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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!

  Reminder: If you are compiling LAMMPS using make, ensure that you run "make yes-NEP" before the final compilation. For cmake, please add "PKG_NEP=on" to enable NEP, along with your other -D flags during the configuration step.

Use the NEP-LAMMPS interface

• atom_style can be atomic and full

• units must be metal

• Specify the pair_style in the same way as other potentials in LAMMPS (the first 2 arguments must be * * so as to span all atom types). For example, if you have a NEP model NEP_HBCN.txt, and your data file just have element carbon, you can set

  pair_style nep   
  pair_coeff * *  NEP_HBCN.txt C
  

  Firstly, we should set pair_style to nep, showed in the first line. Then we need set the NEP potential file and atom types by the command pair_coeff. Two asterisks * * mean every atom type will be set an element type or NULL. NULL means this potential doesn't consider the atom type. In this example, we set atom type 1 in LAMMPS data file to element C in NEP potential file.

• The interface also supports multi-element system and hybrid potentials. 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, the next setting is allowed:

  pair_style hybrid/overlay nep nep ij/cut 1.0
  pair_coeff * * nep 1 NEP_PdCuNiP.txt Cu   Ni   NULL
  pair_coeff * * nep 2 NEP_PdCuNiP.txt NULL NULL Pd
  pair_ceoff 1*2 3 lj/cut 1.0 1.0
  

  The pair_style should be set hybrid/overly or other hybrid methods in LAMMPS. The hybrid potentials should be set after hybrid method. Then, in command pair_coeff we need set potential name again to identify which potential is setting for and the number of the potential if more than one. Here, we set two NEP potentials. The first one just computes the NEP potential between atom type 1 Cu and 2 Ni, and of themselves. The second computes NEP potential of atom type 3 Pd itself.

• 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.