PELE output parameters in Pele++ control file¶
The “PELE_Output” block defines the output options and the paths for all the output files.
The “PELE_Output” block must be defined inside the PeleSimulation command as this parameters must remain the same during the entire Pele simulation.
Output options and parameters.¶
savingMode¶
Use: It tells Pele++ how the accepted models must be saved to disk.
Parameter: ConfigurationSavingMode savingMode
Note for developers: It’s defined in PeleOutputParameters class and its options in the ConfigurationSavingMode enum.
Options:
“savingTrajectory”: It saves the accepted models in a given trajectory file. Model 1 always corresponds to the initial state.
“savingSteps”: It saves the accepted models in different files in a given folder. The file corresponding to accepted step 0 is the initial state.
“savingBoth”: It does both previous things.
Default value: “savingTrajectory”
trajectoryPath¶
Use: Path of the file where all the models are saved to form a trajectory. Model 1 always corresponds to the initial state. Model 2 corresponds to the first recorded accepted step (see saveFrequencyForAcceptedSteps), Model 3 to the second recorded accepted step, and so on. It’s only used in “savingTrajectory” and “savingBoth” options. If the route is invalid, the program cannot write the trajectory, but the execution of the program proceeds.
Parameter: std::string trajectoryFilePath
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “../../trajectory.pdb”
stepsFolder¶
Use: Path of the folder where all the accepted models are saved in separated files. The file numbered as 0 is the initial state. For all other files, the number is the accepted step (thus, n corresponds to the nth accepted step; if savingFrequencyForAcceptedSteps is 2, the values for n will be 2, 4, 6, etc.). It’s only used in “savingSteps” and “savingBoth” options.
Parameter: std::string stepsFolder
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “”
savingFrequencyForAcceptedSteps¶
Use: Accepted steps are saved only if they are multiples of this parameter. Thus, besides the initial state, which is always saved, if savingFrequenceyForAcceptedSteps is n, only accepted steps n, 2*n, etc. are saved.
Parameter: unsigned int savingFrequency
Note for developers: It’s defined in PeleOutputParameters class.
Range: (1, inf)
Default value: 1, which means that every accepted step is saved.
reportPath¶
Use: Path of the file where the Sensors (metrics and tracked variables) values are stored. The first data line corresponds to the initial state (marked with a value of 0 for both Step and AcceptedSteps). Then, there is a data line per accepted step (both Step and AcceptedSteps start counting at 1). If the route is invalid, the execution of the program is aborted.
Parameter: std::string fileReportPath
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “../../test_report.txt”.
initialPdbPath¶
Use: Path of the file where the initial PDB is stored. If the route is invalid, the program cannot write the initial structure, but the execution of the program proceeds. If it is an empty string, no file is created nor PDB is stored.
Parameter: std::string initialPDBPath
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “”.
finalPdbPath¶
Use: Path of the file where the final PDB is stored. If the route is invalid, the program cannot write the final structure, but the program finishes the execution normally. If it is an empty string, no file is created nor PDB is stored.
Parameter: std::string finalPDBPath
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “”.
flushingFrequency¶
Use: When the number of report data lines is a multiple of “flushingFrequency” the report file buffer is flushed to the file. There are as many report data lines as number of accepted steps plus one (the initial state report line). The lower this parameter, the faster you will see your results in the belonging log.
Parameter: unsigned int flushingFrequency
Note for developers: It’s defined in PeleOutputParameters class.
Range: (1, inf)
Default value: 50.
controllerEventsLogPath¶
Use: Path of the log file where all ExplorationController events are logged. Examples of this are: parameter changes, new best explorer election, explorer jump (both forced and requested), explorer finalization… It’s only needed when a Controller for jump events is defined in the control file.
Parameter: std::string controllerEventsLogPath
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “”.
useInterStepLogger¶
Use: Activates the InterStepLogger functionality, which allows taking structural and simulation data within the different stages of a step. It is useful for debugging purposes. Generates a new report and trajectory file, with a suffix to distinguish them from the default outputs, in the subdirectory InterStepLogs.
Parameter: bool useInterStepLogger
Note for developers: It’s defined in PeleOutputParameters class.
Default value: false.
interStepLoggerSuffix¶
Use: Suffix to add to the default output files to generate the names of the interStepLogger output files.
Parameter: std::string interStepLoggerSuffix;
Note for developers: It’s defined in PeleOutputParameters class.
Default value: “_interStep”.
Example¶
"PELE_Output":
{
"reportPath": "../../test_report",
"trajectoryPath": "../../trajectory.pdb",
"stepsFolder": "../../step_",
"savingMode": "savingBoth",
"savingFrequencyForAcceptedSteps": 1,
"initialPdbPath": "../../theInitial.pdb",
"finalPdbPath": "../../theFinal.pdb",
"simulationLogPath": "../../simulationLog.txt",
"controllerEventsLogPath": "../../controllerEventsLog.txt",
"flushingFrequency": 5,
"useInterStepLogger": true
}
Simulations using MPI¶
In simulations using MPI the same parameters are used. Pele++ adds a suffix to all file and folder names to separate the output of each Explorer. The controller process (rank 0) does not output any of these files. Explorers start being numbered at 1 (following their MPI rank).