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Pbc fix

Viacheslav requested to merge pbc_fix into master

Description

Fix related to incorrect PBC application before trajectory writing and sending data to GROMACS. CPMD now needs to know the shift applied to the system that is needed to center QM part (it is needed to unshift everything before writing the trajectory and sending data to GROMACS).

Types of changes

  • Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

  • My code follows the code style of this project.
  • My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • I have updated the CHANGELOG document.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • All new and existing tests passed.

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