NetGen

NetGen and Associated Components

The mechanism generation software was developed using C/C++ code on a Linux I686 machine and compiled using GNU GCC 2.96. This code was built on top of the original automated mechanism generation code already developed. The new code involves use of c++ code to enhance the capability of incorporating experimental data during reaction mechanism generation and interface with the computational quantum chemistry package, Gaussian98. More advanced data structures such as hash tables have been utilized to increase efficiency in looking up reactions and properties from a list.

While building the code several executables have been put together to test various stages of the development process. These executables also serve as useful programs for looking up properties, generating isodesmic reactions, and other tasks that will be useful to practitioners in the field. These are referred to as standalones and are described in more detail below. The final software includes the functions of each standalone and is part of the single executable named “atmos”. The actual mechanism generation software and its use is also detailed below. To calculate any group additivity parameters, the user will need to have a copy of the National Institute of Standards (NIST) group additivity software. This has not been included in this software package.

The software package can be downloaded individually and put together manually by downloading the directory structure followed by each individual link for the standalones and the atmos software discussed below. The full software for implementing atmospheric chemistry can also be downloaded at one time and contains all the standalones and the atmos software.

Standalones

The following standalone executables have been created to fulfill specific individual tasks. They can be run independent of the atmos program. Each individual executable and its task is listed below. All the following files should be downloaded and placed in the src/qz_code/standalones directory.

(1) phandler: This executable takes the name of a .dat file (including its path) as its argument on the command line. It then prints out four options to the user. After the user types in his/her choice, phandler proceeds to find the molecule property for the molecule characterized by the .dat file.

(2) pq: Executable pq provides an interface for the user to type in the .dat file name for a molecule and then will search in databases or run quantum chemical calculations using Gaussian to get the thermochemical properties for the given molecule. It then asks the user if there are any other molecules to be queried. It keeps running until the user chooses not to conduct any further queries.

(3) tomdl: When you need to create .mdl and/or .config file(s) for a molecule, the .dat file name can be passed to the tomdl executable. This program will ask for the choice of one of the semi-empirical methods PM3 or AM1. It then writes an .mdl file (with the name of the molecule suffixed by .mdl) to the directory called “mdlfiles”, and a .config file (with the name of the molecule suffixed by .config) to the directory called “configfiles”.

(4) toinputs: Executable toinputs is very similar to tomdl except that it writes one more file to enable a query to the group additivity database. This file is called “SAndPInput.sp” and saved in the directory called “spfiles”.

(5) runqmmc: In addition to writing the .mdl and .config files for a given molecule, this executable runs qmmc to get the thermochemical properties from Gaussian98.

(6) iso: Executable iso constructs an isodesmic reaction for the molecule defined by the given .dat file. It then prints out the isodesmic reaction in terms of what the products are and their stoichiometric numbers.

(7) isop: In addition to constructing an isodesmic reaction for the target molecule as iso does, isop runs qmmc to get the heat of formation and entropy data for each molecule involved in the constructed isodesmic reaction. It calculates the heat/entropy of reaction based on the qmmc results. Then it searches the group additivity database for the heat of formation and entropy data for all the molecules except the target one. With the group additivity data and the heat/entropy of reaction, the program calculates the heat of formation and entropy for the target molecule.

(8) rxnp: This executable will calculate the reaction properties for a given reaction. If it finds all the molecule properties needed, it will perform the calculations. For each molecule whose properties are unknown, it will construct an isodesmic reaction for that molecule and then calculate the molecule properties for it. If properties are available for all the molecules involved in the reaction, the reaction properties will be calculated. If it cannot get the properties for any of the molecules, it will fail in reaction property calculation.

Atmospheric Chemistry Software

The executable for the software is called atmos. This should be downloaded and placed in the main directory. This executable takes .dat input files which are located in a user's Data directory. Depending on what kind of mechanism generation method is to be used, an input file which contains the list of .dat files to be used as input is specified. The name of this file is Names.dat.CAndR for carbon- and rank-based generation and Names.dat.RateBasedReactive for rate-based generation. The basic command line arguments that are used for running the program are listed below:

-c N: the carbon-count criterion which only allows a species with fewer than the specified number of carbons to react

-x N: the oxygen-count criterion which allows species with fewer than the specified number of oxygens to react

-r N: the rank criterion which does not allow species above a maximum rank N to react

-s N: the number of species in the initial species reactive core for rate-based mechanism generation

-d N: the number of species for which to take reactions from the initial reactions library

-m1: to calculate the rate constants for each reaction and the thermodynamic properties for each species

-a value: this flag can be used alone to specify a particular solar zenith angle or with the -j flag to specify a different spectra

-i filename: the input file containing initial concentrations, temperature, and threshold information for rate-based mechanism generation

The rate-based generation inputfiles are located in the inputfiles directory for several smog chamber experiments. Sample spectral data for Carter's blacklight chambers is also located in the inputfiles directory.

Downloadable Files

Complete download:
Entire software	full.tar.gz
For Individual downloading:
Directory structure	dir_struct.tar.gz
phandler	phandler.tar.gz
pq	pq.tar.gz
tomdl	tomdl.tar.gz
toinputs	toinputs.tar.gz
runqmmc	runqmmc.tar.gz
iso	iso.tar.gz
isop	isop.tar.gz
rxnp	rxnp.tar.gz
atmos	atmos.tar.gz