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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).