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LammpsRelaxWorkChain

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LammpsRelaxWorkChain#

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

  • relax.algo, (Str), optional - The algorithm to be used during relaxation. Defaults to cg.

  • relax.volume, (Bool), optional - Whether or not relaxation of the volume will be performed by using the box/relax fix from LAMMPS. Defaults to False.

  • relax.shape, (Bool), optional - Whether or not the shape of the cell will be relaxed by using the box/relax fix from LAMMPS. Defaults to False

  • relax.positions, (Bool), optional - Whether or not to allow the relaxation of the atomic positions. Defaults to True.

  • relax.steps, (Int), optional - Maximum number of steps during the relaxation. Defaults to 1000.

  • relax.evaluations, (Int), optional - Maximum number of force/energy evaluations during the relaxation. Defaults to 10000.

  • relax.energy_tolerance, (Float), optional - The tolerance that determined whether the relaxation procedure is stopped. In this case it stops when the relative change between outer iterations of the relaxation run is less than the given value. Defaults to 1e-4.

  • relax.force_tolerance, (Float), optional - The tolerance that determines whether the relaxation procedure is stopped. In this case it stops when the 2-norm of the global force vector is less than the given value. Defaults to 1e-4.

  • relax.target_pressure, (Dict), optional - Dictionary containing the values for the target pressure tensor. See the box/relax for more information.

  • relax.max_volume_change, (Float), optional - Maximum allowed change in one iteration (vmax).

  • relax.nreset, (Int), optional - Reset the reference cell every this many minimizer iterations.

  • relax.meta_convergence, (Bool), optional - If True the workchain will perform a meta-convergence on the cell volume. Defaults to True.

  • relax.max_meta_convergence_iterations, (Int), optional - The maximum number of variable cell relax iterations in the meta convergence cycle. Defaults to 5.

  • relax.volume_convergence, (Float), optional - The volume difference threshold between two consecutive meta convergence iterations. Defaults to 0.1.

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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