Identifying all Reactions for a Set of Species

The PopulateReactions module accepts a list of species as input (in the form of adjacency lists) and outputs a list of all possible reactions between those species, according to the RMG reaction family templates (located at %rmg%\databases\RMG_database\kinetics_groups)

Instructions for Use

1. Create a text file in any directory that you like (for the purposes of this example, we’ll create a file named reactions_input.txt).

At the top of the text file, state the temperature of interest. When the module identifies a reaction, it must also grab the kinetics (in the form of modified Arrhenius parameters). In some cases, the RMG kinetics library has multiple kinetics values for the same reaction (e.g. one set valid from 300-500K and another valid from 700-900K). Thus, in order to report the best kinetics, the input file must contain a temperature:

Temperature: 1200 (K)

The next item to supply to the text file is the Solvation field. This feature of RMG is still under construction. For now, please label the Solvation field “off”:

Solvation: off

This should be followed by PrimaryThermoLibrary and PrimaryReactionLibrary blocks, which should each be terminated with the “END” statement. These blocks can be left empty, if desired.

The next item in the text file are the species of interest. For each species of interest, supply a name and an adjacency list. The adjacency list should have the same syntax used to define a species in the condition.txt input file (see RMG manual). Hydrogens can be omitted for simplicity. For example, the adjacency list for 1-butanol and oxygen could be written as:

nBuOH
1 C 0 {2,S}
2 C 0 {1,S} {3,S}
3 C 0 {2,S} {4,S}
4 C 0 {3,S} {5,S}
5 O 0 {4,S}

O2
1 O 0 {2,D}
2 O 0 {1,D}

Thus, the total reactions_input.txt file looks like:

Temperature: 1200 (K)
Solvation: off

PrimaryThermoLibrary:
END

PrimaryReactionLibrary:
END

nBuOH
1 C 0 {2,S}
2 C 0 {1,S} {3,S}
3 C 0 {2,S} {4,S}
4 C 0 {3,S} {5,S}
5 O 0 {4,S}

O2
1 O 0 {2,D}
2 O 0 {1,D}

2. At the command prompt, change to the directory containing the reactions_input.txt file and then execute the command

java -classpath "%rmg%"\bin\RMG.jar PopulateReactions reactions_input.txt

For linux users:

java -classpath $RMG/bin/RMG.jar PopulateReactions reactions_input.txt

To have the output written to file instead of to the screen, use the syntax

java -classpath "%rmg%"\bin\RMG.jar PopulateReactions reactions_input.txt > reactions_output.txt

where reactions_output.txt is the name of the file to be written.

3. Every time a species is found in the input file, the module will:

   • Read in the name and adjacency list of the species
   • Attempt to react the just-read-in species against each of the reaction families located in the %rmg%\databases\RMG_database\kinetics_groups directory
   • Store the results

The reaction families the module will attempt to react the just-read-in species against are either unimolecular or bimolecular.

• If the reaction family is unimolecular, the module attempts to react the current species
• If the reaction family is bimolecular (e.g. A+B–>products), the module assigns the just-read-in species as A and iterates over all previously read-in species (including the just-read-in species) when assigning B. The module then assigns the just-read-in species as B and iterates over all previous species for A.

All reactions generated are reported in the PopRxnsOutput_Rxns.txt file. The top of the file displays:

• The units for the modified Arrhenius parameters reported
• The temperature used in searching for the best kinetics
• Whether the reported Arrhenius parameters are for gas-phase or solution-phase chemistry

Each line after this has the following format (in general):

B+C–>D+F A n Ea Rxn_family exact/estimate: Node1 Node2

where:

• A, n, and Ea are the modified Arrhenius parameters
• Rxn_family is the reaction family template used to generate this reaction. The “Rxn_family” is a folder in the %rmg%\databases\RMG_database\kinetics directory
• Node1/Node2 are the reactive subgroups of the species that RMG identified
• exact/estimate states whether the Rxn_family folder’s rateLibrary.txt file contained data for the Node1-Node2 combination. If so, the kinetics reported are found, exactly as written, in the file. If not, an averaging scheme was performed to arrive at the reported numbers.

The identities of B, C, D, and F are located in the PopRxnsOutput_Spcs.txt file, in the form of adjacency lists.