Output

Output

Summary file

A file called summary_{chemid}.out is written which is a summary of the reaction search (chemid is the id of the well the search started from). This file contains all the successful and failed reaction searches, together with the barrier heights and the product identifiers. Before each successful saddle a comment line # kinbot_stereopath {json} records the stereochemical pathway; tools that read the summary must allow comment lines.

Calculation names

Jobs are named after the species: <name>_well for a well, conf/<name>_<i> for its conformers, hir/<name>_hir_<rotor>_<angle> for rotor scans, <name>_<family>_<atoms> for a TS search and …_IRC_F/_IRC_R for its IRC. <name> is the chemid, with a -s<16 hex> suffix for species with fixed stereochemistry (see Stereochemistry). A newly found product is first optimized as <initial name>_product; the result is then saved under the name of the optimized structure, <optimized name>_well, because the connectivity or stereochemistry can change during that optimization. L2 results carry _high, L0 conformers _semi_emp_. With Sella the optimizer log is <job>_sella.log; conf/<name>_low.<ext> is a copy of the output of the selected lowest conformer.

Database and bookkeeping files

kinbot.db (an ASE database) holds every result: geometry, energy, ZPE, frequencies and, where available, the Hessian; rows named stereochemistry/<job> are not results but the input reference checked before a saved result is reused. .kinbot_run.json records the calculation format and the RDKit version; .kinbot_theory_jobs.json the theory profiles and each job's level (see Restarting).

Master equation files

me/mess_<n>.inp per connected network, listed in me/mess_networks.json; MESS output me/mess_<n>.out and me/mess_<n>.micro. The run script uses mess_command.

PESViewer input file

An input file is written for the PESViewer. To visualize the reactions found, install the code and run:

pesviewer pesviewer.inp

This displays a graph showing the reactant and all products, including the barrier heights and well and product energies. The x-positions of all stationary points can be moved (drag and drop) to make the figure clearer. The figures of the molecules can also be moved (drag and drop).