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1、 1 LAMMPS 简要使用说明简要使用说明 目录目录 lammps 简要使用说明简要使用说明 1 LAMMPS 介绍 . 4 文件 4 1. 系统初始化. 4 units lj/real/metal/si/cgs 4 atom_style angle/atomic/bond/charge/dipole/dpd/ellipsoid/full/granular/molecular/hybrid 5 atom_modify map/first 5 dimension N ,N=2/3 5 boundary x y z, default=boundary p p p . 5 newton flag/
2、flag1 flag2 . 5 communicate single/multi group/cutoff 5 processors Px Py Pz 6 2. 创建模拟晶胞 . 6 lattice none/sc/bcc/fcc/hcp/diamond/sq/sq2/hex/custom scale keyword values . 6 region ID style block/cylinder/prism/sphere/union/intersect args keyword value 6 group ID region/type/id/molecule/subtract/union/
3、intersect. 6 create_box N regionID 7 create_atoms type box/region/single args keyword values . 7 delete_atoms group/region/overlap/porosity args . 7 read_restart file/read_date file. 7 set atom/group/region ID keyword values 8 displace_atoms groupID move/ramp/random args keyword value . 8 displace_b
4、ox groupID parameter args . keyword value . 8 change_box ortho/triclinic 9 replicate nx ny nz 9 3. 设置 9 mass I value . 9 velocity groupID create/set/scale/ramp/zero args keyword value . 9 timestep dt . 9 reset_timestep N 10 neighbor skin bin/nsq/multi 10 neigh_modify keyword values 10 4. 输出 10 dump
5、ID groupID bond/dcd/xtc/xyz/custom N file args . 10 dump_modify dumpID format/scale/image/flush/unwrap/every/precision/region/thresh values . 11 undump dumpID . 11 thermo_style one/multi/custom(args) 11 thermo_modify lost/norm/flush/line/format/temp/press value 12 thermo N . 12 print string . 12 res
6、tart N root . 12 write_restart file 13 echo none/screen/log/both . 13 2 log filename 13 5. FIX 13 fix ID groupID style args 13 系综相关. 14 力和速度的控制 . 15 计算特定量. 16 模拟晶胞的控制 . 17 模拟过程的控制 . 18 unfix fix-id 18 6. COMPUTE . 18 compute ID groupID style args . 18 compute ID groupID ackland/atom 19 compute ID gr
7、oupID centro/atom . 19 compute ID groupID coord/atom cutoff . 19 compute ID groupID damage/atom 19 compute ID groupID displace/atom fixID 19 compute ID groupID group/group group2ID . 20 compute ID groupID ke 20 compute ID groupID ke/atom . 20 compute ID groupID pe (keyword=pair/bond/angle/dihedral/i
8、mproper/kspace) 20 compute ID groupID pe/atom (keyword=pair/bond/angle/dihedral/improper) 20 compute ID groupID pressure tempID keyword=ke/pair/bond/angle/dihedral/improper/kspace/fix . 20 compute ID groupID reduce mode=sum/min/max input1 input2 20 compute ID groupID stress/atom (keyword= ke/pair/bo
9、nd/angle/dihedral/improper/kspace/fix) 20 compute_modify computeID keyword value 20 compute ID groupID temp 21 compute ID groupID temp/com 21 compute ID groupID temp/deform . 21 compute ID groupID temp/partial xflag yflag zflag . 21 compute ID groupID temp/ramp vdim vlo vhi dim clo chi keyword value
10、 21 compute ID groupID temp/region regionID . 21 uncompute compute-ID . 21 7. 势函数 21 pair_style . 21 pair_style tersoff . 22 kspace_style 23 kspace_modify 23 pair_write itype jtype N r/rsq/bitmap inner outer file keyword Qi Qj 23 8. 运行 23 run N upto/start/stop/pre/post/every values. 23 run_style ver
11、let/respa(args) . 23 minimize etol ftol maxiter maxeval 24 min_style cg/sd . 24 min_modify dmax 0.2 (default=0.1) . 24 temper . 24 clear . 24 9. 其他 24 3 variable name delete/index/loop/world/universe/uloop/equal/atom 24 next variables 25 jump file label . 25 label string . 25 if value1 operator valu
12、e2 then command1 else command2 26 include filename 26 shell cd/mkdir/mv/rm/rmdir 26 10. 模拟方法论 . 27 缺陷的生成. 27 晶格常数. 27 迁移 27 表面 27 立方晶系弹性常数 . 22 4 LAMMPS 介绍介绍 LAMMPS= Large-scale Atomic/Molecular Massively Parallel Simulator. http:/lammps.sandia.gov Sandia National Laboratories 命令行选项：-in file 输入文件；-l
13、og file 输出文件；-screen file 屏幕输出文件；-echo style，输入文件内容是否输 出到输出文件和屏幕，style=none/screen/log/both (default=log)。 特点：免费，C+，并行，集成大量势函数 并行：mpirun -nolocal -machinefile node -np $ncpu /opt/lammps/lmp_mpi -in in -screen log.screen 1.0e-6bars reduced LJ pressure, P* = P sigma3 / epsilon 粘度 Poise Poise Pa*s Pois
14、e reduced LJ viscosity, eta* = eta sigma3 / ep- silon / tau 电荷 multiple of electron charge (+1.0 is a pro- ton) multiple of electron charge (+1.0 is a proton) C statcoulombs or esu reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)1/2 偶极 子 charge*Aug charge*Aug C*m statcoulcm = 1018 debye
15、reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma3 epsilon)1/2 5 电场 强度 V/Aug V/Aug V/m statvolt/cm or dyne/esu force/charge, where E* = E (4 pi perm0 sigma epsilon)1/2 sigma / epsilon 1Aug=1e-10 m=1e-8 cm 1ps=1e-12 s, 1fs=1e-15 s, 1ps=1000 fs 1eV=23.0445512 Kc/mol, 1ev=3.8276e-23 Kc, 1eV=
16、1.60217733e-19 J, 1eV=1.60217733e-12 erg, 1mol=6.0221367e23 1J=0.23884 c, 1erg=1e-7 J, 1Kc=4186.8 J, 1Kc=4.1868e10 erg, 1Kc=2.6126e22 eV 1atm=1.01325 bar =101325 Pa, 1bar=100000 Pa atom_style angle/atomic/bond/charge/dipole/dpd/ellipsoid/full/granular/molecular/hybrid default=atom_style atomic 定义使用什么样的原子类型，决定了原子的属性，该命令应该在其他命令前。 style = angle/atomic/bond/charge/dipole/dpd/ellipsoid/full/granular/molecular/hybrid atom_modify map/first 定义并行计算如何求最近邻
