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[求助]
cannot zero langevin force of 0 atoms
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你看这两个group里明明有原子啊？ 为什么会出现这种情况？  未命名.jpg  未命名1.jpg |
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- 【分享】尝试lammps中, 分享中...
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ddll_slsl
木虫 (正式写手)
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2楼2013-05-13 09:44:29
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dimension 3 units real boundary p p f atom_style full neighbor 3.0 bin neigh_modify delay 5 every 1 check yes read_data gufinal2-oh1.data #lattice diamond 3.5667 #region box1 cylinder z 9 16.5 3 3 18 units box #create_atoms 1 region box1 #group tip region box1 # force field pair_style hybrid reax 6.0 1 0 1.0e-6 airebo 2.5 0 0 lj/cut 10.0 pair_coeff * * reax ffield.reax 1 1 1 1 3 2 pair_coeff * * airebo CH.airebo C C C C NULL NULL pair_coeff 1 2*4 lj/cut 0.0654904 3.40 pair_coeff 2 3*4 lj/cut 0.0654904 3.40 pair_coeff 3 4 lj/cut 0.0654904 3.40 pair_coeff 2*4 5 lj/cut 0.101 3.283 pair_coeff 2*4 6 lj/cut 0.0475 3.025 pair_coeff 5 5 lj/cut 0.155402 3.166 pair_coeff 6 6 lj/cut 0.03459 2.65 # 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 3.5 -8 INF units box region th2 block INF INF 29.5 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 variable fg3x equal fcm(g3,x)#x component of the total force on group g3 variable fg3y equal fcm(g3,y) variable fg3z equal fcm(g3,z) variable vg3x equal vcm(g3,x)#x component of velocity of the center of mass of group g3 variable vg3y equal vcm(g3,y)#y 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 variable pg2x equal xcm(g2,x)#x component of position of the center of mass of group g2 variable pg2y equal xcm(g2,y)#y component of position of the center of mass of group g2 variable pg2z equal xcm(g2,z)#z component of position of the center of mass of group g2 variable vg2x equal vcm(g2,x)#x component of velocity of the center of mass of group g2 variable vg2y equal vcm(g2,y)#y component of velocity of the center of mass of group g2 #displace_atoms g3 rotate 21.27 25.45 8.08 0.0 0.0 1.0 10.0 units box #displace_atoms g3 move 0.0 0.0 0.5 units box compute temp1 g3 temp compute temp2 g3 temp/com compute temp3 g12 temp compute temp4 gthg12 temp compute temp5 gthg3 temp compute temp6 gthg3 temp/com compute cf1 g3 group/group gf12 compute ke1 g3 ke compute pe1 g3 pe/atom compute peg3 g3 reduce sum c_pe1 compute pe2 g12 pe/atom compute peg12 g12 reduce sum c_pe2 velocity gfix set 0.0 0.0 0.0 units box #velocity tip 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 10 300 699483 zero yes fix 3 gthg3 langevin 10 10 100 699483 zero yes fix_modify 3 temp temp6 #fix fnvt1 g12 nvt temp 10 10 0.1 drag 2.0 #fix fnvt2 g3 nvt temp 10 10 0.1 drag 2.0 #fix_modify fnvt2 temp temp2 #fix 2 g12 temp/berendsen 10 10 0.3 #fix 3 g3 temp/berendsen 10 10 0.3 #fix_modify 3 temp temp2 fix 4 gfix setforce 0.0 0.0 0.0 #fix ftip tip setforce 0.0 0.0 0.0 #fix ftip1 tip rigid single #relax #min_modify dmax 0.01 #minimize 1.0e-6 2.306e-7 1000 100000 #neigh_modify exclude group gfix gfix #neigh_modify exclude group tip tip timestep 1 thermo 100 thermo_style custom step temp pe ke etotal press pzz c_ke1 c_peg3 c_peg12 c_temp1 c_temp3 c_temp4 c_temp6 v_fg3x v_fg3y v_fg3z & v_pg3x v_pg3y v_pg3z v_vg3x v_vg3y c_cf1 c_cf1[1] c_cf1[2] c_cf1[3] v_pg2x v_pg2y v_pg2z v_vg2x v_vg2y thermo_modify temp temp2 dump 1 all xyz 200 gufinal2-oh.xyz dump 2 all atom 200 gufinal2-oh.lammpstrj run 50000 #Run #variable dz1 equal ramp(17,15.6) #fix fw1 all wall/harmonic zhi v_dz1 0.1 1.0 2.5 units box #fix_modify fw1 energy yes #run 30000 #fix fw1 all wall/harmonic zhi 15.6 0.1 1.0 2.5 units box #fix_modify fw1 energy yes #min_modify dmax 0.01 #minimize 1.0e-6 1.0e-8 1000 100000 #run 40000 velocity g3 set 0.001 NULL NULL sum yes units box run 100000 |
3楼2013-05-13 10:45:13
ddll_slsl
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4楼2013-05-13 10:56:46
5楼2013-05-13 11:10:32
ddll_slsl
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6楼2013-05-13 11:19:38
7楼2013-05-13 16:57:54
ddll_slsl
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8楼2013-05-13 17:02:33
9楼2013-05-13 18:58:56
gswylq
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10楼2013-10-01 22:15:41