Mechanism Input

Input

Accepted file formats

RMS currently supports its own .rms YAML based file format and Chemkin (.inp) format files (if an RMG species_dictionary.txt file is available it can be taken along with the Chemkin file to provide molecular structure information for the Chemkin file species). Chemkin files can be in any units and individual units (quantities specified in Unitful format: 1.0u"m^3") are accepted with the RMS format files. These can be loaded

phaseDict = readinput("src/testing/mech.rms")

or

phaseDict = readinput("chem_annotated.inp";
              spcdict="species_dictionary.txt")

respectively. Note that spcdict is an optional parameter.

Output of Input File Reading

The output of reading an input file in RMS returns a dictionary of phase dictionaries indexed by the name of each phase. Each phase dictionary has an array of Species objects corresponding to the key "Species" and an array of Reaction Objects corresponding to the key "Reactions".

YAML File Formats

RMS uses a YAML format input file. YAML essentially stores information in embedded dictionaries and lists. An example segment from a .rms file is given below.

Phases:
- Species:
  - name: Ar
    smiles: '[Ar]'
    thermo:
      polys:
      - Tmax: 3459.6
        Tmin: 100.0
        coefs: [2.5, 9.24384602e-15, -1.36779837e-17, 6.66184769e-21, -1.00106912e-24,
          -1552.16105, 2.16745116]
        type: NASApolynomial
      - Tmax: 5000.0
        Tmin: 3459.6
        coefs: [2.49999999, 9.20455546e-12, -3.58608293e-15, 6.15198922e-19, -3.92041801e-23,
          -1552.16104, 2.16745122]
        type: NASApolynomial
      type: NASA
    type: Species
  - name: He
    smiles: '[He]'
    thermo:
      polys:
      - Tmax: 3459.6
        Tmin: 100.0
        coefs: [2.5, 9.24384602e-15, -1.36779837e-17, 6.66184769e-21, -1.00106912e-24,
          -1552.16105, -1.28349484]
        type: NASApolynomial
      - Tmax: 5000.0
        Tmin: 3459.6
        coefs: [2.49999999, 9.20455546e-12, -3.58608293e-15, 6.15198922e-19, -3.92041801e-23,
          -1552.16104, -1.28349478]
        type: NASApolynomial
      type: NASA
  name: phase
  Reactions:
  - kinetics: {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}
    products: [oxygen, octane]
    reactants: ['C[CH]CCCCCC', '[O]O']
    type: ElementaryReaction
  - kinetics: {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}
    products: [oxygen, octane]
    reactants: ['CCC[CH]CCCC', '[O]O']
    type: ElementaryReaction

Dashes - denote the beginning of a new key:value pair. If done in series as above under Species: and under Reactions: this makes an array of dictionaries. Colons : denote the beginning of a key:value pair within a dictionary. Key, value pairs following a dash that do not have a dash themselves are part of the same dictionary. You can also define dictionaries and lists as normal within Julia within the YAML.

.rms File Format

In YAML RMS amounts to a dictionary of phase dictionaries. Each phase dictionary has an entry corresponding to "Species", "Reactions" and "name". The "name" corresponds to the name of the phase. Within "Species" and "Reactions" are associated lists of dictionaries that correspond to Species and Reaction objects. Beneath "Species" and "Reactions" the structures all follow the same conventions.

Each dictionary is assumed to correspond to an object within RMS that should be denoted by the type key and to have key:value maps that correspond to all necessary parameters to construct the object corresponding to the type value. Thus, the an Arrhenius rate calculator can be defined as {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}. In that case RMS knows the object from the type value and what to put in the Arrhenius object from the remaining fields. Of course for more complex objects some of the values will correspond to objects themselves and thus be dictionaries with their own type values.

Units can be defined for specific numerical values in the Unitful format 1.0u"m^3. However, currently molecular units are not supported and thus moles must be used (this restriction applies only to .rms files and not to Chemkin format files).