Energies and other thermodynamic properties of reactants/product not accesible

[zarkoivkovicc]

When we have the following peace of code:

    reactant = ade.Molecule(f'Gaussian_XTB/reactant_guess.xyz').to_reactant()
    product = ade.Molecule(f'Gaussian_XTB/product_guess.xyz').to_product()
    ts_guess = ade.Molecule(f'Gaussian_XTB/ts_guess.xyz')
    rxn = ade.Reaction(reactant,product, name=name)
    ts_guess = ade.transition_states.TSguess.from_species(ts_guess)
    rxn.optimise_reacs_prods()
    rxn.ts = ade.TransitionState(ts_guess,bond_rearr=get_bond_rearrangs(reactant,product,name="isomerisation",save=False)[0])
    rxn.ts.optimise(name_ext = "ts")
    ts_check = rxn.ts.is_true_ts
    rxn.calculate_thermochemical_cont()

rxn.delta() type of properties are available, but thermodynamic properties of individual reactants and product accesed, for instance, via rxn.reactant.energy are not available, although they were used to compute reaction properties.

Is there a way these properties can be accessed without explicitely calling calc_thermo() on reactants/products again? Or am I missing something obvious? I took a quick glance at the code and it seems delta properties are calculated by accesing the reactants/products energies through their attributes, so I am confused why I can't access them as well.

[t-young31]

Hi @zarkoivkovicc

autodE reaction reactants and products are the association complexes, containing all the reactants/products

autodE/autode/reactions/reaction.py

Line 499 in 6a6eebe

def reactant(self) -> ReactantComplex:

Reaction.delta calculates based on separated reactants i.e. sum(mol.energy for mol in rxn.reacs)

Hope that's helpful!

[zarkoivkovicc]

Thank you for the quick answer. Indeed, the confusion was from my side as my reaction is an isomerisation, thus reactant and reactive complex are practically the same.