Estimating Species Transport Properties

The TransportDataEstimator utility produces group additivity-based transport property estimates - in particular, the Lennard-Jones sigma and epsilon parameters - without running RMG. As with the transport estimates used by RMG, the TransportDataEstimator utility bases its estimates on group values located in the RMG database.

Instructions for Use

1. Create a text file named input.txt in any directory that you like. The text file should begin with a block to specify the desired Database. The next field should be the PrimaryTransportLibrary, which may be left empty if desired:

   Database: RMG_database
   
   PrimaryTransportLibrary:
   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:

   Tetramethylpentane_2244
   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 input.txt file and then, if you are using a unix-based operating system, execute the command

   $ java -classpath $RMG/bin/RMG.jar TransportDataEstimator input.txt > RMG.log

   If you are using a Windows operating system you can instead run the batch file TransportDataEstimator.bat. Either double-click it or at the command propmpt type:

   > TransportDataEstimator.bat

   The program’s output is automatically written to tran.dat

3. The program will read RMG’s transport database, count groups, and output the species estimated transport properties in CHEMKIN format.

The first entry is the species name (as supplied by you, assuming the number of characters is less than 16). The next entry is the RMG estimate on whether the species is an atom (0), linear (1), or nonlinear (2). The next two entries are the RMG estimates for the Lennard-Jones epsilon and sigma parameters; the units of epsilon are Kelvin while the units of sigma are Angstroms. The next three entries - the dipole moment, polarizability, and rotational relaxation collision number at 298 K - are default values and are not estimated by RMG; these entries are included so that the output tran.dat is CHEMKIN-readable. All remaining information is comments regarding how RMG estimated the Lennard-Jones properties, including the estimated critical properties and which groups in the RMG_databases/transport_groups were matched.