Issue59calculator class

[grahamstockton]

This was a very long time coming. Here are some major changes:

• Calculators now have their own classes that inherit from the generic calculator class
• There is element support, with specific colors for the elements
• Instead of hardcoding, file IO uses the python ase.io package to load any file and then extract what we need
• Some boundary behavior and damping methods have been encapsulated in their own functions
• David's boundary capture method (catching atoms at the edge of a set box hardcoded in) has been implemented