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) /chemkin /pdep /plot /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.