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Maintenance to prepare for features #16

@aalexmmaldonado

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@aalexmmaldonado
  • SimlifyConfig should be moved to the config/core.py and be the parent container for all other configs.
  • Any functions that provide data about the atomistic system are getting moved to atomea. For example, get_com (but not center_structure), get_box_lengths (but not rotate_positions), etc. Things that manipulate the system to get ready for preparation are in simlify.
  • We need to rename the simulation directory to better reflect what we are doing here. We voted for workflows. Some of the structure functions would be moved under workflows.
  • Ensure that we move the PDB writer to atomea.

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