The atomic tools library (atl) is a Python tool aimed at facilitating molecular dynamics simulations,
with essential computational kernels implemented in Fortran.
It is planned to provide an user-friendly tool for carrying out an easier molecular
simulation suitable for the LAMMPS package in terms of preparing input
and performing post-processing of the simulation outputs.
Features:
- Manipulation of LAMMPS molecule topologies, including modifications and merging of molecules.
- Generation of water models (such as SPC/E and TIP5P) and extraction of bond and angle information from
.xyzfile format. - Reading LAMMPS logfiles into Pandas data frames for easy analysis.
- Basic data analysis and visualization capabilities.
- Calculation of the total dipole from input structure files.
- Computation of radial distribution functions (RDF) and lateral RDF.
- Determination of density profiles.
- Calculation of average number of H-bonds and H-bond profiles.
See this example jupyter notebooks.