Dear Sir:
When I encountered a problem when simulating boundary lubrication, the results showed that the alkane molecule overlapped the metal atom. I was considering setting the metal layer as a rigid body, but when the upper and lower metal layers are in contact, does this setting affect the metal? What about layer deformation? Hope you give me some guidance!
Below is my IN file and the result graph：
film
dimension 3
boundary p p f
units real
atom_style full
neighbor 2.0 multi
neigh_modify delay 5
bond_style class2
angle_style class2
improper_style class2
dihedral_style class2#
pair_style hybrid eam/fs lj/class2/coul/cut 10
read_data mixture.data
bond_coeff 1 1.53 299.67 -501.77 679.81
bond_coeff 2 1.101 345 -691.89 844.6
bond_coeff 3 1.53 299.67 -501.77 679.81
bond_coeff 4 1.101 345 -697.89 844.6
angle_coeff 1 110.77 41.453 -10.604 5.129
angle_coeff 2 107.66 39.641 -12.921 -2.4318
angle_coeff 3 112.6700 39.5160 -7.4430 -9.5583
angle_coeff 4 112.6700 39.5160 -7.4430 -9.5583
angle_coeff 5 110.77 41.453 -10.604 5.129
angle_coeff 6 112.6700 39.5160 -7.4430 -9.5583
angle_coeff 7 110.77 41.453 -10.604 5.129
angle_coeff 1 bb 3.3872 1.5300 1.1010
angle_coeff 2 bb 5.3316 1.1010 1.1010
angle_coeff 3 bb 0.0000 1.5300 1.5300
angle_coeff 4 bb 0.0000 1.5300 1.5300
angle_coeff 5 bb 3.3872 1.1010 1.5300
angle_coeff 6 bb 0.0000 1.5300 1.5300
angle_coeff 7 bb 3.3872 1.5300 1.1010
angle_coeff 1 ba 20.7540 11.4210 1.5300 1.1010
angle_coeff 2 ba 18.1030 18.1030 1.1010 1.1010
angle_coeff 3 ba 8.0160 8.0160 1.5300 1.5300
angle_coeff 4 ba 8.0160 8.0160 1.5300 1.5300
angle_coeff 5 ba 11.4210 20.7540 1.1010 1.5300
angle_coeff 6 ba 8.0160 8.0160 1.5300 1.5300
angle_coeff 7 ba 20.7540 11.4210 1.5300 1.1010
dihedral_coeff 1 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
dihedral_coeff 2 -0.1432 0.0000 0.0617 0.0000 -0.1530 0.0000
dihedral_coeff 3 0.0000 0.0000 0.0514 0.0000 -0.1430 0.0000
dihedral_coeff 4 0.0000 0.0000 0.0000 0.0000 -0.1530 0.0000
dihedral_coeff 5 0.0000 0.0000 0.0000 0.0000 -0.1530 0.0000
dihedral_coeff 6 0.0000 0.0000 0.0514 0.0000 -0.1430 0.0000
dihedral_coeff 7 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
dihedral_coeff 8 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000
dihedral_coeff 9 -0.1432 0.0000 0.0617 0.0000 -0.1530 0.0000
dihedral_coeff 10 0.0000 0.0000 0.0000 0.0000 -0.1530 0.0000
dihedral_coeff 1 mbt -14.8790 -3.6581 -0.3138 1.5300
dihedral_coeff 2 mbt -14.2610 -0.5322 -0.4864 1.5300
dihedral_coeff 3 mbt -17.7870 -7.1877 0.0000 1.5300
dihedral_coeff 4 mbt -17.7870 -7.1877 0.0000 1.5300
dihedral_coeff 5 mbt -14.8790 -3.6581 -0.3138 1.5300
dihedral_coeff 6 mbt -17.7870 -7.1877 0.0000 1.5300
dihedral_coeff 7 mbt -14.8790 -3.6581 -0.3138 1.5300
dihedral_coeff 8 mbt -14.8790 -3.6581 -0.3138 1.5300
dihedral_coeff 9 mbt -14.2610 -0.5322 -0.4864 1.5300
dihedral_coeff 10 mbt -17.7870 -7.1877 0.0000 1.5300
dihedral_coeff 1 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010
dihedral_coeff 2 ebt 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
dihedral_coeff 3 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300
dihedral_coeff 4 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300
dihedral_coeff 5 ebt 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300
dihedral_coeff 6 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300
dihedral_coeff 7 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010
dihedral_coeff 8 ebt 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300
dihedral_coeff 9 ebt 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
dihedral_coeff 10 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300
dihedral_coeff 1 at -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700
dihedral_coeff 2 at -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
dihedral_coeff 3 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700
dihedral_coeff 4 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700
dihedral_coeff 5 at 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700
dihedral_coeff 6 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700
dihedral_coeff 7 at -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700
dihedral_coeff 8 at 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700
dihedral_coeff 9 at -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
dihedral_coeff 10 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700
dihedral_coeff 1 aat -16.1640 112.6700 110.7700
dihedral_coeff 2 aat -12.5640 110.7700 110.7700
dihedral_coeff 3 aat -22.0450 112.6700 112.6700
dihedral_coeff 4 aat -22.0450 112.6700 112.6700
dihedral_coeff 5 aat -16.1640 110.7700 112.6700
dihedral_coeff 6 aat -22.0450 112.6700 112.6700
dihedral_coeff 7 aat -16.1640 112.6700 110.7700
dihedral_coeff 8 aat -16.1640 110.7700 112.6700
dihedral_coeff 9 aat -12.5640 110.7700 110.7700
dihedral_coeff 10 aat -22.0450 112.6700 112.6700
dihedral_coeff 1 bb13 0.0000 1.5300 1.1010
dihedral_coeff 2 bb13 0.0000 1.1010 1.1010
dihedral_coeff 3 bb13 0.0000 1.5300 1.5300
dihedral_coeff 4 bb13 0.0000 1.5300 1.5300
dihedral_coeff 5 bb13 0.0000 1.1010 1.5300
dihedral_coeff 6 bb13 0.0000 1.5300 1.5300
dihedral_coeff 7 bb13 0.0000 1.5300 1.1010
dihedral_coeff 8 bb13 0.0000 1.1010 1.5300
dihedral_coeff 9 bb13 0.0000 1.1010 1.1010
dihedral_coeff 10 bb13 0.0000 1.5300 1.5300
improper_coeff 1 0.0000 0.0000
improper_coeff 2 0.0000 0.0000
improper_coeff 3 0.0000 0.0000
improper_coeff 4 0.0000 0.0000
improper_coeff 5 0.0000 0.0000
improper_coeff 6 0.0000 0.0000
improper_coeff 7 0.0000 0.0000
improper_coeff 1 aa 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
improper_coeff 2 aa -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600
improper_coeff 3 aa -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700
improper_coeff 4 aa 0.1184 -1.3199 -1.3199 110.7700 110.7700 112.6700
improper_coeff 5 aa 0.2738 0.2738 -0.4825 107.6600 110.7700 110.7700
improper_coeff 6 aa -0.1729 -0.1729 -0.1729 112.6700 112.6700 112.6700
improper_coeff 7 aa -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700
pair_coeff * * eam/fs Fe_mm.eam.fs Fe NULL NULL NULL
pair_coeff 1 2 lj/class2/coul/cut 0.00172357 3.4927 10
pair_coeff 1 3 lj/class2/coul/cut 0.002521 2.7794 10
pair_coeff 1 4 lj/class2/coul/cut 0.0013844 2.7794 10
pair_coeff 2 2 lj/class2/coul/cut 0.062 3.854 10
pair_coeff 2 3 lj/class2/coul/cut 0.00005535 3.52626 10
pair_coeff 2 4 lj/class2/coul/cut 0.0000304 3.854 10
pair_coeff 3 3 lj/class2/coul/cut 0.023 2.878 10
pair_coeff 3 4 lj/class2/coul/cut 0.0000445 3.52626 10
pair_coeff 4 4 lj/class2/coul/cut 0.04 3.854 10
group Fe1 id 1:7980
group Fe2 id 7981:15960
group mixture molecule 2:1072
fix 1 all nvt temp 300 300 10
fix 2 Fe1 setforce 0 0 0
fix 3 Fe2 setforce 0 0 0
thermo_style custom step temp press density
thermo 2000
timestep 1
dump 1 all xyz 10000 sample.xyz
dump 11 all xyz 10000 cucao.xyz.*
dump_modify 11 element Fe C H C
run_style respa 2 2 pair 1 kspace 2
run 100000
reset_timestep 0
unfix 2
unfix 3
fix 4 Fe1 aveforce 0 0 0.032
fix 5 Fe2 aveforce 0 0 -0.032
run 200000
reset_timestep 0
unfix 4
unfix 5
fix 44 Fe1 setforce 0 0 0
fix 55 Fe2 setforce 0 0 0
fix 7 Fe1 move linear 0.05 0 0 units box
fix 77 Fe2 move linear -0.05 0 0 units box
compute CC C chunk/atom bin/1d z lower 2.867
fix CC C ave/chunk 1 10000 10000 CC vy fx fy fz density/mass density/number file C
compute C1 c7h16 chunk/atom bin/1d z lower 2.867
fix C1 c7h16 ave/chunk 1 10000 10000 C1 vy fx fy fz density/mass density/number file c7h16data
compute C2 Fe1 chunk/atom bin/1d z lower 1.4335
fix C2 Fe1 ave/chunk 1 10000 10000 C2 vy fx fy fz density/mass density/number file Fe1data
compute C3 Fe2 chunk/atom bin/1d z lower 1.4335
fix C3 Fe2 ave/chunk 1 10000 10000 C3 vy fx fy fz density/mass density/number file Fe2data
thermo_style custom step temp press
run 1000000
