谈谈分子模板，手册中提供了几种例子，我们这里用水的作为例子说明，剩下的我找了一些贴出来便于大家参考，欢迎交流！
# Water molecule. SPC/E model.
3 atoms ## 分子模板中的原子总数
2 bonds ## 分子模板中的bond总数
1 angles ## 分子模板中的角总数
Coords
# 原子ID x y z
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
# 原子ID type
1 1
2 2
3 2
Charges
# 原子ID charge
1 -0.8472
2 0.4236
3 0.4236
Bonds
#ID type atom1 atom2
1 1 1 2
2 1 1 3
Angles
#ID type atom1 atom2 atom3
1 1 2 1 3
Shake Flags
# ID flag
1 1 ### 0 ：不属于fix shake 作用的
2 1 ### 1 ：shake two bonds and the angle they form
3 1 ### 2 ：2-atom SHAKE cluster with a single bond
### 3 : 3-atom SHAKE cluster with two bonds
### 4 : 4-atom SHAKE cluster with three bonds
Shake Atoms
1 1 2 3 flag = 1 ： ID a（中心原子） b c （组成的角连接的其他两个atom）
2 1 2 3 flag = 2： ID a（ID of atom in bond with the the lowest ID） b（ID of atom in bond with the the highest ID）
3 1 2 3 flag = 3： ID a（ID of central atom） b,c = IDs of other two atoms bonded to the central atom.
flag = 4： ID a（ID of central atom） b,c = IDs of other three atoms bonded to the central atom.
Shake Bond Types
If flag = 1, a,b,c are listed, where a = bondtype of the bond between the central atom and the first non-central atom (value b in the Shake Atoms section), b = bondtype of the bond between the central atom and the 2nd non-central atom (value c in the Shake Atoms section), and c = the angle type (1 to Nangletypes) of the angle between the 3 atoms.
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
#ID 1-2原子紧邻 1-3 1-4
1 2 0 0 ## 对于atom1 也就是o来说
2 1 1 0
3 1 1 0
##
## atom1
## o
## / \
## atom2 h h atom3
##
## atom1 atom2就是1-2紧邻，atom1 atom3同理；--> 两个相邻原子间隔了1个键
## atom2和atom3呢？三个原子间隔了2个键
## 显然 1-2原子紧邻 2个 ，1-3，1个，1-4，0个
Special Bonds
1 2 3 ### ID 1-2紧邻 1-3
2 1 3 ### 1 2 3 #原子atom1 1-2紧邻的是原子2；1-3紧邻的是原子3
3 1 2 ### 2 1 3
完整代码：
# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2
水分子dimer结构
# dimer molecule
2 atoms
1 bonds
Coords
1 0 0 0
2 1 0 0
Types
1 2
2 3
Bonds
1 1 1 2
Special Bond Counts
1 1 0 0
2 1 0 0
Special Bonds
1 2
2 1
dimer granular molecule
# dimer granular molecule
5 atoms
Coords
1 0 0 0
2 1 0 0
3 2 0 0
4 2 1 0
5 2 2 0
Types
1 1
2 1
3 1
4 1
5 1
Diameters
1 1.0
2 1.0
3 1.0
4 1.0
5 1.0
Masses
1 0.5
2 0.5
3 0.5
4 0.5
5 0.5
CO2 molecule file. TraPPE model.
# CO2 molecule file. TraPPE model.
3 atoms
2 bonds
1 angles
Coords
1 0.0 0.0 0.0
2 -1.16 0.0 0.0
3 1.16 0.0 0.0
Types
1 1
2 2
3 2
Charges
1 0.7
2 -0.35
3 -0.35
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2
LAMMPS data file created for rigid body molecule template
LAMMPS data file created for rigid body molecule template
5 atoms
2.3388800000000005 mass
6.002239704473936 4.99 4.989999999999999 com
116.79265620480001 144.26721336320003 144.26721336320006 -70.05220681600004 -70.05220681600002 -58.238345888000005 inertia
Coords
1 5 5 5
2 5.1 5.0 5.0
3 5.2 5.0 5.0
4 6.2 5.0 5.0
5 7.2 5.0 5.0
Types
1 1
2 1
3 1
4 1
5 1
Diameters
1 1.0
2 0.9
3 1.2
4 1.2
5 1.0
Masses
1 0.5235987755982988
2 0.3817035074111599
3 0.9047786842338602
4 0.9047786842338602
5 0.5235987755982988
这里我给出一个in文件的例子，随机建立2000个水分子
###################
# initial setting #
###################
#----------------------------------------------------------#
variable x equal 50
variable y equal 50
variable z equal 50
#----------------------------------------------------------#
units metal
dimension 3
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
##############
# create box #
##############
#----------------------------------------------------------#
region box block 0 $x 0 $y 0 $z units box
create_box 2 box &
bond/types 1 &
angle/types 1 &
extra/bond/per/atom 2 &
extra/angle/per/atom 1 &
extra/special/per/atom 2
molecule water H2O.txt
create_atoms 0 random 2000 12345 box mol water 12345 units box
#----------------------------------------------------------#
# setting mass
mass 1 16.0
mass 2 1.0
bond_coeff 1 19.51 0.9572
angle_coeff 1 2.40 104.52
write_data 1
