The Master Chemical Mechanism
FACSIMILE is designed to efficiently solve the differential equations involved in modelling the kinetics of chemical systems. FACSIMILE is only one of a wide variety of differential equation solvers available, some of which are free to download from the web. You may be used to a different type of solver and the MCM is available in a variety of formats. A user friendly MS Windows version of FACSIMILE can be purchased to create, modify and use models of chemical systems. The features include model construction wizards which can be used to get started and create simple models. More complex models can be written in the FACSIMILE smart editor or the text editor of your choice.
As an example of a FACSIMILE program using the MCM you can study a model which simulates a chamber experiment: the oxidation of the aromatic compound p-xylene. The file pxyl_030702.fac contains the model for an experiment performed in the EUPHORE chamber during the 2002 EXACT campaign. Open this file in word pad and scroll through the model. Keep in mind that:
The first instructions in the program open a set of files in which the output of the simulation will be recorded. Similar instructions can be used to open any files containing data you want to read into the model. The next, very important step is to declare all of the species names (global VARIABLES) in the model. A VARIABLE is something whose time profile is determined by a differential equation. PARAMETER names, e.g. rate constant names, temperature etc… should also be declared. A PARAMETER is an auxiliary quantity whose time profile is not part of the coupled differential equations. A PARAMETER may be constant during integration or may be calculated as a function of TIME, VARIABLEs or other PARAMETERs.
Each section of the model is defined by various routines in the program:
At the end of the file is the instruction to BEGIN the integration and the STOP command to terminate the program. For more detailed information on writing FACSIMILE models look at the user guide in the FACSIMILE manual.
Once the model file is set up, simply open FACSIMILE, and then open the model using the "open existing FACSIMILE model" button and press "run loaded FACSIMILE model" button. (NOTE: you are advised to run FACSIMILE models from a folder on the C drive. If the path and file name are too long, FACSIMILE will truncate the file name and will fail to find the model).
Running the model creates the output files in the same directory as the model. If you run this same model again the files will be overwritten. In order to keep them, copy them to another folder or change the output file names for each model run.
FACSIMILE has options to view the output as text or in a plot. However, we will want to compare the model result with the chamber data so it is more convenient to plot it in MS Excel or a similar package (e.g. Origin).Go to section 2