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SimlifyConfigshould be moved to theconfig/core.pyand 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 notcenter_structure),get_box_lengths(but notrotate_positions), etc. Things that manipulate the system to get ready for preparation are in simlify. - We need to rename the
simulationdirectory to better reflect what we are doing here. We voted forworkflows. Some of thestructurefunctions would be moved underworkflows. - Ensure that we move the PDB writer to atomea.
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