This project has reached the end of its development as a LAMMPS force field typing library. Feel free to browse the code, but please check out lammps_interface if you want a library to automatically generate LAMMPS input files for molecular dynamics simulations. This library is mainly developed for MOFs and supports several force fields such as UFF, UFF4MOF, Dreiding, BTWFF.
Topology analysis and force field assignment for Lammps simulation package.
Python 3.5 is required with additional libraries listed in requirements.txt file.
You can install by cloning the repository and installing requirements as follows:
git clone https://github.com/WilmerLab/lammps-data-file.git`
cd lammps-data-file
pip install -r requirements.txtFile loading and saving are handled using IPMOF library which utilizes ASE python library. Any format supported by ASE can be used to load and save files.
To determine topology, bonds, angles, and dihedrals can be calculated for a given structure.
Bonds are extrapolated using covalent radii calculated by Pyykkö et al. and a skin distance of 0.45 Å.
For periodic structures bonds that asdasd the boundary can be extrapolated using unit cell vectors. This information is required for Lammps simulations.
Angles are determined using bond list. For each bond pair that shares an atom a 3-element tuple is listed with common atom index in the middle, small index first and large index last.
Dihedrals are determined using bond list. For a given bond two other bonds that share one of the atoms in that bond are selected. If those bonds also share an atom dihedral is discarded as that means it's a closed structure. Otherwise a 4-element tuple is listed as using two atoms of the original bond in the middle in same order and adding smaller index first and larger index last.
A combination of UFF and UFF4MOF force field is used for assigning force field parameters.
Lammps input files and data files can be created with UFF parameters for a given structure.