DFT Calculations

Generate a dft template file using atl_gen_configuration_file -t dft.

Attention

All keys are mandatory unless stated otherwise.

General - [general]

General settings for the DFT script.

  • log_path:

    • Description: Path where the logs will be stored.

    • Type: (str, PosixPath)

    • Default: '/tmp/'.

  • result_file_path:

    • Description: Path for the results file (extxyz format).

    • Type: (str, PosixPath)

    • Default: 'dft_calculation_results'.

  • source_db:

    • Description: Path to the source database file (.extxyz or ATLAS .xz database format).

    • Type: (optional, str, PosixPath)

  • aiida_group_name:

    • Description: Name of the AiiDA group for the calculations.

    • Type: (str)

    • Example: 'my_dft_run'.

  • max_batch:

    • Description: Maximum number of structures to process in one batch.

    • Type: (int)

    • Default: 100.

  • queue_check_interval_seconds:

    • Description: Interval in seconds to check the queue for submitting new calculations.

    • Type: (int)

    • Default: 240.

  • start_on_struct_idx:

    • Description: Number of structures to skip before starting the calculations.

    • Type: (int)

    • Default: 0.

  • dry_run:

    • Description: If True, a dry-run is performed and no calculations are submitted.

    • Type: (optional, bool)

    • Default: False.

  • selected_structure_type:

    • Description: If specified, only structures of this type will be processed.

    • Type: (optional, str)

    • Possible values are: bulk, surface, cluster.

Calculation - [calculation]

DFT calculation settings.

  • calc_type:

    • Description: Type of calculation.

    • Type: (str)

    • Default: 'static'.

    • Possible values are: static, relaxation.

  • aiida_potential_family:

    • Description: AiiDA potential family name.

    • Type: (str)

    • Example: 'vasp-5.4-PBE-2023'.

  • potential_mapping:

    • Description: Mapping of elements to specific potential labels.

    • Type: (optional, dict)

    • Example:

{'Si': 'Si_GW'}

Kpoints - [kpoints]

K-point settings.

  • kspacing:

    • Description: K-spacing in Å⁻¹ for different phases or a single value for all structures. The k-spacing values will be applied on a per-phase basis, according to the keys added to the dictionary which must match phases in the database. The ATL_DEFAULT key can be used to set a default k-spacing value for all phases not explicitly listed.

    • Type: (dict)

    • Example:

{'ATL_DEFAULT': 0.15, 'alpha': 0.125}

Queue - [queue]

Queue settings for HPC schedulers (e.g., SLURM).

  • code_string:

    • Description: Name of the code as defined in AiiDA.

    • Type: (str)

    • Example: 'vasp@my_cluster'.

  • account:

    • Description: Account to be used for the calculations.

    • Type: (optional, str)

  • qos:

    • Description: Quality of service parameter.

    • Type: (optional, str)

  • node_cpus:

    • Description: Number of CPUs per node.

    • Type: (optional, int)

  • max_wallclock_seconds:

    • Description: Maximum wallclock time in seconds.

    • Type: (int)

    • Default: 16200.

  • max_memory_kb:

    • Description: Maximum memory per node in KB.

    • Type: (optional, int)

  • multiple:

    • Description: Whether to use multiple nodes.

    • Type: (optional, int)

  • custom_scheduler_commands:

    • Description: Custom scheduler commands.

    • Type: (optional, str)

Options_Resources - [queue.options_resources]

Scheduler resource options.

  • tot_num_mpiprocs:

    • Description: Total number of MPI processes.

    • Type: (int)

    • Default: 24.

  • parallel_env:

    • Description: Parallel environment to be used.

    • Type: (str)

    • Default: ' '.

Aiida_Vasp - [aiida_vasp]

Settings for the AiiDA-VASP plugin.

Attention

This section is optional.

  • critical_notifications:

    • Description: Errors and warnings to be treated as critical (general).

    • Type: (optional, dict)

Parser_Settings - [aiida_vasp.parser_settings]

Parser settings for aiida-vasp.

  • add_kpoints:

    • Description: Whether to add k-points information to the parsed results.

    • Type: (optional, bool)

    • Default: True.

Critical_Notifications - [aiida_vasp.parser_settings.critical_notifications]

Critical error and warning notifications to be treated as important.

  • add_edddav_zhegv:

    • Description: Add EDDDAV ZHEGV error notification.

    • Type: (optional, bool)

    • Default: True.

  • add_eddrmm_zhegv:

    • Description: Add EDDRMM ZHEGV error notification.

    • Type: (optional, bool)

    • Default: True.

  • add_not_hermitian:

    • Description: Add not hermitian error notification.

    • Type: (optional, bool)

    • Default: True.

  • add_brmix:

    • Description: Add BRMIX error notification.

    • Type: (optional, bool)

    • Default: True.

  • add_bandocc:

    • Description: Add band occupation error notification.

    • Type: (optional, bool)

    • Default: False.

Incar - [incar]

INCAR settings for different structure types.

  • bulk:

    • Description: INCAR settings for bulk structures.

    • Type: (optional, dict)

  • surface:

    • Description: INCAR settings for surface structures.

    • Type: (optional, dict)

  • cluster:

    • Description: INCAR settings for cluster structures.

    • Type: (optional, dict)