lammps胶体输出的日志文件

LAMMPS (7 Aug 2019)

Big colloid particles and small LJ particles

units lj
atom_style sphere
dimension 2

lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10 x,y,z方向的晶格间距
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5) 一个垂直正交的box
1 by 1 by 1 MPI processor grid 1×1×1 MPI处理器网格 单线程运算
create_atoms 1 box
Created 900 atoms
create_atoms CPU = 0.000734329 secs

set group all type/fraction 2 0.96 23984
861 settings made for type/fraction 39个colloid 861个solvent

set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass

velocity all create 1.44 87287 loop geom

multi neighbor and comm for efficiency

neighbor 1 multi
neigh_modify delay 0
comm_modify mode multi

colloid potential

pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5

fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d

#dump 1 all atom 1000 dump.colloid

#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5

#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5

thermo_style custom step temp epair etotal press vol
thermo 1000

timestep 0.005

run 50000
Neighbor list info … 邻域列表信息
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5 主列表截止距离
ghost atom cutoff = 13.5 镜像原子截止距离
binsize = 1.75, bins = 172 172 6 bin模拟盒子划分为若干bins，小箱子的尺寸与截断半径有关，利用小箱子构建邻域列表，箱子大小和xyz方向个数
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes每MPI通道内存分配
Step Temp（温度） E_pair（相互作用能）TotEng（总能量） Press（压力） Volume （体积）
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9572809 -0.00036743274 1.9547388 0.017982269 98935.161
2000 2.068567 -0.0010518227 2.0652168 0.019466739 96307.439
3000 2.1787472 0.0045846363 2.180911 0.029249545 68560.31
4000 2.1979309 0.0017234058 2.1972121 0.048831814 42699.657
5000 2.1541368 0.0068842503 2.1586276 0.07471981 28571.492
6000 2.111318 0.0024189699 2.1113911 0.091799665 21611.61
7000 2.078952 0.0060036925 2.0826458 0.1163485 17868.764
8000 2.0644858 0.0046356539 2.0668276 0.12915961 15516.79
9000 2.0550606 0.0061855134 2.0589627 0.14904895 13860.769
10000 2.0330017 0.025290725 2.0560335 0.17633992 12549.63
11000 2.0375798 0.019721674 2.0550375 0.21088857 11447.056
12000 2.0441411 0.015774575 2.0576444 0.21642751 10486.01
13000 2.0450352 0.012187773 2.0549507 0.22801307 9736.5468
14000 2.0310192 0.017214942 2.0459775 0.26631268 9155.57
15000 2.0372941 0.013988097 2.0490185 0.26904975 8593.0723
16000 2.0317823 0.024301045 2.0538258 0.32296842 8105.8641
17000 2.0404395 0.014004183 2.0521765 0.28844629 7693.8625
18000 2.0253783 0.026482368 2.0496103 0.33892867 7337.2926
19000 1.9993858 0.054582837 2.0517471 0.37056996 7021.9563
20000 2.0250976 0.025553447 2.0484009 0.38595959 6776.6695
21000 2.0110196 0.048246457 2.0570316 0.46314066 6520.9712
22000 2.0012178 0.051450005 2.0504442 0.50011911 6286.566
23000 2.0226109 0.031787722 2.0521512 0.43613089 6119.8217
24000 2.0134913 0.042411775 2.0536659 0.4577662 5943.5984
25000 2.0093422 0.051178345 2.0582879 0.48096234 5761.3544
26000 2.0248309 0.032810165 2.0553913 0.50986378 5597.7711
27000 2.0434002 0.023550572 2.0646803 0.50645895 5412.714
28000 2.016281 0.044759023 2.0587997 0.5280788 5286.4223
29000 2.0077475 0.0601743 2.0656909 0.57877433 5141.1547
30000 2.0020028 0.057996828 2.0577752 0.58202549 5051.5118
31000 2.0272724 0.036923011 2.0619429 0.57737892 4951.4005
32000 1.9961882 0.072148507 2.0661187 0.66956459 4853.7897
33000 2.0195419 0.048574609 2.0658725 0.59963748 4785.5398
34000 1.9847192 0.08791774 2.0704317 0.67472077 4692.0829
35000 2.0232089 0.05359142 2.0745523 0.70512517 4591.1869
36000 2.0132717 0.064582747 2.0756175 0.64191182 4513.5395
37000 2.0099041 0.062627912 2.0702987 0.68667086 4435.1025
38000 2.0052872 0.075715262 2.0787744 0.82912244 4344.0961
39000 1.996695 0.079486362 2.0739628 0.80007632 4274.6786
40000 2.0287984 0.049071765 2.075616 0.68699011 4205.1065
41000 1.9991681 0.079251544 2.0761983 0.76990476 4167.3826
42000 2.0052219 0.078415454 2.0814093 0.8006196 4115.727
43000 1.9969265 0.085572469 2.0802802 0.82495686 4070.1484
44000 2.0220264 0.067086318 2.086866 0.83855059 4022.2122
45000 2.042858 0.049644184 2.0902324 0.81644527 3951.1191
46000 1.9826432 0.10101728 2.0814575 0.90870473 3933.6594
47000 2.006566 0.085716015 2.0900525 0.90397394 3891.4349
48000 2.0040466 0.090560783 2.0923807 0.99847747 3834.7163
49000 2.0220363 0.081815852 2.1016054 0.94394569 3797.9118
50000 2.0137006 0.085147019 2.0966102 1.0177029 3745.546
Loop time of 5.23707 on 1 procs for 50000 steps with 900 atoms

Performance: 4124443.939 tau/day, 9547.324 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
提供全局循环计时摘要。循环时间是模拟运行的总挂钟时间。提供性能行是为了方便，以帮助预测运行所需物理模拟所需的时间。CPU 使用线路提供每个 MPI 任务的 CPU 利用率;它应该接近 OpenMP 线程数量的 100%（或不使用 OpenMP 的 1 个线程）。较低的数字对应于由于文件 I/O 或线程利用率不足而导致的延迟。

MPI task timing breakdown:
MPI 任务部分将 CPU 运行时间（以秒为单位）细分为主要类别
Section | min time | avg time | max time |%varavg| %total

Pair | 2.4991 | 2.4991 | 2.4991 | 0.0 | 47.72 非粘结力计算
Neigh | 1.1446 | 1.1446 | 1.1446 | 0.0 | 21.86 邻居列表构造
Comm | 0.18446 | 0.18446 | 0.18446 | 0.0 | 3.52 原子的处理器间通信及其特性
Output | 0.0012348 | 0.0012348 | 0.0012348 | 0.0 | 0.02 热力学信息和转储文件的输出
Modify | 1.2466 | 1.2466 | 1.2466 | 0.0 | 23.80 修复程序调用的修复和计算
Other | | 0.161 | | | 3.07
"%varavg"是最大值或最小值与平均值不同的百分比。这表明负载不平衡。接近 0 的百分比是完美的负载平衡。

Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5969 ave 5969 max 5969 min
Histogram: 1 0 0 0 0 0 0 0 0 0
列出了每个处理器存储的拥有的原子（Nlocal）、鬼原子（Nghost）和对邻的数目。最大值和最小值通过显示分布的 10 箱Histogram直方图提供这些值在处理器上的分布。直方图计数的总数等于处理器数。

Total # of neighbors = 5969
Ave neighs/atom = 6.63222
Neighbor list builds = 3145
Dangerous builds = 0
LAMMPS 跟踪的对邻和特殊邻居提供聚合统计信息,计算邻居列表的重建次数以及潜在危险重建的次数。

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:05

分析

当模拟准备就绪时，LAMMPS 将执行各种初始化，并打印有关即将执行的运行的信息，包括模拟所需的内存量（以每个处理器的 MB 为单位）。它还打印系统初始热力学状态的详细信息。在运行过程中，热力学信息会每隔几个时间步定期打印一次。运行结束时，LAMMPS 打印模拟的最终热力学状态和总运行时间。它还附加有关模拟的 CPU 时间和存储要求的统计信息。