MD Restarts
Check-pointing, Continuation and Parameter Changes
As with any other calculation in CASTEP, checkpoint files are written at regular intervals. Should the calculation be interrupted for whatever reason, it is possible to continue from the point at which the checkpoint file was last written.
Check-pointing is performed by dumping all pertinent data to a .check file. The interval at which this check-pointing occurs can be controlled in two ways.
The first option is to specify the number of md steps between checkpoints.
Alternatively, the wall-clock time (in seconds) between backups can be specified with:
Both can be specified but backup_interval will be preferred over num_backup_iter if both are set.
To disable either option, set the corresponding parameter to zero.
The name of the checkpoint file will be the calculation seed-name followed by ".check". This can be overridden with:
To continue an MD calculation from a checkpoint file, ensure that the .check file, the .castep file and the .md file from the previous run are present in the current directory. If the seed-name of the new run is the same as for the old, the command
will suffice. To continue the run from a checkpoint file
my_md_run.check use:
Note the standard CASTEP behaviour is to append new data to the end of existing files (such as .castep and .md) to avoid loosing data from earlier runs. This is not the case for the .check file, which is overwritten with new data. For this reason, the default CASTEP behaviour is to make a backup of the .check file, before over-writing it, so as to minimize the risk of data loss.
Changing Parameters on Continuation
Check-pointing is particularly useful for MD calculations where we often require many thousands of time-steps to extract useful information. Another important benefit is the ability to halt a calculation, and continue from a checkpoint with a revised set of MD parameters. For example one may wish to alter the target thermostat temperature, or the cell relaxation time without having to restart the run from the unequilibrated configuration.
All options described in the above sections can be changed on a restart, i.e. it is possible to change ensemble, thermostat and barostat schemes, relaxation times, time-step, constraints, etc. by specifying new values in the input files for the new run. It is not possible to change the number of atoms/electrons in the cell upon a restart.
Care must be taken when changing parameters on a restart. For example a large discontinuous change in the specified temperature or pressure will perturb a system away from equilibrium. In such cases the system should not be sampled until re-equilibrated.
Although it is possible to change electronic minimisation schemes/parameters on a restart, this is somewhat unwise for obvious reasons.
On-The-Fly Parameter Changes
In fact, molecular dynamics parameters can be changed without having to halt the calculation at all! At the end of each MD step, the parameters file is re-read. Any parameters in this file which differ from those currently in use will be updated before the next MD step commences. It is therefore possible to alter the state of a running calculation by simply making changes to the parameters file while the calculation is running. The same considerations/restrictions which apply to changing parameters on a restart apply to these on the fly changes.