AiiDA Processes

Input and output parameters for all AiiDA work chains and calculation jobs.

chargemol

CalcJob ChargemolCalculation [source]

Calcjob for the chargemol software package.

Inputs
  • charge_density_filename, optional - Name of the cube-file containing the valence density of the system.
  • charge_density_folder, required - Folder containing the carge-density cube files
  • code, optional - 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.
  • kind_info, optional - List containing the atomic number and number of core electrons.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
    • description, optional - Description to set on the process node.
    • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
    • label, optional - Label to set on the process node.
    • options, Namespace
      Namespace Ports
      • account, optional - Set the account to use in for the queue on the remote computer
      • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
      • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
      • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
      • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
      • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
      • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
      • input_filename, optional - Filename to which the input for the code that is to be run is written.
      • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
      • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
      • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
      • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
      • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
      • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
      • priority, optional - Set the priority of the job to be queued
      • qos, optional - Set the quality of service to use in for the queue on the remote computer
      • queue_name, optional - Set the name of the queue on the remote computer
      • rerunnable, optional - Determines if the calculation can be requeued / rerun.
      • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
      • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
      • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
      • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
        Namespace Ports
        • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
        • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
        • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
      • submit_script_filename, optional - Filename to which the job submission script is written.
      • withmpi, optional - Set the calculation to use mpi
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    Namespace Ports
  • parameters, required - Dictionary containing the input parameters.
  • path_atomic_densities, optional - Absolte path to the atomic densities needed for the chargemol calculation.
  • remote_folder, optional - 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.
  • spin_density_filename, optional - Name of the cube-file containing the spin density of the system.
Outputs
  • output_ddec3_populations, optional - Calculated DDEC3 populations.
  • output_ddec6_populations, optional - Calculated DDEC6 populations.
  • output_parameters, required - The output dictionary containing results of the calculation.
  • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
  • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
  • retrieved, required - 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`.

CP2K

CalcJob Cp2kCalculation [source]

Calcjob based on the Cp2kCalculation from the official cp2k-plugin.

Inputs
  • code, optional - 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.
  • file, Namespace -- Additional input files.
    Namespace Ports
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
    • description, optional - Description to set on the process node.
    • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
    • label, optional - Label to set on the process node.
    • options, Namespace
      Namespace Ports
      • account, optional - Set the account to use in for the queue on the remote computer
      • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
      • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
      • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
      • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
      • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
      • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
      • input_filename, optional - Filename to which the input for the code that is to be run is written.
      • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
      • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
      • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
      • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
      • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
      • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
      • priority, optional - Set the priority of the job to be queued
      • qos, optional - Set the quality of service to use in for the queue on the remote computer
      • queue_name, optional - Set the name of the queue on the remote computer
      • rerunnable, optional - Determines if the calculation can be requeued / rerun.
      • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
      • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
      • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
      • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
        Namespace Ports
        • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
        • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
        • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
      • submit_script_filename, optional - Filename to which the job submission script is written.
      • withmpi, optional - Set the calculation to use mpi
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    Namespace Ports
  • parameters, required - The input parameters.
  • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
  • remote_folder, optional - 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, optional - Optional input parameters.
  • structure, optional - The main input structure.
Outputs
  • output_bands, optional - Computed electronic band structure.
  • output_cubes, Namespace -- Calculated cubes.
    Namespace Ports
  • output_eigenvalues, optional - Calculated electronic eigenvalues.
  • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
  • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
  • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
  • output_mulliken_populations, optional - Calculated final Mulliken charges.
  • output_parameters, required - The output dictionary containing results of the calculation.
  • output_pdos, optional - Calculated projected density of states.
  • output_structure, optional - The relaxed output structure.
  • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
  • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
  • retrieved, required - 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`.
WorkChain FindSCFParametersWorkChain [source]

AiiDA work chain to find the mixing parameters to converge the Kohn-Sham equations of a specific system.

Inputs
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
    • system_character, optional - Electronic character of the system, possible options are 'metallic' or 'insulator'. In case this parameter is set to 'metallic' ('insulator') electronic smearing is always (never) applied.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain GeoOptWorkChain [source]

AiiDA work chain to optimize the atomic positions.

Inputs
  • adjust_scf_parameters, optional
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_opt_method, optional - Custom set of parameters used for the optimzation.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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.
  • initial_opt_parameters, optional - ....
  • max_iterations, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • optimization_p, Namespace -- Additional optimization parameters set in the CP2K input file.
    Namespace Ports
    • eps_symmetry, optional - The tolerance parameter used to determine the space group.
    • keep_space_group, optional - Constrain the space group of the structure via spglib.
    • max_dr, optional - Convergence criterion for the maximum geometry change.
    • max_force, optional - Convergence criterion for the maximum force component.
    • rms_dr, optional - Convergence criterion for the root mean square (RMS) geometry change.
    • rms_force, optional - Convergence criterion for the root mean square (RMS) force.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
  • space_group_info, optional - Information of the constrained space group (in case 'keep_spacegroup' is set).
WorkChain CellOptWorkChain [source]

AiiDA work chain to optimize the unit cell of a periodic system.

Inputs
  • adjust_scf_parameters, optional
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_opt_method, optional - Custom set of parameters used for the optimzation.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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.
  • initial_opt_parameters, optional - ....
  • max_iterations, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • optimization_p, Namespace -- Additional optimization parameters set in the CP2K input file.
    Namespace Ports
    • cell_symmetry, optional - The applied cell symmetry which is constrained during cell optimization.
    • eps_symmetry, optional - The tolerance parameter used to determine the space group.
    • keep_angles, optional - Constrain the lattice angles during cell optimization.
    • keep_space_group, optional - Constrain the space group of the structure via spglib.
    • keep_symmetry, optional - Constrain the lattice symmetry during cell optimization.
    • max_dr, optional - Convergence criterion for the maximum geometry change.
    • max_force, optional - Convergence criterion for the maximum force component.
    • pressure_tolerance, optional - Specifies the Pressure tolerance to achieve during the cell optimization.
    • ref_cell_scaling_factor, optional - Scaling factor for the reference cell (CELL_REF).
    • rms_dr, optional - Convergence criterion for the root mean square (RMS) geometry change.
    • rms_force, optional - Convergence criterion for the root mean square (RMS) force.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
  • space_group_info, optional - Information of the constrained space group (in case 'keep_spacegroup' is set).
WorkChain BandStructureWorkChain [source]

AiiDA work chain to calculate the band structure using CP2K.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • path_parameters, optional - Dictionary containing parameters based on SeekPath-output.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • seekpath_parameters, optional - Additional arguments passed to the SeekPath analysis.
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
  • seekpath, Namespace -- Output parameters of SeekPath.
    Namespace Ports
    • conv_structure, optional - Conventional structure generated by SeekPath.
    • explicit_kpoints, optional - Explicit kpoints generated by SeekPath.
    • path_parameters, optional - Path parameters used in the calculation generated by SeekPath.
    • primitive_structure, optional - Primitive structure used for the calculation generated by SeekPath.
WorkChain EigenvaluesWorkChain [source]

AiiDA work chain to calculate the band structure with cp2k.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain PDOSWorkChain [source]

AiiDA work chain to calculate the projected density of states.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • maximum_cell_length, optional
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • minimum_cell_length, optional
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • resolve_atoms, optional
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
  • wfn_cube_list, optional - List of orbitals stored as cube data.
  • wfn_n_homo, optional - Print a certain of occupied orbitals as cube data.
  • wfn_n_lumo, optional - Print a certain of unoccupied orbitals as cube data.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain PartialChargesWorkChain [source]

AiiDA work chain to calculate the partial charges of the atoms.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • chargemol, Namespace -- ...
    Namespace Ports
    • code, optional - 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.
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - Dictionary containing the input parameters.
    • path_atomic_densities, optional - Absolte path to the atomic densities needed for the chargemol calculation.
    • remote_folder, optional - 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.
    • spin_density_filename, optional - Name of the cube-file containing the spin density of the system.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • critic2, Namespace -- ...
    Namespace Ports
    • code, optional - 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.
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - List of input parameters (each item is parsed as a line in the input file).
    • remote_folder, optional - 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.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • store_cubes, optional - Whether to store the electron density cube file (only supported for chargemol and critic2).
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • chargemol, Namespace -- Output parameters of chargemol.
    Namespace Ports
    • output_ddec3_populations, optional - Calculated DDEC3 populations.
    • output_ddec6_populations, optional - Calculated DDEC6 populations.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • critic2, Namespace -- Output parameters of critic2.
    Namespace Ports
    • output_bader_populations, optional - Calculated Bader populations.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_planes, Namespace -- Calculated planes.
      Namespace Ports
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain CubeWorkChain [source]

AiiDA work chain to calculate and store cube files using CP2K.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • cube_types, required - List of cubes that are calculated and stored.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain PlanarFieldsWorkChain [source]

AiiDA work chain to calculate the planar fields.

Inputs
  • adjust_scf_parameters, optional - Restart calculation with adjusted parameters if SCF-clycles are not converged.
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • critic2, Namespace -- Input parameters of critic2.
    Namespace Ports
    • code, optional - 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.
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • remote_folder, optional - 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.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • field_types, optional - The field type that is calculated, up to now only 'deformation_density' and 'elf' are supported.
  • handler_overrides, optional - 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, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • plane_vectors, required - Plane vectors and number of points given in crystallographic coordinates and angstrom for (partial) periodic boundary conditions and non-periodic boundary conditions, respectively.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • store_cubes, optional - Whether to store the cube files that are input for the planes.
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
Outputs
  • cp2k, Namespace -- Output parameters of CP2K.
    Namespace Ports
    • output_bands, optional - Computed electronic band structure.
    • output_cubes, Namespace -- Calculated cubes.
      Namespace Ports
    • output_eigenvalues, optional - Calculated electronic eigenvalues.
    • output_hirshfeld_populations, optional - Calculated final Hirshfeld charges.
    • output_kind_info, optional - Kind information including the number of core/valence electrons for each kind.
    • output_motion_step_info, optional - Information of each step for an optimization or molecular dynamics simulation.
    • output_mulliken_populations, optional - Calculated final Mulliken charges.
    • output_parameters, required - The output dictionary containing results of the calculation.
    • output_pdos, optional - Calculated projected density of states.
    • output_structure, optional - The relaxed output structure.
    • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
    • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    • retrieved, required - 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`.
  • critic2, Namespace
    Namespace Ports
    • deformation_density, Namespace -- Critic2 outputs of the deformation density plane calculation.
      Namespace Ports
      • output_bader_populations, optional - Calculated Bader populations.
      • output_parameters, required - The output dictionary containing results of the calculation.
      • output_planes, Namespace -- Calculated planes.
        Namespace Ports
      • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
      • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
      • retrieved, required - 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`.
    • elf, Namespace -- Critic2 outputs of the elf plane calculation.
      Namespace Ports
      • output_bader_populations, optional - Calculated Bader populations.
      • output_parameters, required - The output dictionary containing results of the calculation.
      • output_planes, Namespace -- Calculated planes.
        Namespace Ports
      • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
      • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
      • retrieved, required - 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`.
    • total_density, Namespace -- Critic2 outputs of the total density plane calculation.
      Namespace Ports
      • output_bader_populations, optional - Calculated Bader populations.
      • output_parameters, required - The output dictionary containing results of the calculation.
      • output_planes, Namespace -- Calculated planes.
        Namespace Ports
      • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
      • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
      • retrieved, required - 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`.
  • run_time_stats, required - Information on the run time of the work chain.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.
WorkChain ElectronicPropertiesWorkChain [source]

Work chain to optimize the unit cell and calculate different electronic properties.

Inputs
  • chargemol, Namespace -- Details about the used chargemol code.
    Namespace Ports
    • code, optional - Chargemol-code to be used for the calculations.
    • metadata, optional - Forwards extra information to the calculation job (e.g. for the scheduler).
    • path_atomic_densities, optional - Absolte path to the atomic densities needed for the chargemol calculation.
  • clean_workdir, optional - Clean woring directory after calculation.
  • cp2k, Namespace -- Details about the used CP2K code.
    Namespace Ports
    • code, required - CP2K code to be used for the calculations.
    • metadata, optional - Forwards extra information to the calculation job (e.g. for the scheduler).
  • critic2, Namespace -- Details about the used critic2 code.
    Namespace Ports
    • code, optional - Critic2-code to be used for the calculations.
    • metadata, optional - Forwards extra information to the calculation job (e.g. for the scheduler).
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • structural_p, Namespace -- Structure and system-specific parameters.
    Namespace Ports
    • scf_parameters, optional - Initial parameters that converge the SCF-cycles.
    • structure, required - The input structure.
    • system_character, optional - Electronic character of the system, possible options are 'metallic' or 'insulator'. In case this parameter is set to 'metallic' ('insulator') electronic smearing is always (never) applied.
  • workflow, Namespace -- Parameters that define the workflow.
    Namespace Ports
    • calc_band_structure, optional - Whether the band structure should be calculated.
    • calc_eigenvalues, optional - Whether the eigenvalues should be calculated.
    • calc_partial_charges, optional - Whether the partial charges should be calculated.
    • calc_pdos, optional - Whether the projected density of states (pDOS) should be calculated.
    • custom_protocol, optional - Use a custom protocol to set the parameters of the work chain.
    • protocol, optional - Protocol type to be used for the calculations. The default value is 'standard'.
    • run_cell_optimization, optional - Whether a unit cell optimization should be performed.
Outputs
  • bader_populations, optional - The Bader populations of the system.
  • band_structure, optional - The electronic band structure of the crysal.
  • ddec6_populations, optional - The DDEC6 populations of the system.
  • eigenvalue_info, optional - Contains all calculated eigenvalues for all k-points.
  • general_info, optional - Information on the constrained space group.
  • hirshfeld_populations, optional - The Hirshfeld populations of the system.
  • mulliken_populations, optional - The Mulliken populations of the system.
  • optimized_structure, optional - Optimized unit cell of the crystal.
  • pdos, optional - The projected density of states of the crystal.
WorkChain SurfaceOptWorkChain [source]

Work chain to converge the slab size and optimize the atomic positions of the converged slab.

Inputs
  • adjust_scf_parameters, optional
  • always_add_unocc_states, optional - Always include some unoccupied states even if smearing is not used.
  • bulk_reference, Namespace -- Reference total energies of bulk systems.
    Namespace Ports
  • clean_workdir, optional - If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
  • cp2k, Namespace
    Namespace Ports
    • code, optional - 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.
    • file, Namespace -- Additional input files.
      Namespace Ports
    • metadata, Namespace
      Namespace Ports
      • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
      • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
      • description, optional - Description to set on the process node.
      • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
      • label, optional - Label to set on the process node.
      • options, Namespace
        Namespace Ports
        • account, optional - Set the account to use in for the queue on the remote computer
        • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
        • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
        • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
        • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
        • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
        • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
        • input_filename, optional - Filename to which the input for the code that is to be run is written.
        • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
        • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
        • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
        • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
        • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
        • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
        • priority, optional - Set the priority of the job to be queued
        • qos, optional - Set the quality of service to use in for the queue on the remote computer
        • queue_name, optional - Set the name of the queue on the remote computer
        • rerunnable, optional - Determines if the calculation can be requeued / rerun.
        • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
        • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
        • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
        • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
          Namespace Ports
          • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
          • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
          • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
        • submit_script_filename, optional - Filename to which the job submission script is written.
        • withmpi, optional - Set the calculation to use mpi
      • store_provenance, optional - If set to `False` provenance will not be stored in the database.
    • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
      Namespace Ports
    • parameters, required - The input parameters.
    • parent_calc_folder, optional - Working directory of a previously ran calculation to restart from.
    • remote_folder, optional - 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, optional - Optional input parameters.
  • custom_opt_method, optional - Custom set of parameters used for the optimzation.
  • custom_scf_method, optional - Custom set of parameters used to converge the Kohn-Sham equations.
  • enable_roks, optional - Use restricted open-shell instead of unrestricted open-shell calcualtions.
  • factor_unocc_states, optional - Factor to determine the number of unoccupied orbitals.
  • handler_overrides, optional - 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.
  • initial_opt_parameters, optional - ....
  • max_iterations, optional - Maximum number of iterations the work chain will restart the process to finish successfully.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • description, optional - Description to set on the process node.
    • label, optional - Label to set on the process node.
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets.
    • basis_sets, optional - Basis sets used for the different species.
    • cutoff_values, optional - Cut-off values for the grids.
    • kpoints_ref_dist, optional - Reference distance between two k-points in reciprocal space.
    • pseudo_file, optional - File containing the used pseudopotentials.
    • xc_functional, optional - Exchange-correlation functional used for the calculation.
  • optimization_p, Namespace -- Additional optimization parameters set in the CP2K input file.
    Namespace Ports
    • eps_symmetry, optional - The tolerance parameter used to determine the space group.
    • keep_space_group, optional - Constrain the space group of the structure via spglib.
    • max_dr, optional - Convergence criterion for the maximum geometry change.
    • max_force, optional - Convergence criterion for the maximum force component.
    • rms_dr, optional - Convergence criterion for the root mean square (RMS) geometry change.
    • rms_force, optional - Convergence criterion for the root mean square (RMS) force.
  • preopt_numerical_p, Namespace -- .
    Namespace Ports
    • basis_file, optional - File containing the used basis sets for the pre-optimization steps.
    • basis_sets, optional - Basis sets used for the different species for the pre-optimization steps.
    • cutoff_values, optional - Cut-off values for the grids for the pre-optimization steps.
  • preopt_optimization_p, Namespace -- .
    Namespace Ports
    • max_dr, optional - Convergence criterion for the maximum geometry change.
    • max_force, optional - Convergence criterion for the maximum force component.
    • rms_dr, optional - Convergence criterion for the root mean square (RMS) geometry change.
    • rms_force, optional - Convergence criterion for the root mean square (RMS) force.
  • scf_extended_system, optional - Apply larger number of scf-cycles for extended systems.
  • scf_method, optional - Method used to converge the SCF-cycles, options are: `density_mixing` or `orbital_transformation`
  • slab_conv, Namespace -- .
    Namespace Ports
    • criteria, optional - Convergence criteria to choose the slab size.
    • threshold, optional - Convergence threshold for the surface or formation energy.
  • structural_p, Namespace
    Namespace Ports
    • maximum_slab_size, optional - Vacuum at the bottom and top of the slab.
    • minimum_slab_size, optional - Vacuum at the bottom and top of the slab.
    • periodic, required - Whether the cell direction normal to the surface plan is periodic or not.
    • surface, required - Vacuum at the bottom and top of the slab.
    • vacuum, required - Vacuum at the bottom and top of the slab.
    • vacuum_factor, optional - Vacuum at the bottom and top of the slab.
Outputs
  • cp2k, Namespace -- Output data of the last CP2K calculation.
    Namespace Ports
  • path_parameters, optional - K-path parameters for the slab.
  • primitive_slab, optional - Primitive unrelaxed surface slab.
  • scf_parameters, required - Information on the SCF-Parameters that converge the Kohn-Sham equations.

critic2

CalcJob Critic2Calculation [source]

Calcjob for the critic2 software package.

Inputs
  • charge_density_folder, required - Folder containing the carge-density cube files
  • code, optional - 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.
  • kind_info, optional - List containing the number of valence and core electrons for each element.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
    • description, optional - Description to set on the process node.
    • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
    • label, optional - Label to set on the process node.
    • options, Namespace
      Namespace Ports
      • account, optional - Set the account to use in for the queue on the remote computer
      • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
      • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
      • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
      • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
      • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
      • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
      • input_filename, optional - Filename to which the input for the code that is to be run is written.
      • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
      • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
      • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
      • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
      • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
      • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
      • priority, optional - Set the priority of the job to be queued
      • qos, optional - Set the quality of service to use in for the queue on the remote computer
      • queue_name, optional - Set the name of the queue on the remote computer
      • rerunnable, optional - Determines if the calculation can be requeued / rerun.
      • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
      • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
      • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
      • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
        Namespace Ports
        • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
        • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
        • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
      • submit_script_filename, optional - Filename to which the job submission script is written.
      • withmpi, optional - Set the calculation to use mpi
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    Namespace Ports
  • parameters, required - List of input parameters (each item is parsed as a line in the input file).
  • remote_folder, optional - 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.
Outputs
  • output_bader_populations, optional - Calculated Bader populations.
  • output_parameters, required - The output dictionary containing results of the calculation.
  • output_planes, Namespace -- Calculated planes.
    Namespace Ports
  • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
  • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
  • retrieved, required - 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`.

enumlib

CalcJob EnumlibCalculation [source]

`CalcJob` implementation for the enum.x code of the enumlib library.

Inputs
  • code, optional - 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.
  • concentration_restrictions, optional - Dictionary to restrict the concentrations during the enumeration. The element is used as the key and the values are lists that have to be of the following shape: [numerator1, numerator2, denominator]. The concentration will then be limited to the range numerator1/denominator - numerator2/denominator.
  • elements_to_enumerate, optional - Dictionary that consists of elements (custom kind names are possible as well) of sites that should be enumerated as keys. The values are lists that specify the elements that will be placed on the site positions during the enumeration.
  • eps, optional - Small real number that is used as an epsilon to compare two numbers (to avoid finite precision errors).
  • max_cell_size, required - Maximum size of the enumerated super cells compared to the parent cell.
  • metadata, Namespace
    Namespace Ports
    • call_link_label, optional - The label to use for the `CALL` link if the process is called by another process.
    • computer, optional - When using a "local" code, set the computer on which the calculation should be run.
    • description, optional - Description to set on the process node.
    • dry_run, optional - When set to `True` will prepare the calculation job for submission but not actually launch it.
    • label, optional - Label to set on the process node.
    • options, Namespace
      Namespace Ports
      • account, optional - Set the account to use in for the queue on the remote computer
      • additional_retrieve_list, optional - List of relative file paths that should be retrieved in addition to what the plugin specifies.
      • append_text, optional - Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
      • custom_scheduler_commands, optional - Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the `prepend_text` is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
      • environment_variables, optional - Set a dictionary of custom environment variables for this calculation
      • environment_variables_double_quotes, optional - If set to True, use double quotes instead of single quotes to escape the environment variables specified in ``environment_variables``.
      • import_sys_environment, optional - If set to true, the submission script will load the system environment variables
      • input_filename, optional - Filename to which the input for the code that is to be run is written.
      • max_memory_kb, optional - Set the maximum memory (in KiloBytes) to be asked to the scheduler
      • max_wallclock_seconds, optional - Set the wallclock in seconds asked to the scheduler
      • mpirun_extra_params, optional - Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] ... exec.x
      • output_filename, optional - Filename to which the content of stdout of the code that is to be run is written.
      • parser_name, optional - Set a string for the output parser. Can be None if no output plugin is available or needed
      • prepend_text, optional - Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
      • priority, optional - Set the priority of the job to be queued
      • qos, optional - Set the quality of service to use in for the queue on the remote computer
      • queue_name, optional - Set the name of the queue on the remote computer
      • rerunnable, optional - Determines if the calculation can be requeued / rerun.
      • resources, required - Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
      • scheduler_stderr, optional - Filename to which the content of stderr of the scheduler is written.
      • scheduler_stdout, optional - Filename to which the content of stdout of the scheduler is written.
      • stash, Namespace -- Optional directives to stash files after the calculation job has completed.
        Namespace Ports
        • source_list, optional - Sequence of relative filepaths representing files in the remote directory that should be stashed.
        • stash_mode, optional - Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode`.
        • target_base, optional - The base location to where the files should be stashd. For example, for the `copy` stash mode, this should be an absolute filepath on the remote computer.
      • submit_script_filename, optional - Filename to which the job submission script is written.
      • withmpi, optional - Set the calculation to use mpi
    • store_provenance, optional - If set to `False` provenance will not be stored in the database.
  • min_cell_size, optional - Minimum size of the enumerated super cells compared to the parent cell.
  • monitors, Namespace -- Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
    Namespace Ports
  • path_to_makeStr, required - Absolute path to the `makeStr.py` executable
  • remote_folder, optional - 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.
  • sites_to_enumerate, optional - List that contains a list for each site consisting of the elements that should be enumerated at that site. Custom kind names like `Ni1` or `Ca0` are also possible.
  • structure, required - The parent structure that will be enumerated.
  • structures_hard_cutoff, optional - Maximum number of structures. If more structures are created, an error will be raised (default: No cutoff)
  • structures_to_return, optional - List that specifies the range/indices of structures that should be returned.
Outputs
  • output_structures, Namespace
    Namespace Ports
  • remote_folder, required - Input files necessary to run the process will be stored in this folder node.
  • remote_stash, optional - Contents of the `stash.source_list` option are stored in this remote folder after job completion.
  • retrieved, required - 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`.