Fix cost calculation when icgroup is missing in a simulation
Added ABRatioCellDOF along with 2 other small changes
Added Reference Trajectory simulation.
Add bond, bend and dihedral StateItems to keep track of their energy contributions
Fix XYZ conversion for non-standard cases
FF Generator can now combine multiple parameter files
System.subsystem
Report cell parameters of System object
Cut bonds to/from fragment
Fix bug in generator in case of log level silent
Reset hessian in QN if update fails
Fix Steven's NAN issue
Reorganize test files
A tester for the optimizer and an improved quasi-newton
Minor improvements and one broken test
Make trust radius algorithm a little less agressive
Improve trust radius algorithm
More opttest cases
XYZ trajectory output for opttest
Added do_ei option to EpotBonds-, EpotBends- and EpotDihedsStateItem