Structure and topology generation

Non-reactive force fields for molecular dynamics simulations typically consist of non-bonded and bonded interaction terms. The latter require an explicit specification of the interatomic bonding topology, i.e. which atoms are involved in bond, angle and dihedral interactions. matscipy provides efficient tools to generate this topology for an atomic structure based on matscipy’s neighbour list, and then assign the relevant force field parameters to each interaction term. matscipy also includes the input and output routines for reading and writing the corresponding control files for LAMMPS.

• Setups for non-reactive simulations with LAMMPS
• Topology building for LAMMPS non-reactive MD simulations of amorphous carbon
  • Assignment of the different atom types
  • Generation of the bonding topology and LAMMPS input files