Doxygen
From PHASTA Wiki
Doxygen is a documentation program that is used relatively widely for documenting large code bases. It can be used for C, C++, Fortran, Python, and plenty more. It is widely supported and has been used for quite awhile.
Find out more detailed information at Doxygen's website or at it's documentation site.
Running Doxygen
Note: To run Doxygen on the PHASTA Group Machines, you must be on viz003
and have a gcc compiler loaded into your environment.