Transition state file names

[ffmulks]

Hi there (@t-young31 and co),

I have some issues extracting the finally used data for database uploads from reaction calculations. The automatic transition state search generates a lot of files. The final single point is self-explanatorily placed in the single point folder but for OPT and FREQ, I am not quite sure which file is ultimately used.

I assume the files TS_<TS_ID>adhl_optts* are generally what I am looking for. What is unclear to me here is if the ones additionally denoted as "conf" are earlier iterations before a final "OptTS Freq" call or if the "conf" indicates that after the initial TS search, this is the end result of additionally sampling conformers.

This should be easy enough to confirm but neither of final single points in the respective output files them matches the collected optimisation energy (which it does for the reactants and products collected in the respective folder).

Could you clarify for me which file is what I would be looking for here?

Thank you
Florian

[ffmulks]

My bad, I suppose it is the optts_conf file. I got confused in the ORCA outputs with the nomenclature of the final single point energies. Please correct me if I am wrong, though.

[t-young31]

Hey @ffmulks – sorry for being so slow to reply to this (was on holiday without a laptop for the past few weeks)

I don't think there's a way to tell, as the _conf files may be not from the final TS if it doesn't optimise to a true TS, in which case there's a fallback to the TS without the conformer search. See

autodE/autode/transition_states/transition_state.py

Line 302 in 161818c

if _ts.is_true_ts and _ts.energy < self.energy:

Best way might be to match the geometry? Something like:

"""
Calculate the closest match to a target molecule from .xyz files in a folder
Usage:

    python <script>.py <target_structure>.xyz <folder_name>
"""
import sys
from pathlib import Path
import autode as ade


def molecules_in_directory(directory_name):
    """Generator for autodE molecules from xyz files in a folder"""
    for path in Path(directory_name).iterdir():
        if path.suffix == ".xyz":
            yield ade.Molecule(str(path))


if __name__ == '__main__':

    target = ade.Molecule(sys.argv[1])
    rmsd_molecules = {}

    for possible in molecules_in_directory(sys.argv[2]):
        if possible.atomic_symbols != target.atomic_symbols:
            continue

        rmsd = ade.geom.calc_rmsd(possible.coordinates, target.coordinates)
        rmsd_molecules[rmsd] = possible

    min_rmsd = min(rmsd for rmsd in rmsd_molecules.keys())
    closest_match = next(m for rmsd, m in rmsd_molecules.items() if rmsd == min_rmsd)
    print(
        f"Closest match: {closest_match.name}\n"
        f"RMSD {round(min_rmsd, 3)} Å"
    )