Solving issues #145 and #144 #147
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SimoneMartino98
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Dec 17, 2025
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I also solved (I think) the issue #144 , avoiding the "netCDF4 is not available. Writing AMBER ncdf files will be slow." message every time dynsight is imported in a script. |
andrewtarzia
approved these changes
Dec 17, 2025
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Related Issues: close #145
Requested Reviewers: @andrewtarzia @SimoneMartino98
In the LENS and neighbor_list code, if the simulation box is not provided in the Universe, it is computed by the code. But in the case of system without PBC, the box was computed anew even if it was present.
With 2D system, this new box had zero thickness, and this lead to the code crashing with divisions by zero.
I solved the problem by only computing the box anew if it's not present in the Universe.
All previous tests still pass, and I added new tests on 2D systems to ensure everything works.