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Add new box_factory

Micael Oliveira requested to merge box_factory into develop

Description

Adds new box_factory which initializes box_t classes via the function box_factory_create to replace read_box() from simul_box_init. box_t now has a bounding_box_l component which will replace simulation box's lsize later on.

Checklist

  • I have checked that my code follows the Octopus coding standards
  • I have added tests for all the new features added in this request.

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