Improved Lewis structure analysis and allow containers

• Added access to the new PM6-ORG parameterization and made it the default, though PM7
  is still preferred for materials simulation. PM6-ORG handle organic and biomolecules
  well.
• Made the Lewis structure analysis more robust and added information to the output.
• Provided an option for the Lewis structure calculation to set the charge of the
  system to that calculaed by the Lewis structure.
• Added support for containers
• Made default to run serially, since parallel doesn't provide much benefit.
• Fixed bug in analysis if optimization doesn't converge.