NEP_CPU

What does this repository contain?

• A standalone C++ implementation (a class called NEP3) of the neuroevolution potential (NEP) as introduced in the GPUMD package (https://github.com/brucefan1983/GPUMD). We stress that there is no external dependence. Even though the class name is NEP3, the implementation works for all versions of NEP.

• An interface of the NEP3 class to the CPU version of LAMMPS (https://github.com/lammps/lammps). It can be run with MPI.

The standalone C++ implementation of NEP

• The NEP3 C++ class is defined in the following three files:

  • src/nep.h
  • src/nep.cpp
  • src/dftd3para.h

• There is an option to use tables to speed up the calculations for the radial functions in NEP. To enable it, one can change line 20 of src/nep.h:

// #define USE_TABLE_FOR_RADIAL_FUNCTIONS

• The following folders contain some testing code and results:

  • test/
  • test_dftd3/

• The NEP3 C++ class is used as an engine powering the following Python packages:

  • calorine: https://gitlab.com/materials-modeling/calorine
  • PyNEP: https://github.com/bigd4/PyNEP
  • somd: https://github.com/initqp/somd

The NEP-LAMMPS interface

Build the NEP-LAMMPS interface

• step 1: Copy the files in src/ into interface/lammps/USER-NEP/ such that you have the following files in interface/lammps/USER-NEP/:

  • nep.h
  • nep.cpp
  • dftd3para.h
  • pair_NEP.h
  • pair_NEP.cpp
  • install.sh

• Step 2: Now you can copy the USER-NEP/ folder into YOUR_LAMMPS_PATH/src/ and start to compile LAMMPS in your favorite way. Good luck!

Use the NEP-LAMMPS interface

• atom_style can be atomic and full

• units must be metal

• Specify the pair_style in the following way:

  pair_style nep YOUR_NEP_MODEL_FILE.txt  # YOUR_NEP_MODEL_FILE.txt is your NEP model file (with path)
  pair_coeff * *                          # This format is fixed

• For multi-element system, the atom types must be carefully set. Take a NEP model NEP_PdCuNiP.txt as an example. In this NEP model file, the first line is nep3 4 Pd Cu Ni P. Then in your LAMMPS input file, you must set

  • Pd atoms to type 1
  • Cu atoms to type 2
  • Ni atoms to type 3
  • P atoms to type 4

• Some atom types can be missing in the simulated system. For example you can use the above NEP model to simulate a CuNi binary alloy. It is important to make sure to still set Cu atoms to type 2 and Ni atoms to type 3. In this case, atom types 1 and 4 are missing.

• One can hybrid NEP with other potentials in LAMMPS, for example lj/cut

  pair_style hybrid lj/cut 1.0 nep YOUR_NEP_MODEL_FILE.txt  
  pair_coeff 1*4 1*4 nep YOUR_NEP_MODEL_FILE.txt
  pair_coeff 1*5 5 lj/cut 1.0 1.0

  This will set the interaction of elements of type 1-5 and elements of type 5 to lj/cut, as well as lj/cut/coul/long.

• If you want to calculate the heat current correctly, use the following command to get the 9-component per-atom virial:

  compute 1 all centroid/stress/atom NULL

Citation

• If you directly or indirectly use the NEP3 class here, you are suggested to cite the following paper:

  • Zheyong Fan, Yanzhou Wang, Penghua Ying, Keke Song, Junjie Wang, Yong Wang, Zezhu Zeng, Ke Xu, Eric Lindgren, J. Magnus Rahm, Alexander J. Gabourie, Jiahui Liu, Haikuan Dong, Jianyang Wu, Yue Chen, Zheng Zhong, Jian Sun, Paul Erhart, Yanjing Su, Tapio Ala-Nissila, GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations, The Journal of Chemical Physics 157, 114801 (2022).

• If you use the LAMMPS interface of the NEP3 class, a proper citation for LAMMPS is also suggested.