LAMMPS is designed to be a fast, parallel engine for molecular dynamics (MD) simulations. As such, LAMMPS itself provides only a modest amount of functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS does not:
Our group has also written and released a separate toolkit called Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Thus it addresses several of the above bullets. Pizza.py is written in Python and is available for download from this page.
LAMMPS non-feature details are discussed in this section of the LAMMPS documentation.
Features that LAMMPS does not currently have, but which are planned for future releases, are discussed in this section of the LAMMPS documentation.
A few tools for pre- and post-processing tasks, including a simple (but fast) visualization tool called xmovie are provided as part of the LAMMPS package; they are described in this section of the LAMMPS documentation. Many people use other codes or write their own tools for these tasks.
Alternative MD codes that can be used in place of or in conjunction with LAMMPS, as well as visualization packages that can be used with LAMMPS output data are listed on this page.