N, O, Si, S, and Cl atoms. The network adjusts automatically when elements or species are disabled.

Most reaction rates come from the UMIST 2000 database [@Le-Teuff.Y00The-UMIST-database-for-astrochemistry-1999] as updated for the Leiden workshop and described by @Roellig2007. We also predict the freeze-out of , , and  on grains, using the data given in @Hasegawa1993. Both time-steady and time-dependent chemical evolution calculations are possible.

The effects of cosmic rays and suprathermal secondary electrons can be very important in molecular regions [@1968ApJ...152..971S] and are treated as described by @FerlandMushotzky1984 and @FerlandFabianEtAl2009. Non-thermal particles can both excite and dissociate the gas. @Ferland1994 and @FerlandFabian2002 describe the treatment of chemistry in an X-ray dominated filaments in cool-core galaxy clusters. @Shaw2008 describe an application to the local ISM.

The treatment of  is fully self consistent with its surroundings [@Shaw2005]. Formation on grain surfaces is treated using the derived grain properties and the @Cazaux.S04H2-Formation-on-Grain-Surfaces catalysis rates. Destruction by photoexcitation in electronic states is treated by computing the radiation field at each point. This includes line self shielding, the attenuation by continuous opacity sources such as grains, photoelectric opacity of the heavy elements, and Rayleigh scattering, and emission by the cloud itself.  , the resonance lines, and 