计算材料学 上海交通大学

分子动力学实验

1. 空位形成能

2. 表面、界面能

3. 层错能

4. 晶格常数与体弹模量

5. 熔化

SJTU.CMS.

April 2012

You and Your Computer

你手机的计算能力，已经超越了NASA 1969 年拥有的计算能力的总和。NASA 用那些计算能力发射人上了月球，而你用更强的计算能力发射愤怒的小鸟去砸猪。

Linux

分子动力学五要素

1. 粒子间相互作用势

2. 初始条件

3. 边界条件

4. 求解牛顿运动方程

5. 粒子运动轨迹

LAMMPS Molecular Dynamics Simulator

AtomEye: atomistic configuration viewer

Basic Linux Commands

NAME SYNOPSIS DESCRIPTION

pwd pwd print name of working directory mkdir mkdir□haha make directory

cd cd□haha change directory

cd□..upper directory

cd back home

gedit gedit□a edit a file

cat cat□a concatenate files

ls ls list

cp cp□a□b copy file a to file b cp□–r□A□B copy a file folder

rm rm□b remove

[Tab]

*

1. 空位形成能

Point Defects: Vacancy

Model system: Cu, fcc, a0= 3.61 Å

Tasks:

1. generate a point defect within an

equilibrium lattice

2. calculate the formation energy

Model system Cu

Initial conditions fcc lattice

defect-free state, vacancy

Supercell N, PBCs Interatomic potentials EAM (Cu) Ensembles Minimize

(1) Copy the file folder to home and then get into it. $cp□-r□share/md□.

$cd□md

$cd□1_vacancy

$ls

(2) What is the setup in input file

$gedit□in.vacancy

(3) Run LAMMPS

$lmp□-in□in.vacancy

(4) After running, view the configuration

$ A.i686□a0.cfg

(5) View the result data

$cat□data

Atomeye命令

Tab 键切换视角k, Alt + H, Alt + +/-改变颜色Delete / Insert下一帧/上一帧PgUp/ PgDn原子变大/变小滚轮放大/缩小↑↓ ← → 方向键旋转

q关闭

units metal boundary p p p atom_style atomic

lattice fcc 3.61

region box block 0 6 0 6 0 6create_box 1 box create_atoms 1 box pair_style eam/alloy pair_coeff * * jin_copper_lammps.setfl Cu timestep 0.005

variable E equal pe variable N equal atoms compute pe all pe/atom

dump 1 all cfg 1 a*.cfg id type xs ys zs c_pe run 0

fix extra all print 1 "pefect lattice, 0K: atoms = $N, energy = $E“

region centerpoint block 3 3.05 3 3.05 1 1.05

delete_atoms region centerpoint

run 0

fix extra all print 1 "^ an atom deleted, 0K: atoms = $N, energy = $E"

周期边界条件指定fcc 晶体box 大小Cu 的EAM 势删除一个原子

Vacancy formation energy：

1 pefect lattice, 0K: atoms = 864, energy = -3015.371512

2 an atom deleted, 0K: atoms = 863, energy = -3010.585469

3 after minimization: atoms = 863, energy = -3010.624033

2. 表面、界面能

Planar Defects: Surface and Grain Boundary

Model system: Cu, fcc, a0= 3.610 Å

Tasks:

1.Surface energies of (111) and (100);

2.Grain boundary energies