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Linear and efficient neighbour finder #393

Merged
merged 17 commits into from
Feb 16, 2024
Merged

Commits on Feb 15, 2024

  1. Configuration menu
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  2. neighs in python syntax and added tests

    pfebrer authored and zerothi committed Feb 15, 2024
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  3. remove print statement

    pfebrer authored and zerothi committed Feb 15, 2024
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  4. cython was using the python sqrt

    pfebrer authored and zerothi committed Feb 15, 2024
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  5. make R larger than cell work

    pfebrer authored and zerothi committed Feb 15, 2024
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  6. remove itertools

    pfebrer authored and zerothi committed Feb 15, 2024
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  7. ran black and isort

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  8. small clean-ups, and fixed requirements

    future.annotations requires Cython>=3
    
    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  9. fixed names of neighbor finder

    changed class and argument names to make them simpler.
    
    Also changed default of overlap to False.
    The internal R is now an array, regardless, but
    it can have either ndim 0 or 1, depending on
    whether it is an array or not.
    
    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  10. added Pol as author in Citation

    This is not to diminish other contributors.
    Pol has made tremendous contributions.
    This is a delicate decision, and is in no
    way a discouragement of other contributions made.
    
    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  11. moved neighbor code to new folder

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  12. cleaned documentation and return value

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  13. ran black

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  14. fixed sort order

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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  15. fixed cmake for neighbor location

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. fixed memory problems in the finder

    In some cases (when the bin-size is big) the
    maximum pairs it would allow could be quite big.
    When the bins has many atoms, the error in the
    actual neighbors can be significant, leading
    to memory problems.
    
    Now the finder uses a maximum of 200MB of initial
    neighbor lists. This results in incremental re-allocations
    which is a bit more heavy, but it reduces the chances of
    running out of memory.
    
    One can change the default memory by changing the
    class variable: Neighbor.memory accordingly.
    
    Added it to the documentation.
    
    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 16, 2024
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  2. allowed tuple input of bin_size

    Signed-off-by: Nick Papior <[email protected]>
    zerothi committed Feb 16, 2024
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