配置文件

Crystal MD 从 v0.4.0 开始，使用 yaml 格式开始作为配置文件的格式（v0.2.0 和 v0.3.x 使用 toml 格式)。

1.示例

以下展示了Crystal MD配置文件的部分示例：

# <a href='https://yaml.org'>yaml</a> configure file for Crystal-MD application,# writen by <a href='mailto:genshenchu@gmail.com'>genshen</a>"
title: "Crystal-MD Configure File"version: "0.4.0"contributors:  original_author: "BaiHe"  original_author_email: "baihe_ustb@163.com"  developers: ["BaiHe<baihe_ustb@163.com>", "ChuGenshen<genshenchu@gmail.com>"]  organization: "USTB"
simulation:  phasespace: [50, 50, 50]  cutoff_radius_factor: 1.96125  lattice_const: 2.85532  def_timesteps_length: 0.001
potential:  type: "setfl"  file_path: "FeCuNi.eam.alloy"
creation:  create_phase: true  create_seed: 466953  create_t_set: 600  alloy:    create_seed: 1024    ratio:      Fe: 97      Cu: 2      Ni: 1
output:  dump:    atoms_dump_mode: "copy"    atoms_dump_file_path: "crystal_mdl.{}.out"    origin_dump_path: "crystal_mdl.origin.out"    atoms_dump_interval: 10    by_frame: true  thermo:    interval: 0  logs:    logs_mode: "console"    logs_filename: ""
stages:  - name: rescale    step_length: 0.001    steps: 4    rescale:      t: 600      every_steps: 2
  - name: collision    step_length: 0.0001    steps: 8    set_v:      collision_step: 2      lat: [2, 2, 2, 0]      energy: 6.8      direction: [1.0, 1.0, 1.0]
  - name: run    step_length: 0.001    steps: 6

2.使用配置文件

你可以在运行Crystal MD程序时，通过命令行参数指定配置文件路径，程序能够读取配置文件，以进行后续模拟，例如：

mpirun -n 4 /path/of/CrystalMD  -c /path/of/config.yaml

或者：

mpirun -n 4 /path/of/CrystalMD  --conf=/path/of/config.yaml