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Version: v0.5.0 (unreleased)

配置文件

MISA-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 MISA-MD 配置文件的部分示例:

# <a href='https://yaml.org'>yaml</a> configure file for MISA-MD application,
# writen by <a href='mailto:genshenchu@gmail.com'>genshen</a>"

title: "MISA-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
types:
- name: Fe
mass: 55.845
weight: 97
- name: Cu
mass: 63.546
weight: 2
- name: Ni
mass: 58.6934
weight: 1

output:
atom_dump:
presets:
- name: my_dump
region: [ 25.0, 25.0, 25.0, 80.4, 80.4, 80.4 ]
mode: "copy"
file_path: "misa_mdl.{}.out"
by_frame: true
- name: collision_dump
mode: "copy"
file_path: "before_collision.{}.out"
by_frame: true
thermo:
interval: 0
logs:
logs_mode: "console"
logs_filename: ""

stages:
- name: rescale
step_length: 0.001
steps: 4
dump:
use: my_dump
every_steps: 2
rescale:
t: 600
every_steps: 2

- name: collision
step_length: 0.0001
steps: 8
dump:
use: collision_dump
every_steps: 1
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 MISA-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/misamd  -c /path/of/config.yaml

或者:

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