From 87967bd7634bdc96e2c34c740fc4a145fb67d409 Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Sun, 12 Jan 2025 09:47:29 +0200 Subject: [PATCH] f reation --- arc/reaction/reaction.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/arc/reaction/reaction.py b/arc/reaction/reaction.py index 2a39536448..3a968466c3 100644 --- a/arc/reaction/reaction.py +++ b/arc/reaction/reaction.py @@ -53,6 +53,8 @@ class ARCReaction(object): preserve_param_in_scan (list, optional): Entries are length two iterables of atom indices (1-indexed) between which distances and dihedrals of these pivots must be preserved. Used for identification of rotors which break a TS. + kinetics (Dict[str, float], optional): The high pressure limit rate coefficient calculated by ARC. + Keys are 'A' in cm-s-mol units, 'n', and 'Ea' in kJ/mol. Attributes: label (str): The reaction's label in the format `r1 + r2 <=> p1 + p2` @@ -64,10 +66,12 @@ class ARCReaction(object): r_species (List[ARCSpecies]): A list of reactants :ref:`ARCSpecies ` objects. p_species (List[ARCSpecies]): A list of products :ref:`ARCSpecies ` objects. ts_species (ARCSpecies): The :ref:`ARCSpecies ` corresponding to the reaction's TS. - dh_rxn298 (float): The heat of reaction at 298K. - kinetics (Arrhenius): The high pressure limit rate coefficient calculated by ARC. - rmg_kinetics (List[dict]): The Arrhenius kinetics from RMG's libraries and families. Each dict has 'A', 'n', amd 'Ea' - parameters as keys, and a 'comment' key with a description of the source of the kinetics. + dh_rxn298 (float): The heat of reaction at 298K in J/mol. + kinetics (Dict[str, float]): The high pressure limit rate coefficient calculated by ARC. + Keys are 'A' in cm-s-mol units, 'n', and 'Ea' in kJ/mol. + rmg_kinetics (List[Dict[str, float]]): The Arrhenius kinetics from RMG's libraries and families. + Each dict has 'A' in cm-s-mol units, 'n', and 'Ea' in kJ/mol as keys, + and a 'comment' key with a description of the source of the kinetics. long_kinetic_description (str): A description for the species entry in the thermo library outputted. ts_xyz_guess (list): A list of TS XYZ user guesses, each in a string format. multiplicity (int): The reaction surface multiplicity. A trivial guess will be made unless provided. @@ -96,12 +100,13 @@ def __init__(self, reaction_dict: Optional[dict] = None, species_list: Optional[List[ARCSpecies]] = None, preserve_param_in_scan: Optional[list] = None, + kinetics: Dict[str, float] = None, ): self.arrow = ' <=> ' self.plus = ' + ' self.r_species = r_species or list() self.p_species = p_species or list() - self.kinetics = None + self.kinetics = kinetics self.rmg_kinetics = None self.long_kinetic_description = '' self._family = None