Options for Run: Restarting a simulation, suppressing output, continuing output

Under default conditions a ``restart file'' will be written, once per output-block. If a simulation is interrupted (due to hardware problems for example), it can be restarted from the last completed block (here 12) by

  sim.Run(20000, restartBlock=12)
where the original number of time-steps should be specified, and the last completed block can be found by looking at the file ``LastComplete_restart.txt'' in TrajectoryFiles. It is possible to suppress writing of restart files (so restarts will not be possible), and all other output, by calling

  sim.Run(20000, suppressAllOutput=True)
This might be done for example, during an initial period of equilibration, although if this is planned to take a long time, it may be advisable to allow restart files to be written, in case of possible interruptions.

To avoid re-initializing the output, so that repeated calls to Run will append to the existing energies and trajectory files, do

  sim.Run(20000, initializeOutput=False)
This will give an error if Run was not called previously in the normal way (initializeOutput=True, which is its default value).

Heine Larsen 2017-07-21