Add alchemical groups #15
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This has now been tested and is ready to be merged. |
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This PR adds support for associating modifications with alchemical groups, allowing for more complex transformations. Users can define multiple alchemical groups that can be transformed independently. This is particularly useful when applying different transformations to different regions of a system, or when using multiple instances of the same modification type for the same group of atoms (for example, to transform one set of LJ parameters into another).