in文件——生成水盒子的快捷方法

1.in文件

# TIP4P/2005 water system

variable temp index 300.0
variable filename1 index nve

units real
atom_style full
boundary p p p

pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 10.5 8.0
pair_modify mix arithmetic tail yes
kspace_style pppm/tip4p 1.0e-6
bond_style harmonic
angle_style harmonic

read_data tip4p-2005.data
replicate 20 10 10 #复制扩胞为20a*10b*10c = 62*31*31，6000 atoms，2000个水分子

pair_coeff 1 1 0.1852 3.1589
pair_coeff * 2 0 0

bond_coeff 1 0 0.9572 # o*-h*
angle_coeff 1 0 104.5200 # h*-o*-h*

mass 1 15.9994
mass 2 1.008

set type 1 charge -1.1128 #TIP4P/2005 的水模型，data文件中也要相应修改 pair、bond、angle系数
set type 2 charge 0.5564

neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes

write_data waterbox.data #输出

################################# nve equilibrium ############################
#模拟过程中，水分子的键长和健角使用shake方法保持不变
fix WT all shake 0.0001 100 0 b 1 a 1 #约束bond、angle和原子质量，设置刚性

velocity all create 300.0 4928459 rot yes dist gaussian
variable density equal mass(all)*10/(6.0221417930*vol)
timestep 1
thermo 1000
thermo_style custom step temp lx ly lz press pxx pyy pzz vol epair ebond eangle pe ke etotal density v_density
dump 1 all atom 1000 ${filename1}.lammpstrj

fix 1 all nve
run 100000

write_restart ${filename1}.restart
write_data ${filename1}.data

2.另外准备一个元胞的data

#LAMMPS 'data.' description

3 atoms
2 bonds
1 angles

2 atom types
1 bond types
1 angle types

0.0 3.1 xlo xhi
0.0 3.1 ylo yhi
0.0 3.1 zlo zhi

Atoms

1 1 1 -1.1128 1.55000 1.55000 1.50000
2 1 2 0.5564 1.55000 2.30695 2.08588
3 1 2 0.5564 1.55000 0.79305 2.08588

Bonds

1 1 1 2
2 1 1 3

Angles

1 1 2 1 3