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做高分子模拟拉伸试验，链始终不断 已有3人参与
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我用lammps来模拟PETG的拉伸试验，无论这个程序跑多久，erate值是多少，链始终拉不断。即使在ovito中观察到链已经被拉到足够长，他还是不断。所以我的问题就是怎么才能把它拉断。下面是我的源文件： variable project index "PETG" # project name variable project index "petg" # project name variable source index ../build # data directory variable params index ../build # parameter directory variable temperature index 300 # system temperature variable tdamp index 100 # temperature damping variable dielectric index 1 # medium dielectric variable kappa index 4 # electrostatics kappa variable cutoff index 9.5 # standard cutoff variable charge_cutoff index 9.5 # charge cutoff variable precision index 0.001 # kspace precision variable lseed index 723853 # langevin seed variable vseed index 1486234 # velocity init seed variable tequil index 50000 # equilibration time variable trun index 10000000 # run time variable frestart index 0 # 0: equil, 1: restart variable dtrestart index 100000 # delta restart time variable dtdump index 100000 # delta dump time variable dtthermo index 1000 # delta thermo time variable timestep index 0.5 # integration time step variable tfreq index 10 # profile sampling freq variable nsample index 1000 # profile conf sampling variable dtime equal ${tfreq}*${nsample} # profile dtime variable restart index ${params}/${project}.restart # New Variables for output variable p1 equal "time" variable p2 equal "vol" variable p3 equal "pe" variable p4 equal "temp" variable p5 equal "etotal" variable p6 equal "density" variable p7 equal "mol" if "${frestart} != 0" then & "variable data index ${restart}" & else & "variable data index ${project}.data" & # LAMMPS atomistic input script echo screen units real atom_style full # Interaction potential definition pair_style lj/class2/coul/long ${cutoff} ${charge_cutoff} bond_style harmonic special_bonds lj/coul 0 0 1 if "${frestart} != 0" then "read_restart ${data}" else "read_data ${data}" include ${project}.params # Integration conditions (check) timestep ${timestep} kspace_style pppm/cg ${precision} dielectric ${dielectric} fix mom all momentum 100 linear 1 1 1 angular # Set thermo output thermo 1000 thermo_style custom step pe etotal temp time vol density # Calculate the mean squared displacement for Multiple chunks of atoms compute cc1 all chunk/atom molecule compute msd1 all msd/chunk cc1 #fix msd1 all ave/time 1000 1 1000 c_msd1 ######################################################### # Equilibration # ######################################################### # STAGE1 NVT from 1000 to 300 K reset_timestep 0 timestep ${timestep} #velocity all create ${temperature} 1231 fix 1 all nvt temp 1000 300 100 drag 0.1 run 5000 unfix 1 # STAGE2 NPT from 300K to 300K fix 1 all npt temp 300 300 100 iso 0 0 1000 drag 0.1 run 5000 unfix 1 # Output file fix def1 all print 1000 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6} ${p7}" file equilibration.txt screen no dump 1 all cfg ${dtdump} equi.dump.* mass type xs ys zs id mol q x y z mol #dump_modify 1 element o_2 ho2 oh c hc c1 c_1 o_1 cp c_0 ho ############################################### ############################################### variable simname equal PETG variable equisteps equal 50000 variable thermosteps equal 100 variable strain_rate equal 1e-5 ############################################### # Deformation reset_timestep 0 thermo ${thermosteps} timestep 0.5 fix 1 all npt temp 300 300 25 y 0.0 0.0 500 z 0.0 0.0 500 nreset 1000 fix 2 all deform 1 x erate ${strain_rate} units box remap x variable tmp equal "lx" variable L0 equal ${tmp} variable strain equal "(lx - v_L0)/v_L0" variable p1 equal "step" variable p2 equal "dt" variable p3 equal "pe" variable p4 equal "ke" variable p5 equal "etotal" variable p6 equal "v_strain" variable p7 equal "-pxx/10000*1.01325" variable p8 equal "-pyy/10000*1.01325" variable p9 equal "-pzz/10000*1.01325" variable p10 equal "lx" variable p11 equal "ly" variable p12 equal "lz" variable p13 equal "press" variable p14 equal "pxy" variable p15 equal "pxz" variable p16 equal "pyz" variable p17 equal "temp" variable t2 equal "epair" variable t3 equal "ebond" variable t4 equal "eangle" variable t5 equal "edihed" fix def1 all print 100 "${p1} ${p6} ${p7} ${p8} ${p9} ${p10} ${p11} ${p12} ${p13} ${p14} ${p15} ${p16} ${p17}" file PETG_npt.def1.txt screen no title "step v_strain pxx pyy pzz lx ly lz press pxy pxz pyz temp" fix def2 all print 100 "${p1} ${t2} ${t3} ${t4} ${t5}" file PETG_npt.def2.txt screen no fix myprint all print 100 "${p1} ${p2} ${p3} ${p4} ${p5}" file PETG_npt.engergy.txt screen no title "step dt pe ke etotal" dump 2 all custom 10000 dump_npt.mole.* id type mol fx fy fy mass x y z thermo_style custom step dt pe ke etotal pxx pyy pzz lx ly lz epair ebond eangle edihed run 20000 write_restart ${project}.restart2 write_data data.* print "All Done!" 我问过我的导师，他说可以用一下fix bond/react来试一下，可是我发现那个指令需要拓扑结构（molecule指令）。 （语句表达比较混乱，望见谅） |
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