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LAMMPS (13 Oct 2016)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 53 53 1
Memory usage per processor = 2.478 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
Performance: 3873826.669 tau/day, 8967.191 timesteps/s
99.1% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
Other | | 0.0372 | | | 6.67
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
compute vacf all vacf
fix 4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf
# factor of 0.5 is for 2d
fix 5 all vector 1 c_vacf[4]
variable vacf equal 0.5*dt*trap(f_5)
thermo_style custom step temp c_vacf[4] v_vacf
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.853 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
2000 0.97606079 -0.0015179052 0.23974121
3000 0.97924866 -0.013873067 0.21877575
4000 0.98568451 0.026969065 0.24052934
5000 0.97551815 0.050232557 0.24508207
6000 0.98482252 -0.0018424259 0.25686293
7000 0.9672559 0.018499957 0.27279836
8000 0.9836541 -0.022683127 0.27022734
9000 0.99087147 0.0071767632 0.25267902
10000 0.99663166 -0.011971734 0.2645822
11000 0.97776688 0.01601675 0.27801788
12000 0.98246011 0.0085456779 0.29207728
13000 0.98788732 0.0054252587 0.29148533
14000 0.96872483 0.0087976064 0.29645689
15000 0.98955796 -0.060068996 0.28904116
16000 0.99855196 -0.0066979853 0.24964957
17000 0.98600861 0.021334454 0.23410452
18000 0.98696963 -0.01971883 0.23190572
19000 0.9881192 -0.022828159 0.20882183
20000 0.98527319 -0.0085783561 0.20610922
21000 0.99015191 -0.0061019744 0.20199693
22000 0.97972418 -0.04380952 0.22099864
23000 0.98911012 -0.0031381071 0.19304223
24000 0.98810498 0.023131507 0.18483784
25000 0.96961962 -0.020892151 0.17128259
26000 0.99118408 0.02918818 0.15353531
27000 0.98515159 -0.026417648 0.1457756
28000 0.98951677 0.010372147 0.13321212
29000 0.9832026 0.00058150905 0.13262151
30000 0.98449493 0.0012256712 0.13576655
31000 0.96585993 0.0053021384 0.10734708
32000 0.98758117 -0.011513109 0.11473375
33000 0.98875584 -0.0089140499 0.13003947
34000 0.98007229 0.023423116 0.145185
35000 0.98415295 -0.0078343607 0.16513809
36000 0.98101154 0.025471963 0.1296799
37000 0.97606878 -0.016931612 0.11515595
38000 0.97220293 -0.015288346 0.12046935
39000 0.979783 0.039556949 0.10596988
40000 0.98375673 0.0098704124 0.15651085
41000 0.97506523 -0.029457701 0.14822207
42000 0.97106749 -0.024867475 0.12266294
43000 0.97717259 0.010866403 0.14228602
44000 0.98541435 -0.031545234 0.13017093
45000 0.97678287 -0.011024372 0.11824999
46000 0.98169719 0.011925437 0.1390346
47000 0.99471466 0.0048178625 0.13076123
48000 0.98332437 0.045576305 0.12667585
49000 0.98126947 -0.044123768 0.13582991
50000 0.98809751 0.014296599 0.12323107
51000 0.95919516 -0.0091171161 0.1494511
52000 0.98097913 0.010081012 0.12805794
53000 0.97774072 0.043349117 0.14524942
54000 0.99096915 0.021179196 0.1355801
55000 0.97652739 -0.015118967 0.14955035
56000 0.99185306 0.0018045061 0.16706629
57000 0.96289342 0.0095090659 0.19215008
58000 0.97871716 -0.028989119 0.20370326
59000 0.98637393 0.0067841088 0.21820001
60000 0.98009845 0.011559251 0.24504916
61000 0.99416712 0.0099372548 0.24882366
62000 0.97612483 0.014677063 0.25146482
63000 0.97786531 -0.0047938112 0.26052305
64000 0.99080668 -0.01632121 0.24744267
65000 0.97952497 0.0070583633 0.22323997
66000 0.98095955 0.036296232 0.2151706
67000 0.98370788 -0.0040313363 0.22236193
68000 0.96931818 0.0231486 0.20397659
69000 0.98512552 -0.017450997 0.21854935
70000 0.98065743 0.046916694 0.2080453
71000 0.98971283 0.010974871 0.21628306
72000 0.99890324 -0.023780184 0.23385876
73000 0.98649924 0.012862733 0.23458964
74000 0.98723422 -0.0096252165 0.23873216
75000 1.0025633 -0.070387674 0.2275029
76000 0.97859959 0.0058897922 0.22954358
77000 0.97973006 -0.0082868083 0.25189797
78000 0.9903944 -0.042368536 0.26564349
79000 0.96847518 -0.050630573 0.25344248
80000 0.99171112 0.012126001 0.23257751
81000 0.97202573 -0.029816198 0.27354387
82000 0.99368438 0.030082951 0.27859495
83000 0.97932483 -0.0081664387 0.27409123
84000 0.99078651 0.056610231 0.27593659
85000 0.98973457 0.020424285 0.31002605
86000 0.9835873 -0.0016980943 0.30158255
87000 0.97180564 -0.0051924508 0.27401969
88000 0.99743353 -0.030700753 0.24105471
89000 0.98993437 0.0087866525 0.23913724
90000 0.9926071 -0.014023378 0.24202489
91000 0.98800458 0.033613695 0.2238248
92000 0.98501879 -0.0406599 0.21809043
93000 0.98810082 0.027637634 0.21550897
94000 0.97563748 0.0014112208 0.18954766
95000 0.97283448 0.0093796591 0.17838358
96000 0.9883071 0.033049994 0.18594703
97000 0.97717678 0.01070451 0.19203994
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
Performance: 3987213.825 tau/day, 9229.662 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
Other | | 0.6383 | | | 5.89
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
Nghost: 204.75 ave 213 max 197 min
Histogram: 1 1 0 1 0 3 0 1 0 1
Neighs: 2800.62 ave 2959 max 2661 min
Histogram: 1 1 1 2 0 0 0 1 1 1
Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:11
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