LammpsBaseWorkChain

The LammpsBaseWorkChain is a WorkChain wrapper for the LammpsBaseCalculation that includes the capabilities of the AiiDA BaseRestartWorkchain. That is it allows for automatic error handling and restarting of calculations if certain conditions are met.

Right now the restart capabilities are limited to:

• Restarting an structural optimization from the last parsed structure if the minimization threshold was not reached.

• Restarting a calculation that ran out of walltime by attempting to start from the last stored structure, if no structure is found restart from scratch but with 50% more walltime.

The inputs for the LammpsBaseWorkChain are quite similar to those from the LammpsBaseCalculation, with the only difference being, that for the Workchain the are encapsulated inside the lammps namespace.

Inputs:

• lammps.structure, (StructureData) - Structure used in the LAMMPS calculation.

• lammps.potential, (LammpsPotentialData) - Potential used in the LAMMPS calculation. See LammpsPotentialData.

• lammps.parameters, (Dict) - Parameters that control the input script generated for the LAMMPS calculation. See Parameters.

• lammps.settings, (Dict), optional - Additional settings that control the LAMMPS calculation. One can control if extra files will be copied to the repository by specifying settings["additional_retrieve_list"] = ["foo", "bar"]. It is also possible to do pattern matching via globs patterns by settings["additional_retrieve_list"] = [('path/sub/*c.txt', '.', None)], for more information see the pattern matching in the aiida-core documentation.

• lammps.input_restartfile (SinglefileData), optional - Input restart file to continue from a previous LAMMPS calculation.

• lammps.parent_folder, (RemoteData), optional - An optional working directory of a previously completed calculation to restart from.

• store_restart, (Bool), optional - Whether to store the restart file in the repository. Defaults to False.

Note

LAMMPS can produce binary restart files which contain all the atomic positions, forces and other computed variables until when the are asked to be printed. One can control this by passing a dictionary called restart to the settings input. The available options for the restart are:

• print_final, (bool) - whether to print a restart file at the end of the calculation. Defaults to False. See write_restart.

• print intermediate, (bool) - whether to print restart files periodically throughout the calculation. Defaults to False. See restart.

• num_steps, (int) - how often is the intermediate restart file printed. Defaults to 10% of the total number of steps.

Outputs:

• results, (Dict) - The parsed data extracted from the lammps output file.

• trajectories (LammpsTrajectory) - The data extracted from the lammps trajectory file, includes the atomic trajectories and the site and time dependent calculation parameters.

• time_dependent_computes, (ArrayData) - The data with the time dependent computes parsed from the lammps.out.

• restartfile, (SinglefileData), optional - The restart file of a LAMMPS calculation.

• structure, (StructureData), optional - The output structure of the calculation.

• remote_folder, (RemoteData) - Folder in the remote machine where the calculation was performed.

• remote_stash, (RemoteStashData), optional – Contents of the stash.source_list option are stored in this remote folder after job completion.

• retrieved, (FolderData) - Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added.