forked from lijiext/lammps
246 lines
11 KiB
Groff
246 lines
11 KiB
Groff
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 0.554412 on 8 procs for 5000 steps with 3200 atoms
|
|
|
|
Performance: 3896017.421 tau/day, 9018.559 timesteps/s
|
|
98.9% CPU use with 8 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
|
|
Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
|
|
Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
|
|
Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
|
|
Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
|
|
Other | | 0.04251 | | | 7.67
|
|
|
|
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
|
|
|
|
# factor of 4 in 2 variables is for 2d
|
|
|
|
compute msd all msd com yes
|
|
variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
|
|
fix 9 all vector 10 c_msd[4]
|
|
variable fitslope equal slope(f_9)/4/(10*dt)
|
|
|
|
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
|
|
|
|
# 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_msd[4] v_twopoint v_fitslope
|
|
0 0.97069905 0 0 5e+20
|
|
1000 0.98138076 4.0484996 0.20242494 0.18046446
|
|
2000 0.97606079 9.2121392 0.23030346 0.2091528
|
|
3000 0.97924866 14.815034 0.24691721 0.22619184
|
|
4000 0.98568451 20.516817 0.25646019 0.23715506
|
|
5000 0.97551815 27.33922 0.27339219 0.24709999
|
|
6000 0.98482252 34.37734 0.28647782 0.25735178
|
|
7000 0.9672559 41.696689 0.29783348 0.26654059
|
|
8000 0.9836541 48.340277 0.30212673 0.27440308
|
|
9000 0.99087147 56.042692 0.31134828 0.28113047
|
|
10000 0.99663166 63.69663 0.31848314 0.28767921
|
|
11000 0.97776688 71.144109 0.32338231 0.29344527
|
|
12000 0.98246011 78.301774 0.32625739 0.29849471
|
|
13000 0.98788732 85.061923 0.32716124 0.3026655
|
|
14000 0.96872483 91.1658 0.32559214 0.30601023
|
|
15000 0.98955796 97.278388 0.32426129 0.3084275
|
|
16000 0.99855196 104.23997 0.3257499 0.31049883
|
|
17000 0.98600861 110.66055 0.3254722 0.31220348
|
|
18000 0.98696963 116.90111 0.32472531 0.31352676
|
|
19000 0.9881192 124.21305 0.32687644 0.31480062
|
|
20000 0.98527319 131.09874 0.32774685 0.31596198
|
|
21000 0.99015191 137.89263 0.32831579 0.31705324
|
|
22000 0.97972418 146.68982 0.33338595 0.31833889
|
|
23000 0.98911012 155.1264 0.33723129 0.31979515
|
|
24000 0.98810498 162.88634 0.33934653 0.32131187
|
|
25000 0.96961962 170.37907 0.34075814 0.32276215
|
|
26000 0.99118408 179.26511 0.34474059 0.32427111
|
|
27000 0.98515159 185.90764 0.3442734 0.32574529
|
|
28000 0.98951677 192.12183 0.34307469 0.32700292
|
|
29000 0.9832026 196.99457 0.33964581 0.32799023
|
|
30000 0.98449493 203.48475 0.33914124 0.3287171
|
|
31000 0.96585993 210.06193 0.33880956 0.32935775
|
|
32000 0.98758117 218.94174 0.34209646 0.33001591
|
|
33000 0.98875584 225.96489 0.34237104 0.33072947
|
|
34000 0.98007229 233.5792 0.34349882 0.3314385
|
|
35000 0.98415295 241.98148 0.34568783 0.33216634
|
|
36000 0.98101154 250.30876 0.34765106 0.33295272
|
|
37000 0.97606878 258.2127 0.34893608 0.33377673
|
|
38000 0.97220293 266.40464 0.35053242 0.33459273
|
|
39000 0.979783 272.8578 0.34981769 0.33539728
|
|
40000 0.98375673 279.87598 0.34984497 0.33609699
|
|
41000 0.97506523 288.07676 0.35131312 0.33677708
|
|
42000 0.97106749 296.11647 0.3525196 0.33751312
|
|
43000 0.97717259 304.46747 0.35403194 0.33823441
|
|
44000 0.98541435 312.57228 0.35519578 0.3389771
|
|
45000 0.97678287 321.82674 0.35758527 0.33973306
|
|
46000 0.98169719 329.78197 0.35845866 0.34051748
|
|
47000 0.99471466 337.11283 0.35863066 0.34127239
|
|
48000 0.98332437 346.0754 0.3604952 0.34202442
|
|
49000 0.98126947 356.11859 0.36338631 0.34282132
|
|
50000 0.98809751 365.65248 0.36565248 0.34368171
|
|
51000 0.95919516 373.91833 0.36658659 0.34454516
|
|
52000 0.98097913 381.26492 0.36660089 0.34538506
|
|
53000 0.97774072 388.81031 0.36680218 0.34618232
|
|
54000 0.99096915 395.56767 0.36626636 0.3469296
|
|
55000 0.97652739 401.72735 0.36520668 0.34760374
|
|
56000 0.99185306 407.28834 0.3636503 0.34819906
|
|
57000 0.96289342 414.75298 0.3638184 0.34871992
|
|
58000 0.97871716 424.69443 0.36611588 0.34927986
|
|
59000 0.98637393 433.14205 0.36706953 0.34986296
|
|
60000 0.98009845 438.14533 0.36512111 0.35040349
|
|
61000 0.99416712 446.08007 0.3656394 0.35088379
|
|
62000 0.97612483 450.90846 0.36363585 0.35132647
|
|
63000 0.97786531 455.36749 0.36140277 0.35167458
|
|
64000 0.99080668 458.04873 0.35785057 0.3519105
|
|
65000 0.97952497 461.31241 0.3548557 0.3520506
|
|
66000 0.98095955 463.91727 0.35145248 0.35207764
|
|
67000 0.98370788 468.93 0.34994776 0.35204043
|
|
68000 0.96931818 471.07765 0.34638063 0.35192685
|
|
69000 0.98512552 474.59146 0.34390685 0.35174053
|
|
70000 0.98065743 478.66071 0.3419005 0.35149002
|
|
71000 0.98971283 482.57357 0.33984054 0.35119434
|
|
72000 0.99890324 485.32018 0.3370279 0.35084345
|
|
73000 0.98649924 490.19497 0.33574998 0.35043722
|
|
74000 0.98723422 496.04991 0.33516886 0.35003351
|
|
75000 1.0025633 501.6313 0.33442087 0.34962094
|
|
76000 0.97859959 505.97813 0.33288035 0.34921013
|
|
77000 0.97973006 510.55334 0.33152814 0.3487692
|
|
78000 0.9903944 515.06966 0.33017286 0.34830833
|
|
79000 0.96847518 518.76483 0.32833217 0.3478214
|
|
80000 0.99171112 524.18127 0.32761329 0.34733349
|
|
81000 0.97202573 529.09959 0.32660468 0.3468315
|
|
82000 0.99368438 535.80271 0.32670897 0.34633058
|
|
83000 0.97932483 543.08233 0.32715803 0.34586259
|
|
84000 0.99078651 547.57861 0.32593965 0.34540839
|
|
85000 0.98973457 552.24581 0.32485048 0.34493584
|
|
86000 0.9835873 557.3493 0.32404029 0.34446152
|
|
87000 0.97180564 564.93434 0.32467491 0.34400358
|
|
88000 0.99743353 571.39837 0.32465817 0.3435667
|
|
89000 0.98993437 577.81703 0.32461631 0.3431411
|
|
90000 0.9926071 583.39378 0.32410765 0.342724
|
|
91000 0.98800458 591.08741 0.3247733 0.34232767
|
|
92000 0.98501879 596.10133 0.32396811 0.34193949
|
|
93000 0.98810082 604.02652 0.32474544 0.3415681
|
|
94000 0.97563748 609.43676 0.32416849 0.341209
|
|
95000 0.97283448 615.15754 0.32376713 0.34084828
|
|
96000 0.9883071 622.30912 0.32411933 0.34049871
|
|
97000 0.97717678 628.84457 0.32414669 0.34016355
|
|
98000 0.97190208 634.37377 0.32366009 0.3398341
|
|
99000 0.98687379 640.66666 0.32356902 0.33950845
|
|
100000 0.97559757 646.96406 0.32348203 0.33919036
|
|
Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
|
|
|
|
Performance: 4505729.040 tau/day, 10429.928 timesteps/s
|
|
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
|
|
Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
|
|
Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
|
|
Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
|
|
Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
|
|
Other | | 0.7686 | | | 8.02
|
|
|
|
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: 0:00:10
|