nemd_example

Simple examples for non-equilibrium molecular dynamics (NEMD) simulation with LAMMPS package. Muller-Plathe method is employed.

Prerequisite

• python>=3.0
• ase
• pubchempy

How to Use

To make LAMMPS input scripts:

cd ~/example
PYTHONPATH=$PYTHONPATH:../nemd
python mk_graphite_nemd.py -n 4 -m 3

To make LAMMPS input scripts and run jobs:

cd .../example
sh mkneme.sh
cd ./{created_directory}
lmp_mpi < nemd0.in > log0.txt
lmp_mpi < nemd1.in > log1.txt

To analys results after the calculations:

sh ../analyze_{direction_of_heat_flow (in/out)}.sh

Citation

If you use these scripts, please cite them with:

• M. Ohnishi et al., Phys. Rev. B 95, 155405 (2017).