Ctrl+K
Ctrl+K

LammpsMDWorkChain

Contents

LammpsMDWorkChain#

This is a subclass of the LammpsBaseWorkChain which focuses on MD simulations specifically. It overrides any set of parameters given in the md block (see Parameters) and instead directly exposes them to the user in the md input 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.

  • md.steps, (Int), optional - Number of steps in the MD simulation. Defaults to 1000.

  • md.algo, Str, optional - Type of time integrator used for MD simulations in LAMMPS (run_style). Defaults to verlet.

  • md.integrator, (Str), optional - Type of thermostat used for the MD simulation in LAMMPS, e.g. fix npt. Defaults to npt.

  • md.integrator_constraints, (Dict), optional - Set of constraints that are applied to the thermostat. Defaults to {"temp":[300,300,100], "iso":[0.0, 0.0, 1000]}.

  • md.velocity, (List), optional - List with the information describing how to generate the velocities for the initialization of the MD run.

  • md.respa_options, (List), optional - List with the information needed to setup the respa options.

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.

Contents