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jmforever123新虫 (初入文坛)
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[求助]
石墨烯上的水滴的模拟 已有1人参与
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本人模拟的是石墨烯表面的水分子的运动情况，但用vmd显示后，石墨烯片总是破坏掉了，感觉z方向要使用非周期性边界条件，但是水分子有长程力作业，pppm又必须使用周期性边界条件，本人菜鸟，求大神指教。谢谢。 dimension 3 boundary p p p atom_style full read_data h2o.data pair_style hybrid lj/cut/tip4p/long 2 1 1 1 0.1546 10.0 12.0 lj/cut 10.0 tersoff pair_coeff 1 1 lj/cut/tip4p/long 0.0000 0.0000 pair_coeff 1 2 lj/cut/tip4p/long 0.0000 0.0000 pair_coeff 2 2 lj/cut/tip4p/long 0.16275 3.16435 pair_coeff 1 3 lj/cut 0.0000 0.0000 pair_coeff 2 3 lj/cut 0.3876 3.262 pair_coeff * * tersoff SiC.tersoff NULL NULL C kspace_style pppm/tip4p 1.0e-4 bond_style harmonic bond_coeff 1 450 0.9572 angle_style harmonic angle_coeff 1 55 104.52 timestep ${dt} thermo $d  graphene.png |
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10楼2016-06-16 14:36:50
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jmforever123: 金币+5, ★★★很有帮助 2016-06-14 15:19:55
感谢参与，应助指数 +1
jmforever123: 金币+5, ★★★很有帮助 2016-06-14 15:19:55
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这里有个例子，你参考一下能用不 units metal dimension 3 boundary p p f atom_style full read_data mixed-graph-water.dat neighbor 3.0 bin neigh_modify delay 0 every 1 check yes # set potential function and parameters ### Create Groups ### group hy type 2 # H_water group ox type 3 # O_water set group ox charge -0.8476 #给氢 氧原子带电 set group hy charge 0.4238 region box block INF INF INF INF INF INF units box group graphite type 1 group boxes region box ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### ### 设置氢氧原子间的作用 pair_style hybrid/overlay rebo lj/cut/coul/long 10.0 pair_coeff * * rebo ./potential/CH.airebo C NULL NULL pair_coeff 1 2 lj/cut/coul/long 0.0 0.0 # C-H pair_coeff 1 3 lj/cut/coul/long 0.013 2.71 # C-O pair_coeff 2 2 lj/cut/coul/long 0.0 0.0 # H-H pair_coeff 2 3 lj/cut/coul/long 0.0 0.0 # H-O pair_coeff 3 3 lj/cut/coul/long 0.0067 3.166 # O-O bond_style harmonic bond_coeff 1 7.669 1.0 angle_style harmonic angle_coeff 1 1.829 109.47 kspace_style pppm 1.0e-5 #final npt relaxation kspace_modify slab 3.0 thermo 1 thermo_style custom step pe etotal press temp thermo_modify norm no dump myatom all custom 500 atom.dat id group slab type 1 # graphite_slab group water type 2 3 timestep 0.0001 velocity all create 10.0 482748 dist gaussian fix freaze_slab slab move linear 0.0 0.0 0.0 #This can be useful for boundary or other atoms, whose movement can influence nearby atoms. # move style args fix zwall water wall/reflect zhi EDGE # wall/reflect face arg ... keyword value ... fix 1 all nve fix 2 all temp/rescale 10 10.0 10.0 0.02 1.0 ##温度设置为10度 # temp/rescale N Tstart Tstop window fraction fix shake_1 water shake 1e-5 500 0 b 1 a 1 # 算法固定键长键角 化学键的断裂、生成 dump 1 graphite custom 1 graphite.lammpstrj id type xs ys zs # style tol iter N constraint values constraint values dump dcd_1 all dcd 100 nve_10.dcd run 10000 write_restart restart.10.* unfix 2 unfix shake_1 undump dcd_1 fix 3 all temp/rescale 10 10.0 100.0 0.02 1.0 fix shake_2 water shake 1e-5 500 0 b 1 a 1 dump dcd_2 all dcd 100 nve_10_100.dcd run 10000 write_restart restart.10_100.* unfix 3 unfix shake_2 undump dcd_2 fix 4 all temp/rescale 10 100.0 200.0 0.02 1.0 fix shake_3 water shake 1e-5 500 0 b 1 a 1 fix shake_3 water shake 1e-5 500 0 b 1 a 1 dump dcd_3 all dcd 100 nve_100_200.dcd run 10000 write_restart restart.100_200.* unfix 4 unfix shake_3 undump dcd_3 fix 5 all temp/rescale 10 200.0 298.0 0.02 1.0 fix shake_4 water shake 1e-5 500 0 b 1 a 1 dump dcd_4 all dcd 100 nve_200_298.dcd run 10000 write_restart restart.200_298.* unfix 5 unfix shake_4 undump dcd_4 fix 6 all temp/rescale 10 298.0 298.0 0.02 1.0 fix shake_5 water shake 1e-5 500 0 b 1 a 1 dump dcd_5 all dcd 100 nve_298_298.dcd run 10000 write_restart restart.298.* |
2楼2016-06-13 19:54:50
jmforever123
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3楼2016-06-13 20:06:07
jmforever123
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4楼2016-06-14 15:17:10
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