7. Analyzing the Output Files

You will see that a sucessfully executed RMG job will create multiple output files and folders: output.html (if generateOutputHTML=True is specified) /cantera_from_ck /cantera1 (if generateCanteraYAML1=True is specified) /cantera2 (if generateCanteraYAML2=True is specified) /chemkin /pdep /plot /rms /solver /species RMG.log

7.1. The Chemkin Folder

The /chemkin folder will likely have a large number of chemkin formatted files. In general, these can be disregarded, as you will be mainly interested in chem.inp, the chemkin formatted input file with a species list, thermochemical database, and a list of elementary reactions. All of inp files appended with numbers are those that have been generated by RMG as it runs and the mechanism is still in progress of enlarging. chem_annotated.inp is provided as a means to help make sense of species syntax and information sources (i.e., how RMG estimated indivual kinetic and thermodynmic parameters). In addition, a species dictionary, species_dictionary.txt, is generated containing all the species in your mechanism in the format of an adjacency list. Either chemkin file, in addition to the dictionary, may be used as inputs in the tools section of this website to better visualize the species and reactions. Alternatively, if the input option generateOutputHTML= is set to True, you will be able to visualize 2D images of all species and reactions in your mechanism as image files and in an html file, output.html. Once you are able to visualize the mechanism, several useful tools exist. For example, in the Reaction Details section, you’ll see the following with check-box fields beside them:

  • Kinetics

  • Comments

  • Chemkin strings

If you check the last box, chemkin strings, you can then search for strings corresponding to seemingly nonsensical named species (e.g. S(1234)) that may show up in any analyses/simulations you perform (e.g., with Cantera or Chemkin). Further, under Reaction Families, you can selectively view the reactions that been generated based on a particular RMG reaction family or library.

7.2. The Species Folder

If generateOutputHTML=True is specified as an RMG input option, the species folder will be populated with png files with 2D pictures of each species in your final mechanism. Otherwise, it will contain no files, or files generated from pressure dependent jobs.

7.3. The Pdep Folder

The /pdep folder will contain files associated with the pressure-dependent reactions that RMG has generated, if you requested such a job. These files are formatted as input files for Arkane, which can be run independently. This can be useful if one wants to visualize the potential energy surface corresponding to any particular network.

7.4. The Solver Folder

RMG currently includes a solver for isothermal batch reactors. This is in fact a critical part of the model enlargement algorithm. If you have included simulations in your input file, the solutions will be located in /solver. You will probably only be interested in the files with the largest number tags. Please note that up to and including RMG-Py version 2.3.0 these files showed mole fraction of each species at each step, but they now show amount (number of moles) of each species; you must divide by the sum if you wish to get a mole fraction.

7.5. Cantera Output Folders

RMG can write mechanisms in Cantera YAML format via three distinct routes, producing up to three output folders. All three require Cantera to be installed in the conda environment (it is included in the standard rmg_env).

7.5.1. /cantera_from_ck

This folder is always produced when the Chemkin writer is enabled (generateChemkin=True, the default). After the final RMG iteration, Cantera’s own ck2yaml converter is used to translate the Chemkin-format files in /chemkin into Cantera YAML. This is the most thoroughly tested route and is the recommended output for production use.

7.5.2. /cantera1 (beta)

Note

The cantera1 writer is in beta. It uses the Cantera Python API to construct and serialise the mechanism YAML, rather than writing the YAML by hand. It has been less extensively tested than the cantera_from_ck route. Please report any discrepancies.

This folder is created when generateCanteraYAML1=True is set in the options() block (disabled by default). The writer runs after every RMG iteration (or on the schedule set by saveInterval), so the folder accumulates a history of the growing mechanism.

Files generated:

  • chem{NNNN}.yaml — mechanism snapshot at the iteration when the core contained NNNN species (e.g. chem0042.yaml)

  • chem.yaml — copy of the latest snapshot; always reflects the current model state

  • chem_annotated.yaml — annotated version with SMILES, source, and kinetics comments (written when verboseComments=True for this writer)

  • chem_edge{NNNN}.yaml / chem_edge.yaml / chem_edge_annotated.yaml — edge-model equivalents (written when saveEdge=True)

  • comparison_report.txt — numerical comparison of chem.yaml against the cantera_from_ck translation (written at the end of the run if both writers are enabled; see below)

7.5.3. /cantera2 (beta)

Note

The cantera2 writer is in beta. It generates Cantera YAML directly from RMG’s internal Python data structures, without going through the Chemkin intermediate. While it should produce valid mechanisms, it has been less extensively tested than the cantera_from_ck route. Please report any discrepancies.

This folder is created when generateCanteraYAML2=True is set in the options() block (disabled by default). Like cantera1, it runs at every iteration (or on the configured schedule).

Files generated:

  • chem{NNNN}.yaml / chem.yaml — latest mechanism snapshot and its labelled history

  • chem_annotated.yaml — annotated version (written when verboseComments=True)

  • chem_edge{NNNN}.yaml / chem_edge.yaml / chem_edge_annotated.yaml — edge-model equivalents (written when saveEdge=True)

  • comparison_report.txt — numerical comparison against the cantera_from_ck translation (written at the end of the run if both writers are enabled)

7.5.4. Comparison Reports

When a direct-writer folder (cantera1 or cantera2) is used alongside the Chemkin writer, RMG automatically compares the final chem.yaml from that folder against the cantera_from_ck/chem.yaml produced by ck2yaml. The comparison checks differences in the yaml data. Not all differences are necessarily problematic. Results are written to comparison_report.txt inside the relevant direct-writer folder.

If you find that the two routes disagree in a problematic way, please open an issue on the RMG-Py GitHub repository and include the comparison_report.txt and a minimal reproducing input.py.

7.6. The RMS YAML Folder

The /rms folder contains the mechanism in ReactionMechanismSimulator (RMS) YAML format. This writer is enabled by default (generateRMSYAML=True) and writes at every iteration, unless configured otherwise by saveInterval.