Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/DIFFUSE/log.vacf.2d.1Feb14
e1d589bc8ddbefficient_neuronet

Last Change
Raw File

log.vacf.2d.1Feb14
View Options

LAMMPS (12 Feb 2014)
# 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
Memory usage per processor = 2.06238 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 0.97069909 -1.5851114 0 -0.61471562 0.90108296
Loop time of 0.556362 on 8 procs for 5000 steps with 3200 atoms
Pair time (%) = 0.242478 (43.5828)
Neigh time (%) = 0.0590148 (10.6073)
Comm time (%) = 0.0862918 (15.51)
Outpt time (%) = 0.000148952 (0.0267725)
Other time (%) = 0.168428 (30.2731)
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 = 2.29126 Mbytes
Step Temp vacf[4] vacf
0 0.97069909 1.9407915 0
1000 0.98259938 0.068345562 0.21424576
2000 0.98866167 0.028205164 0.24370013
3000 0.98066292 0.008852823 0.27439588
4000 0.97384109 0.011903564 0.3159275
5000 0.97843004 0.019295534 0.33596598
6000 0.98703537 0.01070801 0.34517088
7000 0.97169186 -0.0082938435 0.33784119
8000 0.9823893 0.038402174 0.32756669
9000 0.9998457 0.045317593 0.33379383
10000 0.98782869 0.027148675 0.34751149
11000 0.99481941 0.035783937 0.36009047
12000 0.9760981 -0.0010825507 0.36059769
13000 0.97774297 0.048323885 0.36103752
14000 0.96752038 0.0008189784 0.34988029
15000 0.98697717 -0.0339338 0.35841003
16000 0.98385955 0.03729417 0.36378228
17000 0.9839555 -0.0063931744 0.37486488
18000 0.98000182 0.065439765 0.39975619
19000 0.96633821 0.0034363237 0.39585239
20000 0.98641362 -0.020284 0.39696422
21000 0.9763779 0.013683539 0.36183593
22000 0.97984221 -0.0077108606 0.32642476
23000 0.98384014 -0.030550764 0.32775468
24000 0.97601102 -0.0047287909 0.3294707
25000 0.99623187 0.00653461 0.34586445
26000 0.98943691 -0.05047279 0.3283058
27000 0.98992058 -0.01720223 0.30840611
28000 0.97957751 0.020915942 0.3149002
29000 0.99513582 0.03712206 0.30525251
30000 0.99754125 -0.022509889 0.29511243
31000 0.98894929 0.015289267 0.25586423
32000 0.973493 0.015971435 0.25226411
33000 0.99989261 0.026989142 0.29050941
34000 0.97192218 0.043710515 0.29067058
35000 0.99711642 0.047231436 0.27989734
36000 0.97718259 0.0059969847 0.28843181
37000 0.98194807 0.017440303 0.30325718
38000 0.97195138 -0.040449666 0.29696592
39000 0.98219017 0.0063692991 0.28915832
40000 0.98039694 -0.0038122219 0.24799014
41000 0.97621359 0.012624961 0.2374766
42000 0.97460413 -0.0024187 0.24693474
43000 0.9799912 0.015928618 0.26238505
44000 0.96313376 -0.067284605 0.24397772
45000 0.97643796 -0.0039001998 0.22733962
46000 0.98641729 -0.026949085 0.24167989
47000 0.97811939 -0.050859011 0.2335985
48000 0.99744864 -0.008154229 0.2417371
49000 0.97480356 -0.011051498 0.25474033
50000 0.97841509 -0.00531423 0.25357072
51000 0.97865859 0.067722096 0.25086864
52000 0.97415415 0.015863025 0.2516842
53000 0.97984491 0.021332829 0.28226376
54000 0.99289379 -0.0192578 0.28300764
55000 0.98606668 0.029307891 0.27592186
56000 0.98585489 0.0062922121 0.2687204
57000 0.98507959 -0.0068688582 0.27868708
58000 0.98030805 0.013766115 0.31008116
59000 0.98315137 0.033068034 0.32211415
60000 0.98762585 0.050662295 0.30109082
61000 0.96937507 -0.02797113 0.29968066
62000 0.97194792 -0.0032022157 0.2866526
63000 0.99877655 -0.010154313 0.31701083
64000 0.98525211 -0.020415497 0.31774092
65000 0.9833149 0.0087192442 0.31256891
66000 0.97191797 0.0047184494 0.29880531
67000 0.98479592 -0.010779275 0.294197
68000 0.98418943 -0.035264623 0.29993828
69000 0.96953928 -0.028114432 0.27403611
70000 0.98373337 -0.057363336 0.25554163
71000 0.98260952 0.048742037 0.27102884
72000 0.98906053 0.010799224 0.26908376
73000 0.99569597 -0.0092675754 0.26927752
74000 0.97627362 0.013945821 0.2730712
75000 0.97276792 0.015036012 0.25847255
76000 0.97659072 -0.027078556 0.26783118
77000 0.9807196 -0.044553679 0.25993053
78000 0.97398601 -0.00027444729 0.26127735
79000 0.98124212 -0.012488833 0.27454966
80000 0.98506783 -0.015190822 0.2676633
81000 0.97926561 -0.012755191 0.27046398
82000 0.97906184 0.012564185 0.2835038
83000 0.96540502 -0.007372877 0.29622738
84000 0.98726761 0.021015365 0.32432233
85000 0.98133061 0.020043402 0.3540913
86000 0.99142106 0.025350024 0.36697674
87000 0.97917566 0.0061562414 0.37456288
88000 0.99391197 0.0068565008 0.39150922
89000 0.98521911 0.015500816 0.38121119
90000 0.97419059 0.00037609894 0.34181128
91000 0.98687774 -0.0073221495 0.35316892
92000 0.97816545 0.014057005 0.33181146
93000 0.98734859 0.016570523 0.34546487
94000 0.99116168 -0.0068196043 0.36316635
95000 0.99982024 0.076723346 0.38376316
96000 0.99232404 -0.048534983 0.38369657
97000 0.97829693 0.0041180664 0.38022523
98000 0.99878715 -0.00089133295 0.40289006
99000 0.97026354 -0.0039532716 0.43650647
100000 0.98911409 0.028647976 0.4499919
Loop time of 10.5771 on 8 procs for 100000 steps with 3200 atoms
Pair time (%) = 4.88134 (46.1499)
Neigh time (%) = 1.2657 (11.9664)
Comm time (%) = 1.78371 (16.8638)
Outpt time (%) = 0.0207323 (0.196011)
Other time (%) = 2.62565 (24.8239)
Nlocal: 400 ave 410 max 389 min
Histogram: 1 1 1 0 1 1 0 0 1 2
Nghost: 205.375 ave 216 max 194 min
Histogram: 1 0 0 2 2 0 1 0 0 2
Neighs: 2818 ave 3010 max 2683 min
Histogram: 2 0 2 0 1 1 0 1 0 1
Total # of neighbors = 22544
Ave neighs/atom = 7.045
Neighbor list builds = 12748
Dangerous builds = 0
c4science · Help