ARC's API

ARC's API (application programming interface)

ARC (arc/main.py)

class ARC(input_dict=None, project=None, arc_species_list=None, arc_rxn_list=None, level_of_theory='',
conformer_level='', composite_method='', opt_level='', freq_level='', sp_level='', scan_level='', ts_guess_level='',
fine=True, generate_conformers=True, scan_rotors=True, use_bac=True, model_chemistry='', ess_settings=None,
initial_trsh=None, t_min=None, t_max=None, t_count=None, verbose=logging.INFO, project_directory=None)

Attribute	Type	Description
project	str	The project's name. Used for naming the working directory.
project_directory	str	The path to the project directory
arc_species_list	list	A list of ARCSpecies objects (each entry should represent either a stable well, TS guesses are given in the arc_rxn_list)
arc_rxn_list	list	A list of ARCReaction objects
level_of_theory	str	Either sp//geometry levels or a composite method, e.g. 'CBS-QB3', 'CCSD(T)-F12a/aug-cc-pVTZ//B3LYP/6-311++G(3df,3pd)'...
conformer_level	str	Level of theory for conformer searches
ts_guess_level	str	Level of theory for comparisons of TS guesses between different methods
composite_method	str	Composite method
opt_level	str	Level of theory for geometry optimization
freq_level	str	Level of theory for frequency calculations
sp_level	str	Level of theory for single point calculations
scan_level	str	Level of theory for rotor scans
fine	bool	Whether or not to use a fine grid for opt jobs (spawns an additional job)
generate_conformers	bool	Whether or not to generate conformers when an initial geometry is given
scan_rotors	bool	Whether or not to perform rotor scans
use_bac	bool	Whether or not to use bond additivity corrections for thermo calculations
model_chemistry	list	The model chemistry in Arkane for energy corrections (AE, BAC). This can be usually determined automatically.
ess_settings	dict	An optional input parameter: a dictionary relating ESS to servers
initial_trsh	dict	Troubleshooting methods to try by default. Keys are server names, values are trshs
t_min	tuple	The minimum temperature for kinetics computations, e.g., (500, str('K')). An int value is also accepted, and will be converter to a (x, 'K') tuple.
t_max	tuple	The maximum temperature for kinetics computations, e.g., (3000, str('K')). An int value is also accepted, and will be converter to a (x, 'K') tuple.
t_count	int	The number of temperature points between t_min and t_max for kinetics computations

To use this class programmatically, create an instance and set its attributes, then invoke the execute() method.

ARCSpecies (arc/species.py)

class ARCSpecies(is_ts=False, rmg_species=None, mol=None, label=None, xyz=None, multiplicity=None, charge=None,
smiles='', adjlist='', bond_corrections=None, generate_thermo=True, species_dict=None, yml_path=None,
ts_methods=None, ts_number=None, rxn_label=None)

Attribute	Type	Description
label	str	The species' label
multiplicity	int	The species' multiplicity. Can be determined from adjlist/smiles/xyz. The algorithm assumes it's either a singlet or a doublet if not given
charge	int	The species' net charge. Assumed to be 0 be default.
is_ts	bool	Whether or not the species represents a transition state
xyz	string	An initial geometry guess
rmg_species	Species	An RMG Species object to be converted to an ARCSpecies object
smiles	str	The SMILES representation
adjlist	str	An RMG adjacency list molecule connectivity graph
mol	Molecule	An RMG:Molecule object used for BAC determination. Does not necessarily describe bond orders.
xyz_mol	Molecule	An RMG:Molecule object derived from the given xyz coordinates, if available. Used when a match between atom order in the molecule and in xyz is desired
mol_list	list	A list of localized structures generated from 'mol', if possible
bond_corrections	dict	The bond additivity corrections (BAC) to be used. Determined from the structure if not directly given.
generate_thermo	bool	Whether ot not to calculate thermodynamic properties for this species
ts_methods	list	Methods to try for generating TS guesses. If Species is a TS and ts_methods is an empty list, then xyz (user guess) must be given. If ts_methods is None, it will be set to the default methods
ts_guesses	list	A list of TSGuess objects for each of the specified methods
yml_path	str	Path to an Arkane YAML file representing a species (for loading the object)
external_symmetry	int	The external symmetry of the species (not including rotor symmetries)
optical_isomers	int	Whether (=2) or not (=1) the species has chiral center/s

Note: An ARCSpecies object does not have to be created for a transition state, unless the user would like to explicitly set arguments. Otherwise, it will be automatically created per ARCReaction object.

ARCReaction (arc/reaction.py)

class ARCReaction(is_ts=False, rmg_species=None, mol=None, label=None, xyz=None, multiplicity=None, charge=None,
smiles='', adjlist='', bond_corrections=None, generate_thermo=True, species_dict=None, yml_path=None,
ts_methods=None, ts_number=None, rxn_label=None)

Attribute	Type	Description
label	str	The reaction's label. Should be in the format 'reactant1 + reactant2(optional) <=> product1 + product2(optional)'
reactants	str	A list of labels corresponding to previously defined ARCSpecies objects
products	str	A list of labels corresponding to previously defined ARCSpecies objects
ts_label	str	A label corresponding to an ARCSpecies object, if defined.
rmg_reaction	Reaction	An RMG Reaction object
ts_methods	list	A list with TS guess methods, default is in settings.py, passed to the TS ARCSpecies object
ts_xyz_guess	list	A list of xyz guesses
multiplicity	int	The surface's multiplicity. Trivial values automatically determined from reactants/products multiplicities
charge	int	The surface's charge. Automatically determined from the reactants