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Day4作业
作业
作业
Zitong Xu
更新于 2024-08-13
推荐镜像 :LAMMPS:23Jun2022-dp2.1.5-latest
推荐机型 :c2_m4_cpu
双击即可修改
代码
文本
[1]
%%writefile in.diffusion
#---------------Initialize Simulation -------------------------
units lj # 使用LJ单位制
dimension 2 # 使用二维空间
boundary p p p # 使用周期性边界条件
atom_style atomic # 使用普通原子
variable t equal 0.5 # 定义系统温度
#-------------- Create Atoms Intial Conditions----------------
lattice sq 1.0 # 使用简单正方晶格,晶格常数为1.0
region box block 0 100 0 100 -0.5 0.5 # 定义盒子的范围
create_box 2 box # 在盒子中创建两种类型的原子
create_atoms 1 random 2500 12345 box # 随机创建2500个类型为1的原子
create_atoms 2 random 2500 54321 box # 随机创建2500个类型为2的原子
mass 1 1.0 # 设置原子1质量
mass 2 3.0 # 设置原子2质量,并按照作业要求设定为不同粒子
#---------------- Define Simulation Parameters----------------
pair_style hybrid lj/cut 2.5 soft 5.0 # 使用hybrid混合两种势
pair_coeff 1 1 lj/cut 1.0 1.0 2.5 # 类型为1的原子之间为LJ势
pair_coeff 2 2 lj/cut 1.0 1.0 2.5 # 类型为2的原子之间为LJ势
pair_coeff 1 2 soft 5.0 # 类型为1和2的原子之间为soft势
#--------------- Run MD Simulation ----------------------------
compute eng all pe/atom # 计算每个原子的势能
compute eatoms all reduce sum c_eng # 计算所有原子的总势能
thermo_style custom step temp epair etotal press c_eatoms # 定义输出的热力学量
thermo 1000 # 每1000步输出一次热力学量
dump id all atom 100 dump.lammpstrj # 每100步将所有原子的状态输出到dump.lammpstrj文件中
minimize 1e-4 1e-6 1000 10000 # 防止随机生成的原子重叠能量过大
velocity all create $t 87287 # 赋予所有原子初始速度
fix nvt all nvt temp $t $t 0.01 # 使用NVT系综,温度为t,时间常数为0.01
run 50000 # 运行50000步
Writing in.diffusion
代码
文本
[2]
!lmp -i in.diffusion
Warning:
This LAMMPS executable is in a conda environment, but the environment has
not been activated. Libraries may fail to load. To activate this environment
please see https://conda.io/activation.
LAMMPS (23 Jun 2022 - Update 1)
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 /opt/deepmd-kit-2.1.5/lib/deepmd_lmp
Lattice spacing in x,y,z = 1 1 1
Created orthogonal box = (0 0 -0.5) to (100 100 0.5)
  1 by 1 by 1 MPI processor grid
Created 2500 atoms
  using lattice units in orthogonal box = (0 0 -0.5) to (100 100 0.5)
  create_atoms CPU = 0.002 seconds
Created 2500 atoms
  using lattice units in orthogonal box = (0 0 -0.5) to (100 100 0.5)
  create_atoms CPU = 0.000 seconds
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 38 38 1
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair soft, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Setting up cg style minimization ...
  Unit style    : lj
  Current step  : 0
Per MPI rank memory allocation (min/avg/max) = 7.075 | 7.075 | 7.075 Mbytes
   Step          Temp          E_pair         TotEng         Press         c_eatoms   
         0   0              5.0637488e+15  5.0637488e+15  1.5191246e+16  5.0637488e+15
      1000   0             -2.2238562     -2.2238562      2.4537066     -2.2238562    
Loop time of 5.22828 on 1 procs for 1000 steps with 5000 atoms

100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
    5.06374880431566e+15  -2.22328314271219  -2.22385624354953
  Force two-norm initial, final = 1.5674736e+22 38.101405
  Force max component initial, final = 1.0813852e+22 8.3143077
  Final line search alpha, max atom move = 0.005428131 0.045131151
  Iterations, force evaluations = 1000 1586

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.8049     | 3.8049     | 3.8049     |   0.0 | 72.78
Neigh   | 1.131      | 1.131      | 1.131      |   0.0 | 21.63
Comm    | 0.032366   | 0.032366   | 0.032366   |   0.0 |  0.62
Output  | 0.051384   | 0.051384   | 0.051384   |   0.0 |  0.98
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.2087     |            |       |  3.99

Nlocal:           5000 ave        5000 max        5000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1045 ave        1045 max        1045 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 387
Dangerous builds = 0
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Setting up Verlet run ...
  Unit style    : lj
  Current step  : 1000
  Time step     : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.075 | 6.075 | 6.075 Mbytes
   Step          Temp          E_pair         TotEng         Press         c_eatoms   
      1000   0.5           -2.2238562     -1.7239562      2.7036566     -2.2238562    
      2000   0.4949906     -2.0884178     -1.5935262      1.8208201     -2.0884178    
      3000   0.49742189    -2.1764669     -1.6791445      1.0956713     -2.1764669    
      4000   0.49767735    -2.1690414     -1.6714636      0.86460694    -2.1690414    
      5000   0.50159325    -2.1670865     -1.6655936      0.68350406    -2.1670865    
      6000   0.50213256    -2.1394782     -1.637446       0.53366013    -2.1394782    
      7000   0.51577911    -2.1306671     -1.6149911      0.50028334    -2.1306671    
      8000   0.50077102    -2.1061593     -1.6054884      0.42328939    -2.1061593    
      9000   0.49530855    -2.0985198     -1.6033103      0.32179694    -2.0985198    
     10000   0.49619446    -2.072605      -1.5765098      0.32620387    -2.072605     
     11000   0.48840769    -2.058302      -1.569992       0.2292908     -2.058302     
     12000   0.49943046    -2.0418714     -1.5425409      0.22001855    -2.0418714    
     13000   0.50017682    -2.0114187     -1.5113419      0.2442835     -2.0114187    
     14000   0.49424865    -2.0088018     -1.514652       0.17439343    -2.0088018    
     15000   0.50714146    -1.9721381     -1.4650981      0.18736809    -1.9721381    
     16000   0.50343834    -1.9698293     -1.4664917      0.15999903    -1.9698293    
     17000   0.50068879    -1.9453976     -1.4448089      0.16554229    -1.9453976    
     18000   0.51411346    -1.950727      -1.4367164      0.15088806    -1.950727     
     19000   0.50688169    -1.9443484     -1.4375681      0.18801815    -1.9443484    
     20000   0.50041875    -1.9265457     -1.426227       0.14969453    -1.9265457    
     21000   0.5145349     -1.9274468     -1.4130148      0.13929095    -1.9274468    
     22000   0.49953013    -1.9317925     -1.4323623      0.1648356     -1.9317925    
     23000   0.50656224    -1.9305855     -1.4241246      0.15276985    -1.9305855    
     24000   0.49243139    -1.9164986     -1.4241657      0.15298029    -1.9164986    
     25000   0.5033437     -1.9202001     -1.4169571      0.13307823    -1.9202001    
     26000   0.49878801    -1.9172587     -1.4185704      0.13139242    -1.9172587    
     27000   0.49377212    -1.9197226     -1.4260492      0.16187951    -1.9197226    
     28000   0.49606137    -1.9280161     -1.4320539      0.12520829    -1.9280161    
     29000   0.49867061    -1.9026841     -1.4041133      0.18282532    -1.9026841    
     30000   0.49605919    -1.9076036     -1.4116436      0.19854189    -1.9076036    
     31000   0.48730354    -1.9081954     -1.4209894      0.16014957    -1.9081954    
     32000   0.4961979     -1.8997865     -1.4036878      0.14549662    -1.8997865    
     33000   0.49926113    -1.8891543     -1.389993       0.13228389    -1.8891543    
     34000   0.49053736    -1.9008015     -1.4103622      0.13725469    -1.9008015    
     35000   0.50081009    -1.8936883     -1.3929784      0.16566779    -1.8936883    
     36000   0.50127899    -1.8850226     -1.3838439      0.15614537    -1.8850226    
     37000   0.48588156    -1.8921728     -1.4063884      0.15600445    -1.8921728    
     38000   0.50381926    -1.8839801     -1.3802616      0.12077484    -1.8839801    
     39000   0.49882167    -1.9057592     -1.4070373      0.15219859    -1.9057592    
     40000   0.49836124    -1.9051593     -1.4068977      0.10461306    -1.9051593    
     41000   0.48770979    -1.8904725     -1.4028602      0.13075343    -1.8904725    
     42000   0.49377673    -1.8873972     -1.3937193      0.12483865    -1.8873972    
     43000   0.49910008    -1.8931826     -1.3941823      0.11410788    -1.8931826    
     44000   0.49671487    -1.8899772     -1.3933617      0.1210732     -1.8899772    
     45000   0.50455286    -1.8991947     -1.3947428      0.14018836    -1.8991947    
     46000   0.50126495    -1.8772986     -1.3761339      0.084781182   -1.8772986    
     47000   0.50066613    -1.8975293     -1.3969633      0.12742051    -1.8975293    
     48000   0.51034155    -1.8870678     -1.3768284      0.14531825    -1.8870678    
     49000   0.49790812    -1.884302      -1.3864935      0.14077895    -1.884302     
     50000   0.50261033    -1.8829514     -1.3804416      0.13353632    -1.8829514    
     51000   0.49860333    -1.8747559     -1.3762523      0.065797304   -1.8747559    
Loop time of 48.9533 on 1 procs for 50000 steps with 5000 atoms

Performance: 441236.546 tau/day, 1021.381 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 30.091     | 30.091     | 30.091     |   0.0 | 61.47
Neigh   | 11.147     | 11.147     | 11.147     |   0.0 | 22.77
Comm    | 0.53752    | 0.53752    | 0.53752    |   0.0 |  1.10
Output  | 2.5576     | 2.5576     | 2.5576     |   0.0 |  5.22
Modify  | 4.1913     | 4.1913     | 4.1913     |   0.0 |  8.56
Other   |            | 0.429      |            |       |  0.88

Nlocal:           5000 ave        5000 max        5000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1077 ave        1077 max        1077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4723
Dangerous builds = 2279
Total wall time: 0:00:55
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