Transform particles first to the elements local coordinate system, then compute Particle-Matter interaction

fixing bug that prevented usage of negative angles in combination with X,Y,Z,THETA,PHI,PSI instead of ELEMEDGE

 moving startTimer/stopTimer outside loop over particles and - avoiding string
 comparison inside loops over particles

src/Classic/Structure/LossDataSink.cpp

- openH5(mode): passed mode argument was not used, H5_O_RDONLY was
  hard-coded in case of H5hut 2 (fixes issue #29)
- save(): read number of steps after opening file in append mode

Closes #29

See merge request !7

- openH5(mode): passed mode argument was not used, H5_O_RDONLY was
  hard-coded in case of H5hut 2 (fixes issue #29)
- save(): read number of steps after opening file in append mode