This adds some new methods to the atom_two table that will make use of the new frame column and the change to the atom0 and atom1 indexing. The get_bond method will get the bond distance between any two referenced atoms over the different frames. The use of this can be in a geometry optimization to track a bond distance over the course of the optimization.
Things left to do:
[ ] Extend this for the periodic cells
[ ] Test the functionality in the different functions to get the interatomic distances
[ ] Make sure this can work in a molecular dynamics calculation
[ ] Make sure that all of the atom parsers have the new adx column
This will close #205 and close #211
This adds some new methods to the
atom_two
table that will make use of the newframe
column and the change to theatom0
andatom1
indexing. Theget_bond
method will get the bond distance between any two referenced atoms over the different frames. The use of this can be in a geometry optimization to track a bond distance over the course of the optimization.Things left to do:
adx
columnFor testing: