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in文件:
dimension 3
units metal
boundary p p f
atom_style full
neighbor 3.0 bin
neigh_modify delay 5 every 1 check yes
read_data gufinal2.data
# force field
pair_style hybrid airebo 2.5 0 0 lj/cut 10.0
pair_coeff * * airebo CH.airebo C C C C
pair_coeff 1 2*4 lj/cut 0.00284 3.40
pair_coeff 2 3*4 lj/cut 0.00284 3.40
pair_coeff 3 4 lj/cut 0.00284 3.40
# define region before define group
region rfix block INF INF INF INF INF -8 units box
region r1 block INF INF INF INF -8 -4.5 units box
region r2 block INF INF INF INF -4.5 -1 units box
region r3 block INF INF INF INF -1 INF units box
region th1 block INF INF INF 2 -8 INF units box
region th2 block INF INF 31 INF -8 INF units box
group gfix region rfix
group g1 region r1
group g2 region r2
group g3 region r3
group gth1 region th1
group gth2 region th2
group gth union gth1 gth2
group gthg12 subtract gth g3
group gthg3 subtract gth gthg12
group g12 union g1 g2
group gf12 union gfix g12
# compute and velocity
compute temp6 gthg3 temp/com
variable vg3x equal vcm(g3,x)#x component of velocity of the center of mass of group g3
variable pg3x equal xcm(g3,x)#x component of position of the center of mass of group g3
variable pg3y equal xcm(g3,y)#y component of position of the center of mass of group g3
variable pg3z equal xcm(g3,z)#z component of position of the center of mass of group g3
velocity gfix set 0.0 0.0 0.0 units box
velocity g12 create 10 4928459 rot yes dist gaussian units box
velocity g3 create 10 4928459 rot yes dist gaussian units box
# fixes
fix 1 all nve
fix 2 gthg12 langevin 10 10 0.3 699483 zero yes
fix 3 gthg3 langevin 10 10 0.1 699483 zero yes
fix_modify 3 temp temp6
fix 4 gfix setforce 0.0 0.0 0.0
#relax
min_modify dmax 0.01
minimize 1.0e-6 1.0e-8 1000 100000
neigh_modify exclude group gfix gfix
timestep 0.001
thermo 100
thermo_style custom step v_pg3x v_pg3y v_pg3z v_vg3x
dump 1 all xyz 200 gufinal2.xyz
dump 2 all atom 200 gufinal2.lammpstrj
run 50000
velocity g3 set 1.00 NULL NULL units box sum yes
run 100000
盒子尺寸:
0.000000000 85.2168 xlo xhi
0.000000000 34.4332 ylo yhi
-8.500000000 18.257102924 zlo zhi
模拟的是碳纳米管在石墨烯上运动,z方向原子不会丢失。
只改 boundary p p f 这句, v_pg3x v_pg3y v_pg3z v_vg3x 结果不一样。
修改data文件里的 -8.500000000 18.257102924 zlo zhi 使盒子尺寸稍微变化一点,结果也不一样。 |
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