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LammpsBaseCalculation

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LammpsBaseCalculation#

The LammpsBaseCalculation performs a single stage LAMMPS calculation, the input is generated by a set of parameters passed as a dictionary. The inputs accepted are the following:

Inputs:#

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

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

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

  • 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.

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

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

  • metadata.options.input_filename, (str), optional - Name of the input file for the calculation. Defaults to input.in.

  • metadata.options.structure_filename, (str), optional - Name of the file where the structure is stored. Defaults to structure.dat

  • metadata.options.output_filename, (str). optional - Name of the main output file for LAMMPS. Defaults to lammps.out.

  • metadata.options.variables_filename, (str), optional - Name of the file where the final values of the thermodynamic variables are stored. Defaults to aiida_lammps.yaml.

  • metadata.options.trajectory_filename, (str), optional - Name of the file where the trajectories are stored. Defaults to aiida_lammps.trajectory.dump.

  • metadata.options.restart_filename, (str), optional - Name of the restart file to be written. Defaults to lammps.restart.

  • metadata.options.parser_name, (str), optional - Name of the parser to be used for this calculation. Defaults to lammps.base.

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.

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