1. Lammps 安装-简单运行

从lammps官网下载windows版本的程序：https://packages.lammps.org/windows.html，在Installing LAMMPS on Windows 标题下点击“64-bit Windows download area”，下载程序，我下载的是“LAMMPS-64bit-Python-latest-MPI.exe”，双击程序即可安装。

后面说在windows上并行运算LAMMPS，需要安装MPICH2，点击官网“mpich2-1.4.1p1-win-x86-64.msi”，下载后双击即可安装。

在安装目录下有文件夹Examples，其中是运行案例，拷贝Examples/peptide文件夹到桌面，启动命令行，进入peptide文件夹，输入：lmp -pk omp 8 -sf omp -in in.peptide.lmp；

C:\Users\li\Desktop\peptide>lmp -pk omp 8 -sf omp -in in.peptide.lmp
LAMMPS (28 Mar 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
Loaded 1 plugins from D:\software\lammps\LAMMPS 64-bit 28Mar2023-MPI with Python\plugins
set 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0
  special bond factors coul:  0        0        0
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.005 seconds
  read_data CPU = 0.063 seconds
Finding SHAKE clusters ...
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.001 seconds
84 atoms in group peptide
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long/omp, perpetual
      attributes: half, newton on, omp
      pair build: half/bin/newton/omp
      stencil: half/bin/3d
      bin: standard
Setting up Verlet run ...
  Unit style    : real
  Current step  : 0
  Time step     : 2
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        7
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 22.54 | 22.54 | 22.54 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005
PotEng   =     -6372.3766 E_bond   =        16.5572 E_angle  =        36.3726
E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945
E_coul   =     26772.2646 E_long   =    -33907.9271 Press    =      -837.0112
------------ Step             50 ----- CPU =     0.192885 (sec) -------------
TotEng   =     -5247.5537 KinEng   =      1132.4000 Temp     =       281.4745
PotEng   =     -6379.9537 E_bond   =        12.2118 E_angle  =        31.7365
E_dihed  =        18.8145 E_impro  =         2.3611 E_vdwl   =       658.1785
E_coul   =     26804.4441 E_long   =    -33907.7003 Press    =     -1331.7946
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.111     7.80613e-07        9
Bond:    6   0.997     1.06181e-06        6
Bond:    8   1.08      6.20292e-07        7
Bond:   10   1.111     6.23284e-07        8
Bond:   12   1.08      2.67996e-07        9
Bond:   14   0.96      0                  1
Bond:   18   0.957201  5.3796e-06      1280
Angle:  31   104.52    0.000502278      640
------------ Step            100 ----- CPU =      0.39917 (sec) -------------
TotEng   =     -5257.9979 KinEng   =      1078.0553 Temp     =       267.9663
PotEng   =     -6336.0532 E_bond   =        14.4829 E_angle  =        43.4429
E_dihed  =        15.2569 E_impro  =         2.3160 E_vdwl   =       708.3273
E_coul   =     26786.6829 E_long   =    -33906.5621 Press    =      -648.6819
------------ Step            150 ----- CPU =     0.613116 (sec) -------------
TotEng   =     -5287.2799 KinEng   =      1098.6028 Temp     =       273.0737
PotEng   =     -6385.8827 E_bond   =        17.4925 E_angle  =        32.8594
E_dihed  =        15.1624 E_impro  =         1.6522 E_vdwl   =       736.9675
E_coul   =     26717.2655 E_long   =    -33907.2821 Press    =      -333.1830
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     2.18698e-07        9
Bond:    6   0.997     1.50562e-07        6
Bond:    8   1.08      6.57498e-08        7
Bond:   10   1.111     5.54188e-07        8
Bond:   12   1.08      1.98839e-07        9
Bond:   14   0.96      0                  1
Bond:   18   0.957201  3.59627e-06     1280
Angle:  31   104.52    0.000388336      640

命令解释：
-pk omp 8：使用多线程进行计算；
-sf omp：启用了多线程后，还必须在LAMMPS中选择启用了多线程的样式；
-in in.peptide.lmp：lammps的输入文件；