Action: RESTART
| Module | setup |
|---|---|
| Description | Usage |
| Activate restart. |   |
Further details and examples
Activate restart.
Many MD calculations are run on supercomputer facilities that limit the amount of time an individual calculation can run for. As MD simulations take a long time to complete, you often have to restart your calculations and build up your trajectories by running a chain of sub-runs. Some MD codes tell PLUMED if the MD has restarted the calculation from a checkpoint file while others do not. To avoid problems we recommend using the RESTART commands and keywords in your input files whenever you are generating trajetories by restarting calculations from a checkpoint file.
RESTART is a Setup directive and, as such, should appear at the beginning of the input file. When you include the RESTART command in your plumed.dat file you are telling PLUMED that you want to restart all the actions. Restarting these actions ensures that, as discussed here, PLUMED appends all the files that are open for writing. Appending to these files makes it easier to analyze results from simulations that have been performed as a chain of several sub-runs.
To consider what this means in practise consider the following input:
 |
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=out
If you run a plumed calculation in a directory which already contains a file called
out that file called out will be renamed bck.0.out so that the data from the new
calculation can be output to a new version of the file out and so that the data in the
old version of the file is not lost.
If by contrast you run the calculation in that same directory with the following input:
|
RESTARTActivate restart. More details 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=out
The data from the new simulation simulation will be appended to the file called out that
was already present in the data.
Notice that it is also possible to enable or disable restart on a per-action basis using the RESTART keyword as illustrated below:
|
d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 d2: 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=d1 FILEthe name of the file on which to output these quantities=out1 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d2 FILEthe name of the file on which to output these quantities=out2 RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
If this input is used any files called out1 are backed up to bck.0.out1. Data from the
new calculation is then appended to any file called out2 that is present in the working directory.
Notice that the RESTART keyword is assigned one of three values:
RESTART=AUTOis the default and means that global settings are usedRESTART=YESmeans that the action is restartedRESTART=NOmeans that the action is not restarted even if there is a global restart command
The following input is thus equivalent to the first input that introduced the RESTART keyword.
|
RESTARTActivate restart. More details d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 d2: 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=d1 FILEthe name of the file on which to output these quantities=out1 RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d2 FILEthe name of the file on which to output these quantities=out2
[!CAUTION] The RESTART directive can have also other important side effects. For methods such as METAD or PBMETAD when the action is told to restart all the hills from the previous run are read in at the start of the calculation so that the bias potential at the start of the restarted simulation is identical to the bias potential at the end of the previous run.
If you are absolutely certain that you do not want to restart any of the actions in your input you can use an input like the example below:
|
RESTARTActivate restart. More details NO switch off restart - can be used to override the behavior of the MD engine d1: 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=d1 FILEthe name of the file on which to output these quantities=out1
The RESTART NO command in this input tells PLUMED that no actions are to be restarted even if the MD
code has told PLUMED that the initial configuration came from a checkpoint file and that the trajectory
is being restarted.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| NO | optional | false | switch off restart - can be used to override the behavior of the MD engine |