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changzhangyong木虫 (小有名气)
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[求助]
Lammps 模拟硅的单轴拉伸边界上出现不正常的原子 求解？
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最近学习Lammps，仿一网站写了in 文件，发现晶向为x:111，y:1-10，z:11-2时,通过ovito观察data或cfg文件，x和z方向边界上有不正常的原子，如下图，把晶向设为x:100，y:010，z:001就不会出现，不知为什么，求各位大神指导。 in文件如下 # Input file for uniaxial compressive loading of single crystal silicon # Mark Tschopp, November 2010 # ------------------------ INITIALIZATION ---------------------------- units metal dimension 3 boundary p p p atom_style atomic variable latparam equal 5.442 # ----------------------- ATOM DEFINITION ---------------------------- lattice diamond ${latparam} orient x 1 1 1 orient y 1 -1 0 orient z 1 1 -2 region whole block 0 12 0 12 0 12 create_box 1 whole create_atoms 1 region whole # ------------------------ FORCE FIELDS ------------------------------ pair_style tersoff pair_coeff * * Si-3.tersoff Si neighbor 0.3 bin neigh_modify delay 5 mass 1 28.0855 write_data Si.0.data # ------------------------- SETTINGS --------------------------------- compute csym all centro/atom 12 compute peratom all pe/atom ###################################### # EQUILIBRATION minimize 1.0e-8 1.0e-8 10000 10000 write_data Si.1.data reset_timestep 0 timestep 0.001 velocity all create 300 12345 mom yes rot no fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 # Set thermo output thermo 1000 thermo_style custom step lx ly lz press pxx pyy pzz pe temp dump 2 all cfg 2000 dump.relaxtion_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz dump_modify 2 element Si # Run for at least 10 picosecond (assuming 1 fs timestep) run 100000 unfix 1 undump 2 # Store final cell length for strain calculations variable tmp equal "ly" variable L0 equal ${tmp} print "Initial Length, L0: ${L0}" ###################################### # DEFORMATION reset_timestep 0 fix 1 all npt temp 300 300 1 x 0 0 1 z 0 0 1 drag 1 variable srate equal 1.0e9 variable srate1 equal "v_srate / 1.0e12" fix 2 all deform 1 y erate ${srate1} units box remap x # Output strain and stress info to file # for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] # p2, p3, p4 are in GPa variable strain equal "(ly - v_L0)/v_L0" variable p1 equal "v_strain" variable p2 equal "-pxx/10000" variable p3 equal "-pyy/10000" variable p4 equal "-pzz/10000" fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Silicon_tension_def1.txt screen no # Use cfg for AtomEye dump 1 all cfg 2000 dump.comp_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz dump_modify 1 element Si # Display thermo thermo 1000 thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press restart 10000 Si.*.inp run 2000000 ###################################### # SIMULATION DONE print "All done"  111.png |
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3楼2017-12-10 19:24:19
2楼2017-12-10 19:05:38
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