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[求助]
請問C原子與H原子間不正常的鍵結
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?????????????(Diamond Like Carbon)?????????????(DLC?????c??????????????x?_)??????????????S?C????1000?wH???(???^?_??????????w?? ??Щ???????????)?? ????????????? tersoff (tersoff1994)?????????? REBO2?? (??????????? AIREBO ?P?? LJ_flag ?? torsion_flag) ??????rebo2????? ?????DLC???Щ??????????h???H?????F?Щ?????????I?Y?????vmd??????????Щ?????O???box???????I?Y(??????L) ???????λ?????????????}??????F?@?N?????????I?Y??? ??????D ??????DLC ????????? ?@?e???????? ------------------------------------------------------- units metal boundary p p s dimension 3 atom_style atomic neighbor 2.0 bin neigh_modify every 5 delay 0 check yes read_data R25-diamond.txt region workpiece block -44.5 44.5 -44.5 44.5 -70 160 units box group workpiece region workpiece #region 1 block -3.0 5.0 INF 10.0 INF INF region diabound block INF INF INF INF INF -55.01 region diathermal block INF INF INF INF -55 -50.01 region dianewdun block INF INF INF INF -50 1 region dlcnewdun block INF INF INF INF 125 142 region dlcthermal block INF INF INF INF 142.01 146 region dlcbound block INF INF INF INF 146.01 INF group diabound region diabound group diathermal region diathermal group dianewdun region dianewdun group dlcnewdun region dlcnewdun group dlcthermal region dlcthermal group dlcbound region dlcbound set group diabound type 1 set group diathermal type 2 set group dianewdun type 3 set group dlcnewdun type 4 set group dlcthermal type 5 set group dlcbound type 6 group dia union diabound diathermal dianewdun group dlc union dlcnewdun dlcthermal dlcbound mass * 12.0107 region hydrogen block -44.5 44.5 -44.5 44.5 1.1 2.0 create_atoms 7 random 1000 568991 hydrogen mass 7 1 group hydro region hydrogen set group hydro type 7 group mobile union diathermal dianewdun dlcnewdun dlcthermal hydro group work union diabound diathermal dianewdun dlcnewdun dlcthermal dlcbound hydro group therm union dlcthermal diathermal pair_style rebo pair_coeff * * CH.airebo C C C C C C H compute 1 all coord/atom 1.75 compute dlcRDF dlcnewdun rdf 100 fix dlcrdf dlcnewdun ave/time 100 1 100 c_dlcRDF file dlc-tmp.rdf mode vector compute k all ke/atom compute p all pe/atom variable b atom c_k*1.602e-19/(1.5*1.3806505e-23) #temp controllers compute new3d mobile temp # Compute stress information for Atomeye visualization compute stressall all stress/atom NULL compute stress1 all reduce sum c_stressall[1] compute stress2 all reduce sum c_stressall[2] compute stress3 all reduce sum c_stressall[3] compute stress4 all reduce sum c_stressall[4] compute stress5 all reduce sum c_stressall[5] compute stress6 all reduce sum c_stressall[6] #equilibrate velocity mobile create 300 699845 temp new3d loop local# thermo 1000 minimize 1.0e-9 1.0e-9 1000000 1000000 fix 1 work nve fix 2 diabound setforce 0 0 0 fix 3 mobile langevin 300 300 0.01 699483 fix_modify 3 temp new3d fix 4 dlcbound setforce 0 0 0 dump 1 all atom 2000 dump.relax.lammpstrj# dump_modify 1 sort id thermo_style custom step temp c_new3d epair emol pe ke etotal ebond press vol c_stress1 c_stress2 c_stress3 c_stress4 c_stress5 c_stress6 thermo 1000 timestep 0.001 run 50000 undump 1 #120528modify displace_atoms dlc move 0 0 -120 units box compute 10 dlcbound reduce sum fx fy fz compute 13 diabound reduce sum fx fy fz # Setup file output (time in ps, pressure in GPa) #variable p1 equal "(ly-v_ly0)/v_ly0" variable p2 equal "-pxx/10000" variable p3 equal "-pyy/10000" variable p4 equal "-pzz/10000" variable p5 equal "-pxy/10000" variable p6 equal "-pxz/10000" variable p7 equal "-pyz/10000" variable p8 equal "pe" # Output stress and strain information to datafile for Matlab post-processing fix equil1 dlcnewdun print 1000 " ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file dlcnewdun.stress.txt screen no# ${p1} fix equil2 dianewdun print 1000 " ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file dianewdun.stress.txt screen no# ${p1} unfix 3 #fix 3 therm langevin 300 300 0.01 699483 #fix 3 dlcthermal langevin 300 300 0.01 699483 fix 3 diathermal langevin 300 300 0.01 699483 velocity dlcbound set 0 0 -0.1 units box fix 10 all ave/time 10 10 100 f_4[1] f_4[2] f_4[3] file force-dlcbound100.txt fix 11 all ave/time 50 10 500 f_4[1] f_4[2] f_4[3] file force-dlcbound500.txt fix 12 all ave/time 100 10 1000 f_4[1] f_4[2] f_4[3] file force-dlcbound1000.txt fix 13 all ave/time 500 10 5000 f_4[1] f_4[2] f_4[3] file force-dlcbound5000.txt fix 14 all ave/time 10 10 100 f_2[1] f_2[2] f_2[3] file force-diabound100.txt fix 15 all ave/time 50 10 500 f_2[1] f_2[2] f_2[3] file force-diabound500.txt fix 16 all ave/time 100 10 1000 f_2[1] f_2[2] f_2[3] file force-diabound1000.txt fix 17 all ave/time 500 10 5000 f_2[1] f_2[2] f_2[3] file force-diabound5000.txt fix 18 all ave/time 10 10 100 c_10[1] c_10[2] c_10[3] file force-dlcbound-sum.txt fix 19 all ave/time 10 10 100 c_13[1] c_13[2] c_13[3] file force-diabound-sum.txt dump 1 all custom 1000 dump.lammpstrj id type x y z c_1 c_k c_p v_b dump_modify 1 sort id dump 4 all custom 1000 dump4.lammpstrj id type x y z ix iy iz fx fy fz c_stressall[1] c_stressall[2] c_stressall[3] c_stressall[4] c_stressall[5] c_stressall[6] dump_modify 4 sort id run 100000 velocity dlcbound set 0 0 0 units box run 100000 #unload velocity dlcbound set 0 0 0.1 units box run 200000 ---------------------------------------------------  left1.jpg |
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