integrator md-vv does not print at nstlog
With integrator md-vv there is no log output at nstlog steps.
Fix log writing (modular simulator)
The current implementation would not write energies to log if
- log was not in sync with energy writing, or
- log writing is more frequent than neighborsearching.
This commit fixes these bugs, restoring the legacy behavior. Moving
forward, it could be discussed whether writing to log file and writing
to energy trajectory could be coupled (i.e., should log writing frequency
be a multiple of energy writing?).