Usually an AutoChem mechanism, model, and assimilation system is set up by running a shell script that defines the species list and the Pick and RoC control files. In the example included with the distribution this script is in the AutoChemV8/Code/ directory and is called qroc-methane. This script is executed from a terminal window by typing:
./qroc-methane
If you want all the documents to be run through LaTeX as well then use the shell script
./qroc-methane-latex
This script is run once only when a new mechanism is to be set up. It only needs to be run again if your species list changes, or if the reaction databases set in the Pick control file is changed. When it's execution is complete the model is ready for compilation.
The example included is for Mac OS X using the IBM xlf fortran compiler. AutoChem has already been run on more than 10 platforms including Mac OS X, various variants of Linux, supercomputers, and windows machines. To port it to your system edit the script. Replace all occurences of makefile.pick-mac and makefile.roc-mac and with the name of two makefiles you will need to create for your system. It is probably better to use different names so the original is always there for you to look at. Edit the makefiles and set the correct compiler by changing the compiler from FC = xlf95 to whatever compiler you use on your system. Also edit the flags, if in doubt the following will probably work: FFLAGS = -c.
Note: For Pick and RoC double precision is not needed. However for the model it is. So for the box model compilation make sure that the double precision flags are set (often an option like -r8). If you are interested in other versions of the code, such as the Kalman filter data assimilation please contact David.Lary@umbc.edu.