LAMMPS has no API document
According to this thread, LAMMPS has no API document available for developers, which is a pity! Similar discuss can be found for Gromacs here, which tells there is no API document neither. Both of them are powerful simulation codes and can be used as libraries, but apparently this is not the encouraged usage. Although in the official user manuals, extending methods are discussed more or less, but those are far from enough to fully get the ideas of the design and architecture of the sophisticated packages. People (developers) often have to turn to the mailing lists and hope to get peer help from other users, which can be misleading without the help from the original software designers. On the other hand, if complete API documents are available for the end users, I believe the community and the software itself will thrive rapidly and become much stronger.