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Output

After running a project, the local project folder will contain the following directory tree (bold represents folders, italics represents files):

  • t3.log: Details of all project execution procedures.
  • t3_restart.yml: T3 restart file. T3 can resume from this if interrupted.
  • iteration_x:
    • RMG:
      • input.py: The RMG input file for iteration x (automatically written by T3).
      • RMG.log: The RMG log file for iteration x.
      • chem_annotated.inp: The Chemkin mechanism file with annotated reaction sources.
      • species_dictionary.txt: Species adjacency list dictionary.
      • chemkin: Additional Chemkin files (transport, species).
      • solver: RMG simulation profiles (if save_simulation_profiles is enabled).
    • SA (if sensitivity analysis is enabled):
      • sa_coefficients.yml: Sensitivity analysis results in YAML format.
      • solver: Raw SA output files (CSV format for RMG adapter).
    • ARC (if QM calculations are performed):
      • restart.yml: The ARC restart file for iteration x.
      • arc.log: The ARC log file for iteration x.
      • calcs: All spawned jobs sorted by species name (including transition states).
      • output: Additional ARC output files and folders.

Key output files

The generated mechanism

The final Chemkin mechanism is in the last iteration's RMG folder:

iteration_N/RMG/chem_annotated.inp
iteration_N/RMG/species_dictionary.txt

These files can be used directly in Cantera, CHEMKIN, or other tools.

Sensitivity analysis results

SA results are saved in YAML format:

iteration_N/SA/sa_coefficients.yml

This file contains the SA coefficients for each observable species, organized per condition. It can be loaded in Python:

from t3.common import sa_dict_from_yaml
from arc.common import read_yaml_file

raw = read_yaml_file('iteration_0/SA/sa_coefficients.yml')
sa_dict = sa_dict_from_yaml(raw)

# Access kinetics SA for the first condition
kinetics = sa_dict['kinetics'][0]
for observable, reactions in kinetics.items():
    print(f'{observable}: {len(reactions)} sensitive reactions')

T3 libraries

T3 creates RMG-compatible thermo and kinetics libraries from the QM calculations. These are stored in the RMG database path under the name specified by library_name (default: T3lib).

Restarting a project

T3 automatically detects existing iteration folders and resumes from where it left off. Simply re-run T3 in the same project directory:

python ~/Code/T3/T3.py input.yml

T3 will scan for iteration_* folders and continue from the latest completed iteration.