Action: CHECKPOINT
| Module | setup |
|---|---|
| Description | Usage |
| Write a PLUMED checkpoint file for an exact restart. |   |
Details and examples
Write a PLUMED checkpoint file for an exact restart.
With this directive PLUMED writes its own checkpoint file, separate from the
one of the MD engine, whenever the MD engine writes its checkpoint (the MD
engine tells PLUMED through the doCheckPoint command of the interface; the
GROMACS patch does so) or, with STRIDE, every STRIDE steps for the engines
that do not send this signal.
The checkpoint stores the internal state of the actions (hills, accumulators,
random number generators, ...) at the start of the checkpointing step, together
with the sizes of all the files that PLUMED has written up to that moment.
When the simulation is restarted from it, every output file is truncated to the
size it had at the checkpoint, so that the lines written after it by the
interrupted run are removed, and the checkpointing step is computed again:
this requires the MD engine to restart from its own checkpoint of the same
step, as GROMACS does with -cpi. The result is an exact continuation of the
interrupted run, at variance with a plain RESTART where files
are only appended.
CHECKPOINT is a setup directive and must come before any action that writes a
file, so put it at the top of the input. The file is written atomically and the
previous checkpoint is kept with the suffix _prev (plumed_prev.cpt for
plumed.cpt); with multiple replicas every replica writes its own file with the
usual replica suffix.
CHECKPOINTWrite a PLUMED checkpoint file for an exact restart. More details FILE the name of the checkpoint file=plumed.cpt d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar
At restart, RESTART_FROM selects the checkpoint to read. The default, AUTO, reads FILE when the MD engine tells PLUMED that the run is restarted (or when RESTART comes before CHECKPOINT) and starts a new run otherwise. A file name reads that checkpoint unconditionally, NO never reads one (the checkpoint is only written). Restarting from a checkpoint implies RESTART.
CHECKPOINTWrite a PLUMED checkpoint file for an exact restart. More details FILE the name of the checkpoint file=plumed.cpt STRIDE write a checkpoint every STRIDE steps, in addition to those requested by the MD engine=1000 RESTART_FROM the checkpoint to restart from: AUTO (FILE, if the MD engine is restarting), NO (never restart from a checkpoint), or the name of a checkpoint file=AUTO d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar
The first step presented by the MD engine after the restart must be the one stored in the checkpoint, otherwise PLUMED stops with an error: this happens when the PLUMED checkpoint and the restart file of the MD engine do not come from the same moment of the simulation. With STRIDE, choose a stride that matches the checkpointing of the MD engine.
An action with the per-action keyword RESTART=NO starts from scratch at the
restart step: its state is not restored from the checkpoint and its files,
trimmed at the checkpoint like all the others, are backed up and rewritten
instead of being appended. This is the way to add a new action with an
internal state to a continuation, or to reset one (e.g. a METAD
that starts depositing again from zero while everything else continues
exactly). The global RESTART NO directive after CHECKPOINT is an error,
since it contradicts the restart from the checkpoint.
The actions that store their state in the checkpoint include METAD, PBMETAD, OPES_METAD, OPES_METAD_EXPLORE, METAINFERENCE (and the ISDB collective variables with DOSCORE), EDS, DRR, MOVINGRESTRAINT, ABMD, EXTENDED_LAGRANGIAN, ACCUMULATE, COLLECT, COMMITTOR, MAXENT, READ, RANDOM_EXCHANGES, LOGMFD, FISST, RESCALE, EMMI, EMMIVOX and EFFECTIVE_ENERGY_DRIFT (exact with a single process, up to rounding with more): they restore their state from it, so that their hills, kernels or status files are not read (the growing ones are truncated). Actions that keep an internal state but do not store it in the checkpoint yet are listed in a warning in the log: for them the restart is the usual file-based one and an exact continuation is not guaranteed.
The content of a checkpoint can be inspected with plumed checkpoint --dump.
Compressed (.gz) output files cannot be truncated and are not allowed
together with CHECKPOINT.
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| FILE | compulsory | plumed.cpt | the name of the checkpoint file |
| STRIDE | compulsory | 0 | write a checkpoint every STRIDE steps, in addition to those requested by the MD engine |
| RESTART_FROM | compulsory | AUTO | the checkpoint to restart from: AUTO (FILE, if the MD engine is restarting), NO (never restart from a checkpoint), or the name of a checkpoint file |