Set/Get coordinates and get gradients from system needs modification

[chemphys]

The get/set coordinates from the system currently implemented return the coordinates AS THEY ARE. This means that will return the reordered coordinates, and add them in the order of the input, messing with the order of the monomers inside the code.

This needs to be addressed.

• Set coordinates should take the coordinates in the original input order, and set them in the system in the actual system order. This can be done by using the original order variable.
• Get coordinates should take the coordinates in the system order, and send them in the original input order.
• Gradients should be returned in the original input order, not in the actual order.

I will work on this and fix it.

[chemphys]

This has been fixed. Closing issue.