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lammps/examples/VISCOSITY/log.nemd.2d.12Sep13
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log.nemd.2d.12Sep13
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LAMMPS (10 Sep 2013)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# NEMD via fix deform and fix nvt/sllod
# settings
variable x equal 20
variable y equal 20
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
variable srate equal 2.7
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
# problem setup
lattice sq2 ${rho}
lattice sq2 0.5999999999999999778
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox prism 0 $y 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 $y -0.1 0.1 0.0 0.0 0.0
region simbox prism 0 20 0 20 -0.1 0.1 0.0 0.0 0.0
create_box 1 simbox
Created triclinic box = (0 0 -0.182574) to (36.5148 36.5148 0.182574) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 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 = 2.07097 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
1000 0.9455393 -1.573329 0 -0.62897162 0.91884199
2000 1.0359047 -1.6229551 0 -0.58834528 0.96136682
3000 1.0171488 -1.5468681 0 -0.53099077 1.1078235
4000 1.0040221 -1.5977142 0 -0.59494717 0.92428924
5000 0.95883045 -1.6087309 0 -0.65109902 0.92015626
Loop time of 0.995848 on 1 procs for 5000 steps with 800 atoms
Pair time (%) = 0.530232 (53.2443)
Neigh time (%) = 0.155753 (15.6403)
Comm time (%) = 0.0214312 (2.15206)
Outpt time (%) = 5.38826e-05 (0.00541073)
Other time (%) = 0.288377 (28.958)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 266 ave 266 max 266 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5604 ave 5604 max 5604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5604
Ave neighs/atom = 7.005
Neighbor list builds = 548
Dangerous builds = 0
unfix 1
unfix 2
# turn on NEMD shear and equilibrate some more
velocity all scale $t
velocity all scale 1
variable xyrate equal ${srate}/lx
variable xyrate equal 2.7000000000000001776/lx
fix 1 all nvt/sllod temp $t $t 0.1
fix 1 all nvt/sllod temp 1 $t 0.1
fix 1 all nvt/sllod temp 1 1 0.1
fix 2 all deform 1 xy erate ${xyrate} remap v
fix 2 all deform 1 xy erate 0.07394254526319743448 remap v
fix 4 all ave/spatial 20 250 5000 y center 0.05 vx units reduced file profile.nemd.2d
compute usual all temp
compute tilt all temp/deform
thermo 1000
thermo_style custom step temp c_usual epair etotal press pxy
thermo_modify temp tilt
run 50000
Memory usage per processor = 2.07189 Mbytes
Step Temp usual E_pair TotEng Press Pxy
5000 2.2074694 1 -1.6087309 0.59597912 1.6684031 -0.13173607
6000 0.91633679 1.0719617 -1.6395918 -0.72440047 0.75849191 -0.095097981
7000 1.0124825 1.1977616 -1.6934341 -0.68221723 0.70703149 -0.15913906
8000 1.0360742 1.244051 -1.6664702 -0.63169111 0.87208594 -0.17196758
9000 0.97397154 1.2397496 -1.6727765 -0.7000224 0.80220669 -0.11127356
10000 0.95658497 1.2726404 -1.6735904 -0.71820119 0.67518534 0.021843949
11000 0.99924023 1.3580428 -1.67571 -0.67771886 0.70353983 -0.095458782
12000 1.0433584 1.3936154 -1.6710176 -0.6289634 0.78515023 -0.10560886
13000 1.0405816 1.4490361 -1.6830775 -0.64379669 0.61832448 -0.11781994
14000 1.0497802 1.4357015 -1.6534549 -0.60498685 0.76907329 0.017545708
15000 0.96121525 1.3821511 -1.6498177 -0.68980398 0.95020534 -0.080877133
16000 1.0267815 1.4361052 -1.6538729 -0.62837492 0.68232896 -0.070333365
17000 0.93630695 1.3935392 -1.6232359 -0.68809929 0.76153713 0.0065771149
18000 1.0096924 1.5362618 -1.6690032 -0.66057292 0.74673844 -0.0020401284
19000 0.98814671 1.4707103 -1.6447486 -0.65783707 0.72488074 -0.13287245
20000 0.99667627 1.5457608 -1.6408152 -0.64538473 0.60598401 -0.0076374847
21000 0.98153893 1.5408205 -1.6148102 -0.63449823 0.80827079 -0.13251983
22000 1.0074242 1.6101043 -1.6422641 -0.63609914 0.90042046 -0.24385712
23000 0.95365942 1.5736051 -1.6412154 -0.68874806 0.8559935 -0.2467715
24000 0.98446077 1.5616505 -1.6395606 -0.65633045 0.73483641 -0.08920475
25000 1.0485516 1.6856359 -1.6399653 -0.5927244 0.84977844 -0.075926647
26000 0.96582655 1.5721629 -1.5882566 -0.62363728 0.81869074 0.090152592
27000 0.97557823 1.6668575 -1.6191458 -0.64478708 0.91081614 -0.19376266
28000 1.0303654 1.6964024 -1.6092391 -0.5801616 0.86334845 -0.17578668
29000 1.0622338 1.7710626 -1.6229948 -0.5620888 0.99336949 -0.14536132
30000 0.96943779 1.6600645 -1.6139092 -0.6456832 0.9989094 -0.02138527
31000 0.93832908 1.6925042 -1.6176446 -0.68048846 0.95346065 -0.17742851
32000 0.9875824 1.725668 -1.6119922 -0.62564431 0.96558919 -0.043195696
33000 0.99760198 1.7058006 -1.6052067 -0.60885172 0.98003863 -0.1333913
34000 1.0279367 1.7569574 -1.599245 -0.5725932 0.92585533 -0.16404413
35000 0.93404083 1.7440669 -1.6103769 -0.67750362 0.85837384 -0.23365559
36000 1.050384 1.8439426 -1.6563916 -0.60732054 0.67392288 -0.10063943
37000 0.94243088 1.7640322 -1.6138567 -0.6726039 0.96591044 -0.027194268
38000 0.98755975 1.8113344 -1.6079596 -0.62163426 1.0223699 -0.201769
39000 1.0420603 1.8627119 -1.5973478 -0.55659 1.0381788 0.12071081
40000 1.0335545 1.8837126 -1.5851743 -0.5529117 0.94822902 -0.10987028
41000 0.94213103 1.8188004 -1.6049587 -0.66400536 0.97923033 0.01154085
42000 1.0356435 1.8901318 -1.6212526 -0.58690373 0.95585859 -0.19557187
43000 0.99015606 1.8799525 -1.6090628 -0.62014448 0.9274227 -0.2300794
44000 1.0161294 1.9551452 -1.6180455 -0.60318623 1.0355228 -0.12706459
45000 0.98674382 1.8916077 -1.6468656 -0.66135521 0.78299308 -0.15774308
46000 1.0113469 1.9533202 -1.5957721 -0.58568941 0.78737351 0.13820702
47000 1.0571363 1.9631114 -1.5772356 -0.52142074 0.95792606 0.029844288
48000 0.94855706 1.8697175 -1.6015863 -0.65421497 0.90993104 -0.34180657
49000 1.0607674 1.9704564 -1.5868247 -0.52738329 1.0716947 -0.034892185
50000 0.97263672 1.9338729 -1.6082924 -0.63687146 1.0235045 -0.16412663
51000 1.0378868 1.9671463 -1.5809392 -0.54434973 1.1981016 0.057155145
52000 1.005245 1.9432386 -1.6053723 -0.60138379 0.96669621 -0.04065554
53000 1.0051888 1.9494803 -1.592364 -0.58843173 0.94235557 -0.082756851
54000 0.98792555 1.9333497 -1.5977723 -0.6110817 1.0539616 -0.052439197
55000 1.0215148 1.9761517 -1.6026169 -0.58237902 0.98461466 -0.014054852
Loop time of 13.2512 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 5.62991 (42.486)
Neigh time (%) = 3.31133 (24.9889)
Comm time (%) = 0.333608 (2.51757)
Outpt time (%) = 0.00183129 (0.0138198)
Other time (%) = 3.97453 (29.9937)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 276 ave 276 max 276 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5608 ave 5608 max 5608 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5608
Ave neighs/atom = 7.01
Neighbor list builds = 11158
Dangerous builds = 0
# data gathering run
variable visc equal -pxy/(v_srate/ly)
fix vave all ave/time 10 100 1000 v_visc ave running start 56000
thermo_style custom step temp press pxy v_visc f_vave
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:664)
thermo_modify temp tilt
#dump 1 all custom 10 dump.nemd.2d id type x y z vx
run 50000
Memory usage per processor = 2.11211 Mbytes
Step Temp Press Pxy visc vave
55000 1.0215148 0.98406243 -0.015573121 0.2106111 0
56000 0.97676391 0.7935725 -0.097217766 1.3147744 0.94442622
57000 0.98121663 0.97189374 -0.09906427 1.3397466 1.0348472
58000 0.99072249 1.0185041 -0.1107535 1.4978319 1.1148823
59000 1.0339566 1.1930503 -0.11512608 1.5569667 1.136778
60000 0.96659848 0.92099027 -0.040929962 0.55353737 1.1425378
61000 0.91281753 0.94424526 0.0057649576 -0.077965366 1.1569145
62000 0.94858877 1.0998838 -0.017149668 0.23193235 1.1483313
63000 0.95337651 0.89712297 -0.11187696 1.5130256 1.2009105
64000 1.0210948 0.9602771 -0.054478663 0.73677019 1.2148796
65000 1.0504997 0.94778551 -0.15854746 2.1441981 1.2093498
66000 0.98082278 1.0669108 -0.079622124 1.0768107 1.2394021
67000 1.004502 1.0176002 0.0064462478 -0.087179144 1.2171347
68000 0.92374901 0.71524627 -0.16232949 2.1953463 1.2280608
69000 1.0515117 1.1458523 0.10895185 -1.4734664 1.2214747
70000 1.0555502 1.076672 -0.042203866 0.57076567 1.19651
71000 0.9770682 1.180182 -0.13504139 1.8263016 1.1565664
72000 1.0086134 1.022067 -0.037398667 0.50578009 1.1850636
73000 1.0162758 1.120033 -0.059765955 0.8082756 1.1911215
74000 0.99405946 0.89203552 -0.24842296 3.3596755 1.1878296
75000 0.98750361 0.94382542 -0.22651557 3.0633996 1.185964
76000 1.0464263 1.2902475 -0.054604453 0.73847137 1.1830982
77000 0.97443033 0.9748021 -0.0188378 0.25476266 1.1807479
78000 1.0458063 1.0029976 -0.073834161 0.99853421 1.1713126
79000 1.0144775 1.218542 0.062883654 -0.8504394 1.1810856
80000 1.0114425 0.86457858 0.0071905047 -0.097244484 1.1826166
81000 0.94134141 0.77988469 -0.12039379 1.6282073 1.1949499
82000 1.0043004 1.1044886 -0.071274637 0.96391918 1.1858594
83000 1.0183148 0.97315487 -0.17878927 2.4179486 1.1847614
84000 1.0089223 0.94988998 -0.14706747 1.9889425 1.186726
85000 0.99683237 1.1387674 -0.093287095 1.261616 1.1950365
86000 0.98703013 0.90123949 -0.071666603 0.96922013 1.1994887
87000 0.98715174 1.0031198 0.073329807 -0.99171332 1.2030095
88000 0.98802533 0.780636 -0.18839651 2.547877 1.206866
89000 0.98607737 1.0366379 -0.16016943 2.1661336 1.2122118
90000 1.0210319 1.0157699 -0.036734636 0.49679972 1.2136124
91000 1.0383205 1.0432409 -0.2294371 3.1029105 1.2119958
92000 1.0552856 1.2186718 -0.013410875 0.18136886 1.2082849
93000 1.0114907 1.075338 0.0035134444 -0.04751587 1.2094306
94000 0.94044675 1.054018 0.085446493 -1.1555795 1.203052
95000 1.0158089 0.97472916 -0.11967767 1.6185225 1.2030168
96000 1.020383 0.89405366 -0.14288077 1.9323215 1.2030977
97000 0.96955936 1.0480423 -0.11860582 1.6040268 1.2056096
98000 1.0091452 0.84288535 -0.1289184 1.7434942 1.1994042
99000 0.99665723 1.0303263 -0.02254625 0.3049158 1.194661
100000 0.94019285 0.98342349 -0.069073187 0.93414673 1.1935304
101000 1.0351616 1.0994068 -0.089112502 1.2051587 1.1778161
102000 0.94550389 1.0840839 -0.093572091 1.2654702 1.1855211
103000 1.0384124 1.0513178 -0.053925313 0.72928668 1.1787243
104000 1.0561611 0.87476291 -0.13807613 1.8673434 1.1807725
105000 1.0046808 0.95999328 0.015725114 -0.21266665 1.1820494
Loop time of 13.826 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 5.72616 (41.4159)
Neigh time (%) = 3.64084 (26.3333)
Comm time (%) = 0.359706 (2.60167)
Outpt time (%) = 0.0011127 (0.00804788)
Other time (%) = 4.09817 (29.6411)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 264 ave 264 max 264 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5616 ave 5616 max 5616 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5616
Ave neighs/atom = 7.02
Neighbor list builds = 12198
Dangerous builds = 0
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