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Add support for general triclinic boxes #104

@mphoward

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@mphoward

LAMMPS now allows the simulation box to be arbitrarily oriented in 3D space for user convenience in some cases. These boxes can be used in both data and dump files, so lammpsio should find a way to support them.

Internally in LAMMPS, coordinates are still put into the "restricted" LAMMPS box, and the dumped outputs are not rotated unless dump modify triclinic/general is used.

This change would require some discussion and thought:

  • Should we allow particles to be stored in non-restricted boxes in lammpsio? Maybe we should always map them back to the restricted box. We could provide a helper method for performing the rotation.
  • How do we maintain compatibility between restricted and general triclinic boxes in the Box and Snapshot?
  • What is the behavior in DumpFiles that may have a general triclinic box, but the coordinates have not been rotated?

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