OpenKIM is an interatomic potential repository and an online framework for making molecular simulations reliable, reproducible, and portable.

以上说明来自网址:OpenKIM

前提

已安装LAMMPS

安装

查看安装方法

在LAMMPS的文件夹/home/peachrl/LAMMPS/lammps-3Mar20/lib/kim中,阅读README,得知将通过cmake进行安装。

安装cmake

  1. CMake下载安装包。

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  2. 将安装包解压,进入cmake-3.18.0-rc2文件夹。

  3. 终端输入./bootstrap

    • 若出现Could NOT find OpenSSL问题,根据提示安装OpenSSL :apt-get install libssl-dev
  4. make -j4

  5. sudo make -j4 install

  6. 查看安装情况cmake --version

image-20200628154236953

安装kim-api

  1. 进入LAMMPS中/home/peachrl/LAMMPS/lammps-3Mar20/lib/kim文件夹。

  2. 下载kim-api-2.1.3。(有不同版本,具体见Obtaining KIM Models

  3. 解压到当前文件夹。

  4. $ cd kim-api-2.1.3

  5. $ mkdir build && cd build

  6. $ cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-2.1.3

    • 若出现No CMAKE_Fortran_COMPILER could be found.,安装gfortran:$ sudo apt install gfortran
  7. $ make -j4

  8. $ make -j4 install

  9. $ printf "${PWD}/installed-kim-api-2.1.3" > ./kim-prefix.txt

  10. 现在可以删除压缩包和安装包了

    $ cd ../../
    $ rm -rf kim-api-2.1.3
    $ rm -rf kim-api-2.1.3.txz

    build LAMMPS with the KIM package installed

  • 进入/home/peachrl/LAMMPS/lammps-3Mar20/src文件夹,重新make ubuntu(之前make过的):
    $ make yes-kim
    $ sudo make ubuntu -j4
  • 移动和改个名:
    $ mv lmp_ubuntu /home/peachrl/LAMMPS/bin/lmp4RMSPm.kim

    添加path

export PATH=/home/peachrl/LAMMPS/lammps-3Mar20/lib/kim/installed-kim-api-2.1.3/bin:$PATH

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使用

==测试算例:LAMMPS自带的算例/home/peachrl/LAMMPS/lammps-3Mar20/examples/reax/CHO,将其改为使用OpenKIM。==

安装所需的KIM Model

在OpenKIM网站上找到需要的势:Sim_LAMMPS_ReaxFF_ChenowethVanDuinGoddard_2008_CHO__SM_584143153761_001

$ source kim-api-activate 
$ kim-api-collections-management install user Sim_LAMMPS_ReaxFF_ChenowethVanDuinGoddard_2008_CHO__SM_584143153761_001

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改写in文件

# KIM potential for CHO system
# .....

kim_init  Sim_LAMMPS_ReaxFF_ChenowethVanDuinGoddard_2008_CHO__SM_584143153761_001  real

read_data   data.CHO
kim_interactions H C O

neighbor    2 bin
neigh_modify    every 10 delay 0 check no

fix     1 all nve
fix             3 all temp/berendsen 500.0 500.0 100.0

timestep    0.25

#dump       1 all atom 30 dump.reax.cho

run     3000

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运行

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