Estimating Species Thermochemistry

The ThermoDataEstimator utility produces group additivity-based thermochemistry estimates without running RMG. As with the thermochemistry estimates used by RMG, the ThermoDataEstimator utility bases its estimates on group values located in the RMG database.

Instructions for Use

1. Create a text file named thermo_input.txt (or some other name of your choice) in any directory that you like. If a GATPFit folder does not already exist in this directory, make it using the following command:

   mkdir GATPFit

The text file should begin with a block to specify a PrimaryThermoLibrary, which may be left empty if desired:

PrimaryThermoLibrary:
END

Next, in the text file, create the adjacency list(s) corresponding to the molecule(s) of interest using 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 2,2,4,4-tetramethylpentane could be written as:

1 C 0 {2,S}
2 C 0 {1,S} {3,S} {4,S} {5,S}
3 C 0 {2,S}
4 C 0 {2,S}
5 C 0 {2,S} {6,S}
6 C 0 {5,S} {7,S} {8,S} {9,S}
7 C 0 {6,S}
8 C 0 {6,S}
9 C 0 {6,S}

2. At the command prompt, change directory to the location of the thermo_input.txt file and GATPFit folder and then execute the command

   $ java -classpath "%rmg%"\bin\RMG.jar ThermoDataEstimator thermo_input.txt

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

$ java -classpath "%rmg%"\bin\RMG.jar ThermoDataEstimator thermo_input.txt > thermo_output.txt

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

3. The program will read RMG’s thermodynamics database, count groups, and output the NASA polynomials in CHEMKIN format, as well as another set of values labeled ThermoData. The format for ThermoData is

   ΔH_f,298 S₂₉₈ C_p,300 C_p,300 C_p,400 C_p,600 C_p,800 C_p,1000 C_p,1500

Units are kcal/mol for ΔH_f,298 and cal/mol*K for the other quantities (entropy and heat capacity). The symmetry number (including contributions from internal rotations) will also be displayed.