that the external |
| trajectory behavior follows the required variable-cell semantics for changing |
| orthorhombic and triclinic cells. The correction must work for |
| general atom counts, cell changes, and crossing directions; do not hard-code the |
| public coordinates or a single frame index. |
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| Preserve ordinary fixed-cell trajectories, the existing handling of missing or |
| singular periodic cells, and the diagnostic behavior for non-sequential frame |
| access. The transformation must also remain coherent when a |
| trajectory is traversed more than once through the normal MDAnalysis API. |
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| The public reproduction is only a small smoke diagnostic. Use the source call |
| graph to determine the complete behavior that needs to be repaired. Do not use the network or add external data files. Keep changes |
| limited to the scientific implementation and any focused tests or comments |
| that are necessary for a general fix. |
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