All plugins

aiida-lammps

status beta AiiDA ~=2.3

General information

Install pip install git+https://github.com/aiidaplugins/aiida-lammps
Source code https://github.com/aiidaplugins/aiida-lammps
Documentation No documentation provided by the package author.
Author(s) Chris Sewell
Contact chrisj_sewell@hotmail.com
Python import import aiida_lammps

Registry checks

W006: 'development_status' key is deprecated. Use PyPI Trove classifiers in the plugin repository instead.
Click any code (W001, E001…) to jump to troubleshooting instructions .

Plugins provided

Calculations 2 Parsers 2 Data 2 Workflows 3

Entry points

CalcJobs and calculation functions aiida.calculations

  • lammps.base

    class: aiida_lammps.calculations.base:LammpsBaseCalculation

    A basic plugin for performing calculations in ``LAMMPS`` using aiida. The plugin will take the input parameters validate them against a schema and then use them to generate the ``LAMMPS`` input file. The input file is generated depending on the parameters provided, the type of potential, the input structure and whether or not a restart file is provided.

    InputRequiredValid typesDescription
    parameters true Dict Parameters that control the input script generated for the ``LAMMPS`` calculation
    potential true LammpsPotentialData Potential used in the ``LAMMPS`` calculation
    structure true StructureData Structure used in the ``LAMMPS`` calculation
    code false AbstractCode, NoneType The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
    input_restartfile false SinglefileData, NoneType Input restartfile to continue from a previous ``LAMMPS`` calculation
    metadata false
    monitors false Dict Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    parent_folder false RemoteData, NoneType An optional working directory of a previously completed calculation to restart from.
    remote_folder false RemoteData, NoneType Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.
    settings false Dict, NoneType Additional settings that control the ``LAMMPS`` calculation
    OutputRequiredValid typesDescription
    remote_folder true RemoteData Input files necessary to run the process will be stored in this folder node.
    results true Dict The data extracted from the lammps output file
    retrieved true 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, but one can add more by specifying them in `CalcInfo.retrieve_list`.
    time_dependent_computes true ArrayData The data with the time dependent computes parsed from the lammps.out
    trajectories true LammpsTrajectory The data extracted from the lammps trajectory file
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    restartfile false SinglefileData The restartfile of a ``LAMMPS`` calculation
    structure false StructureData The output structure.
    Exit statusMessage
    1 The process has failed with an unspecified error.
    2 The process failed with legacy failure mode.
    10 The process returned an invalid output.
    11 The process did not register a required output.
    110 The job ran out of memory.
    120 The job ran out of walltime.
    131 The specified account is invalid.
    140 The node running the job failed.
    150 {message}
    301 the retrieved folder data node could not be accessed.
    302 the stdout output file was not found
    303 the stderr output file was not found
    304 the output file is missing, it is possible that LAMMPS never ran
    305 the file with the lammps log was not found
    306 the file with the final variables was not found
    307 the file with the trajectories was not found
    308 the file with the restart information was not found
    309 The parser detected the lammps error :{error}
    400 The calculation stopped prematurely because it ran out of walltime.
    401 The energy tolerance was not reached at minimization.
    402 The force tolerance was not reached at minimization.
    1001 error parsing the output file has failed.
    1002 error parsing the final variable file has failed.

  • lammps.raw

    class: aiida_lammps.calculations.raw:LammpsRawCalculation

    Plugin with minimal interface to run LAMMPS.

    InputRequiredValid typesDescription
    script true SinglefileData Complete input script to use. If specified, `structure`, `potential` and `parameters` are ignored.
    code false AbstractCode, NoneType The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
    filenames false Dict, NoneType Optional namespace to specify with which filenames the files of ``files`` input should be written.
    files false SinglefileData Optional files that should be written to the working directory.
    metadata false
    monitors false Dict Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    remote_folder false RemoteData, NoneType Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.
    settings false Dict, NoneType Additional settings that control the ``LAMMPS`` calculation
    OutputRequiredValid typesDescription
    remote_folder true RemoteData Input files necessary to run the process will be stored in this folder node.
    results true Dict The data extracted from the lammps out file
    retrieved true 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, but one can add more by specifying them in `CalcInfo.retrieve_list`.
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    1 The process has failed with an unspecified error.
    2 The process failed with legacy failure mode.
    10 The process returned an invalid output.
    11 The process did not register a required output.
    100 The process did not have the required `retrieved` output.
    110 The job ran out of memory.
    120 The job ran out of walltime.
    131 The specified account is invalid.
    140 The node running the job failed.
    150 {message}
    309 The parser detected the lammps error :{error}
    351 the file with the lammps out was not found
    1001 parsing the output file has failed.
CalcJob parsers aiida.parsers

  • lammps.base

    aiida_lammps.parsers.base:LammpsBaseParser

  • lammps.raw

    aiida_lammps.parsers.raw:LammpsRawParser
Data node types aiida.data

  • lammps.potential

    aiida_lammps.data.potential:LammpsPotentialData

  • lammps.trajectory

    aiida_lammps.data.trajectory:LammpsTrajectory
WorkChains and work functions aiida.workflows

  • lammps.base

    class: aiida_lammps.workflows.base:LammpsBaseWorkChain

    Base workchain for calculations using LAMMPS

    InputRequiredValid typesDescription
    lammps true Data
    clean_workdir false Bool If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
    handler_overrides false Dict, NoneType Mapping where keys are process handler names and the values are a dictionary, where each dictionary can define the ``enabled`` and ``priority`` key, which can be used to toggle the values set on the original process handler declaration.
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    metadata false
    store_restart false Bool, NoneType Whether to store the restartfile in the repository.
    OutputRequiredValid typesDescription
    remote_folder true RemoteData Input files necessary to run the process will be stored in this folder node.
    results true Dict The data extracted from the lammps output file
    retrieved true 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, but one can add more by specifying them in `CalcInfo.retrieve_list`.
    time_dependent_computes true ArrayData The data with the time dependent computes parsed from the lammps.out
    trajectories true LammpsTrajectory The data extracted from the lammps trajectory file
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    restartfile false SinglefileData The restartfile of a ``LAMMPS`` calculation
    structure false StructureData The output structure.
    Exit statusMessage
    1 The process has failed with an unspecified error.
    2 The process failed with legacy failure mode.
    10 The process returned an invalid output.
    11 The process did not register a required output.
    300 The calculation failed with an unidentified unrecoverable error.
    301 The sub process excepted.
    302 The sub process was killed.
    401 The maximum number of iterations was exceeded.
    402 The process failed for an unknown reason, twice in a row.

  • lammps.relax

    class: aiida_lammps.workflows.relax:LammpsRelaxWorkChain

    Workchain to relax a structure using the LAMMPS minimization procedure.

    InputRequiredValid typesDescription
    lammps true Data
    relax true
    clean_workdir false Bool If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
    handler_overrides false Dict, NoneType Mapping where keys are process handler names and the values are a dictionary, where each dictionary can define the ``enabled`` and ``priority`` key, which can be used to toggle the values set on the original process handler declaration.
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    metadata false
    store_restart false Bool, NoneType Whether to store the restartfile in the repository.
    OutputRequiredValid typesDescription
    remote_folder true RemoteData Input files necessary to run the process will be stored in this folder node.
    results true Dict The data extracted from the lammps output file
    retrieved true 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, but one can add more by specifying them in `CalcInfo.retrieve_list`.
    time_dependent_computes true ArrayData The data with the time dependent computes parsed from the lammps.out
    trajectories true LammpsTrajectory The data extracted from the lammps trajectory file
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    restartfile false SinglefileData The restartfile of a ``LAMMPS`` calculation
    structure false StructureData The output structure.
    Exit statusMessage
    1 The process has failed with an unspecified error.
    2 The process failed with legacy failure mode.
    10 The process returned an invalid output.
    11 The process did not register a required output.
    403 The underlying LammpsBaseWorkChain failed

  • lammps.md

    class: aiida_lammps.workflows.molecular_dynamics:LammpsMDWorkChain

    Workchain to perform a LAMMPS MD simulation.

    InputRequiredValid typesDescription
    lammps true Data
    md true
    clean_workdir false Bool If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
    handler_overrides false Dict, NoneType Mapping where keys are process handler names and the values are a dictionary, where each dictionary can define the ``enabled`` and ``priority`` key, which can be used to toggle the values set on the original process handler declaration.
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    metadata false
    store_restart false Bool, NoneType Whether to store the restartfile in the repository.
    OutputRequiredValid typesDescription
    remote_folder true RemoteData Input files necessary to run the process will be stored in this folder node.
    results true Dict The data extracted from the lammps output file
    retrieved true 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, but one can add more by specifying them in `CalcInfo.retrieve_list`.
    time_dependent_computes true ArrayData The data with the time dependent computes parsed from the lammps.out
    trajectories true LammpsTrajectory The data extracted from the lammps trajectory file
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    restartfile false SinglefileData The restartfile of a ``LAMMPS`` calculation
    structure false StructureData The output structure.
    Exit statusMessage
    1 The process has failed with an unspecified error.
    2 The process failed with legacy failure mode.
    10 The process returned an invalid output.
    11 The process did not register a required output.
    403 The underlying LammpsBaseWorkChain failed