.. _input_reference: Input YAML Reference ==================== ARC input files are YAML dictionaries passed directly to ``ARC(**input_dict)``. Top-level keys must match arguments accepted by :ref:`arc.main.ARC
`. Entries under ``species`` are converted to ``ARCSpecies`` objects, and entries under ``reactions`` are converted to ``ARCReaction`` objects. Use this page as a practical checklist of accepted keys. For deeper behavior, see the API reference pages for :ref:`ARC
`, :ref:`ARCSpecies `, :ref:`ARCReaction `, and :ref:`Level `. Minimal Shape ------------- .. code-block:: yaml project: my_project species: - label: ethanol smiles: CCO level_of_theory: wb97xd/def2svp ess_settings: gaussian: local Top-Level Keys -------------- Project and execution: * ``project`` - project name. Required for new projects. * ``project_directory`` - local directory for project output. * ``verbose`` - logging level. * ``running_jobs`` - restart state for submitted jobs. * ``output`` - restart/status state for species. * ``output_multi_spc`` - restart/status state for multi-species workflows. Species and reactions: * ``species`` - list of species dictionaries. * ``reactions`` - list of reaction dictionaries. * ``dont_gen_confs`` - species labels for which conformer generation should be avoided when XYZ is supplied. * ``n_confs`` - number of low-energy force-field conformers to keep. Default: ``10``. * ``e_confs`` - conformer energy window in kJ/mol. Default: ``5.0``. * ``allow_nonisomorphic_2d`` - allow optimization even when generated 3D geometry is not isomorphic to the 2D graph. Levels of theory: * ``level_of_theory`` - shortcut for composite or ``sp//opt`` style levels. * ``composite_method`` - composite method level. * ``conformer_level`` - alias for ``conformer_opt_level``. * ``conformer_opt_level`` - conformer optimization level. * ``conformer_sp_level`` - conformer single-point level. * ``ts_guess_level`` - level for TS guess comparison/optimization. * ``opt_level`` - geometry optimization level. * ``freq_level`` - frequency level. * ``sp_level`` - single-point energy level. * ``scan_level`` - rotor scan level. * ``irc_level`` - IRC level. * ``orbitals_level`` - orbitals level. * ``arkane_level_of_theory`` - level used for Arkane atom and bond corrections. * ``adaptive_levels`` - level choices by heavy-atom count. Job selection and resources: * ``job_types`` - dictionary of job type booleans. * ``specific_job_type`` - run one job family; takes precedence over ``job_types``. * ``job_memory`` - memory per job in GB. * ``max_job_time`` - wall-time limit in hours. * ``keep_checks`` - keep ESS checkfiles. * ``trsh_ess_jobs`` - troubleshoot failed ESS jobs. Default: ``true``. * ``trsh_rotors`` - troubleshoot failed rotor scans. Default: ``true``. * ``skip_nmd`` - skip normal-mode-displacement checks. * ``report_e_elect`` - report electronic energy. Software and statmech: * ``ess_settings`` - map ESS names to server names for this project. * ``thermo_adapter`` - thermochemistry adapter. Default: ``Arkane``. * ``kinetics_adapter`` - kinetics adapter. Default: ``Arkane``. * ``compare_to_rmg`` - compare calculated data to RMG database values. Default: ``true``. * ``compute_thermo`` - compute thermodynamic properties. Default: ``true``. * ``compute_rates`` - compute rate coefficients. Default: ``true``. * ``compute_transport`` - compute transport properties. Default: ``false``. * ``bac_type`` - bond additivity correction type: ``p``, ``m``, or ``null``. * ``freq_scale_factor`` - harmonic frequency scaling factor. * ``calc_freq_factor`` - calculate a scaling factor if one cannot be found. Default: ``true``. * ``bath_gas`` - bath gas for OneDMin/Lennard-Jones workflows. Kinetics conditions and TS search: * ``T_min`` - minimum temperature tuple, e.g. ``[500, K]``. * ``T_max`` - maximum temperature tuple, e.g. ``[3000, K]``. * ``T_count`` - number of temperature points. Default: ``50``. * ``ts_adapters`` - TS search adapters to try, such as ``heuristics``, ``AutoTST``, ``GCN``, ``xtb_gsm``, and ``orca_neb``. Species Entries --------------- Each entry under ``species`` may use the following keys: Identity and structure: * ``label`` - species label. * ``smiles`` - SMILES string. * ``inchi`` - InChI string. * ``adjlist`` - RMG adjacency list. * ``xyz`` - XYZ string, XYZ dictionary, list of XYZ entries, or path to a supported coordinate/input/output file. * ``yml_path`` - path to a species YAML file. * ``mol`` - RMG Molecule object when using the Python API. * ``species_dict`` - dictionary representation used in restarts/API workflows. Charge, spin, and TS metadata: * ``charge`` - integer charge. * ``multiplicity`` - spin multiplicity. * ``number_of_radicals`` - radical count override. * ``is_ts`` - whether this species is a transition state. * ``ts_number`` - TS index. * ``rxn_label`` - associated reaction label. * ``rxn_index`` - associated reaction index. * ``irc_label`` - IRC label. Thermo and output behavior: * ``compute_thermo`` - compute thermo for this species. * ``include_in_thermo_lib`` - include species in output thermo library. * ``e0_only`` - compute/store only E0 where applicable. * ``bond_corrections`` - custom bond correction data. * ``bdes`` - bond dissociation energy atom-pair list. * ``checkfile`` - ESS checkfile path. * ``run_time`` - restart/runtime metadata. Conformers, rotors, and geometry controls: * ``force_field`` - force field for conformer generation. Default: ``MMFF94s``. * ``directed_rotors`` - directed rotor scan requests. * ``preserve_param_in_scan`` - internal coordinates to preserve during scans. * ``consider_all_diastereomers`` - consider all diastereomers during conformer generation. * ``fragments`` - fragment atom indices. * ``active`` - active-space metadata. * ``external_symmetry`` - external symmetry number. * ``optical_isomers`` - number of optical isomers. * ``multi_species`` - multi-species label. * ``keep_mol`` - preserve the molecule object. * ``project_directory`` - species-specific project directory metadata. Reaction Entries ---------------- Each entry under ``reactions`` may use the following keys: * ``label`` - reaction label, commonly ``A + B <=> C + D``. * ``reactants`` - list of reactant labels. * ``products`` - list of product labels. * ``r_species`` - reactant ``ARCSpecies`` objects when using the Python API. * ``p_species`` - product ``ARCSpecies`` objects when using the Python API. * ``ts_label`` - associated TS species label. * ``ts_xyz_guess`` - TS guess or list of guesses. * ``xyz`` - alias for ``ts_xyz_guess``. * ``family`` - RMG reaction family. * ``multiplicity`` - reaction PES multiplicity. * ``charge`` - reaction PES charge. * ``preserve_param_in_scan`` - scan constraints for the reaction/TS. * ``kinetics`` - user-supplied kinetics data. * ``reaction_dict`` - dictionary representation used in restarts/API workflows. * ``species_list`` - species object list used when reconstructing from dictionaries. Level Dictionaries ------------------ Any level key can be a string: .. code-block:: yaml opt_level: wb97xd/def2tzvp or a dictionary: .. code-block:: yaml sp_level: method: DLPNO-CCSD(T)-F12 basis: cc-pVTZ-F12 auxiliary_basis: aug-cc-pVTZ/C cabs: cc-pVTZ-F12-CABS software: orca Accepted level dictionary keys are: * ``method`` * ``basis`` * ``auxiliary_basis`` * ``dispersion`` * ``cabs`` * ``method_type`` * ``software`` * ``software_version`` * ``compatible_ess`` * ``solvation_method`` * ``solvent`` * ``solvation_scheme_level`` * ``args`` * ``year`` Use ``year`` only for Arkane correction matching, not inside QC method names. Job Types --------- Current job type keys are: * ``conf_opt`` * ``conf_sp`` * ``opt`` * ``fine`` * ``freq`` * ``sp`` * ``rotors`` * ``irc`` * ``orbitals`` * ``onedmin`` * ``bde`` Legacy aliases are normalized by ARC: * ``fine_grid`` -> ``fine`` * ``lennard_jones`` -> ``onedmin`` Example: .. code-block:: yaml job_types: conf_opt: true opt: true fine: true freq: true sp: true rotors: false ESS Settings ------------ ``ess_settings`` maps software names to configured server names: .. code-block:: yaml ess_settings: gaussian: - local - cluster_a orca: local molpro: cluster_b Supported ESS keys include ``cfour``, ``gaussian``, ``mockter``, ``molpro``, ``orca``, ``qchem``, ``terachem``, ``onedmin``, ``xtb``, ``torchani``, and ``openbabel``. TS adapters such as ``heuristics``, ``AutoTST``, ``GCN``, ``xtb_gsm``, and ``orca_neb`` are configured through ``ts_adapters`` and related installation/settings. Complete Example ---------------- .. code-block:: yaml project: ethanol_reference_demo project_directory: /tmp/arc_ethanol_reference_demo ess_settings: gaussian: local job_types: conf_opt: true opt: true fine: true freq: true sp: true rotors: true irc: false level_of_theory: wb97xd/def2svp sp_level: method: wb97xd basis: def2tzvp software: gaussian job_memory: 14 max_job_time: 24 compute_thermo: true compute_rates: false bac_type: null species: - label: ethanol smiles: CCO multiplicity: 1 charge: 0 .. include:: links.txt