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lammps/examples/VISCOSITY/log.gk.2d.12Sep13
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LAMMPS (10 Sep 2013)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Green-Kubo method via fix ave/correlate
# 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 p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
variable d equal 400*$s
variable d equal 400*5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.5999999999999999778
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 20 0 $y -0.1 0.1
region simbox block 0 20 0 20 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
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
# equilibration run
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
thermo $d
thermo 2000
run 10000
Memory usage per processor = 2.07097 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.56617 -1.535262
2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
6000 1.0384034 -1.6029204 0 -0.56581499 0.82862864
8000 1.03126 -1.5776603 0 -0.54768937 1.122187
10000 1.0159313 -1.6063811 0 -0.59171973 0.9961884
Loop time of 1.89357 on 1 procs for 10000 steps with 800 atoms
Pair time (%) = 1.05965 (55.9602)
Neigh time (%) = 0.227317 (12.0047)
Comm time (%) = 0.0356276 (1.88151)
Outpt time (%) = 5.60284e-05 (0.00295888)
Other time (%) = 0.570923 (30.1506)
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: 5614 ave 5614 max 5614 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5614
Ave neighs/atom = 7.0175
Neighbor list builds = 1103
Dangerous builds = 0
velocity all scale $t
velocity all scale 1
unfix 2
# Green-Kubo viscosity calculation
reset_timestep 0
variable pxy equal pxy
fix SS all ave/correlate $s $p $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 $p $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 $d v_pxy type auto file profile.gk.2d ave running
fix SS all ave/correlate 5 400 2000 v_pxy type auto file profile.gk.2d ave running
variable scale equal 1.0/$t*vol*$s*dt
variable scale equal 1.0/1*vol*$s*dt
variable scale equal 1.0/1*vol*5*dt
variable v11 equal trap(f_SS[3])*${scale}
variable v11 equal trap(f_SS[3])*33.333333333333328596
thermo_style custom step temp press pxy v_v11
run 500000
Memory usage per processor = 2.07097 Mbytes
Step Temp Press Pxy v11
0 1 0.98664157 0.1056765 0.18612539
2000 0.95291404 1.199872 0.16190354 6.3622865
4000 0.97035474 0.95019583 -0.028108952 -0.019331326
6000 0.99784792 1.0066466 0.0085549073 -0.12148778
8000 0.99816414 0.90521139 0.00095639386 0.0098644997
10000 0.9951641 0.96718253 0.090881095 0.50006024
12000 0.93744355 1.2391514 0.014185646 1.4928658
14000 1.000559 0.97734913 -0.096964014 1.3899184
16000 1.002721 1.1185539 0.026144411 1.0983068
18000 0.96861294 1.0439439 0.090245855 1.4107497
20000 0.98664185 0.97686008 -0.27549912 1.3394189
22000 0.97569716 1.0845656 -0.0734503 1.2870138
24000 0.98609865 1.0625182 -0.01142576 1.0253871
26000 0.988828 0.99456937 -0.019918137 0.9418664
28000 0.98671933 0.94373279 -0.21675597 0.94445052
30000 0.98778176 0.8446134 0.15106071 0.9681741
32000 0.97606274 1.0297113 -0.15539564 0.91574182
34000 1.0018246 0.96354339 0.0040827444 0.86638522
36000 1.0106496 0.78936538 -0.075881707 0.85472064
38000 1.002101 0.84613466 0.096875042 0.79935874
40000 0.99674744 1.0228324 0.068840647 0.75555879
42000 0.98994908 0.96088667 -0.067028764 0.89587645
44000 0.96432917 1.0396458 -0.14766862 0.98252655
46000 0.9857594 1.0493731 -0.16618989 0.92998032
48000 0.99435908 1.0474288 -0.099147004 0.96068255
50000 0.98424778 1.0498745 -0.02093585 0.91727045
52000 1.0087964 1.0044041 -0.17322 0.85023294
54000 0.98865025 0.96826791 -0.0040697022 0.78082036
56000 0.99830593 0.85271022 -0.0095598719 0.76991826
58000 1.0067449 0.83099437 -0.0088816687 0.73064231
60000 0.99157769 0.97115433 0.054722168 0.68728526
62000 0.98221722 1.0180359 -0.019303097 0.6924154
64000 1.0107737 0.8729291 0.14432752 0.67840745
66000 0.98057736 1.147233 -0.15209863 0.6829561
68000 0.99861459 1.013 0.096201469 0.64354984
70000 0.99465851 0.99448469 -0.15043327 0.65410181
72000 0.96494888 1.0879386 0.10533378 0.59884711
74000 0.98295883 1.0364372 -0.15043121 0.89748148
76000 1.0006934 1.0423573 -0.019296985 0.96967781
78000 0.97007774 0.89100292 0.082518797 1.0416848
80000 0.9673494 1.0862372 0.0059477626 1.0154864
82000 1.00901 0.91118297 0.11024238 1.0445278
84000 0.99091853 1.029323 0.064448536 1.0177414
86000 0.99769204 1.0031789 0.049276808 1.012145
88000 1.0043966 0.87571549 0.0098902782 1.0258499
90000 0.98664263 0.95754039 -0.078411226 1.0183036
92000 0.97082418 1.0007131 -0.16528157 1.0313541
94000 0.9718415 1.134436 0.13053227 1.0133067
96000 0.97769459 1.1823894 -0.034238523 0.98394844
98000 1.0212676 1.0322511 0.019298484 0.98987481
100000 0.98939854 0.94010891 -0.14270608 0.93622435
102000 0.99029022 1.032313 -0.084354688 0.9349947
104000 0.97710114 0.93914663 -0.061639137 0.95912515
106000 1.0015283 0.94261993 -0.065425987 0.98677831
108000 1.0277867 0.90869174 0.012240704 0.93883613
110000 0.99627564 0.96468532 0.016729662 0.92041863
112000 1.0053403 0.89703815 0.053013062 0.90792399
114000 1.0061962 0.88630948 0.074929857 0.89048522
116000 0.95237809 1.0422611 0.03659581 0.90269348
118000 0.99935668 0.95007176 0.17759824 0.91222275
120000 0.96695648 1.0439211 0.034405839 0.97878534
122000 0.97945456 0.99746187 0.0068417 0.97320581
124000 1.0205146 0.94768233 -0.0059643466 0.97517978
126000 0.99066371 1.1996852 -0.014932912 0.98986369
128000 0.98292228 1.0610561 0.045677014 0.99324967
130000 0.97938306 1.056683 -0.070425405 1.0229877
132000 0.98907671 1.1401504 0.017589327 1.0266663
134000 0.97298779 1.0372376 -0.053985765 1.0140165
136000 1.006034 0.95903957 0.02253597 0.99236069
138000 0.99107129 0.93393363 0.12735171 0.97191787
140000 0.97467096 1.1824765 -0.037275252 0.95115537
142000 0.99599019 0.93770801 -0.0063475745 0.91527534
144000 0.98928711 1.0100989 -0.14030583 0.92830561
146000 1.0252234 0.86035265 -0.10246737 0.93782417
148000 1.014654 0.79624898 0.016043825 0.91183296
150000 1.0025365 0.94434929 0.061147641 0.91181019
152000 0.98239056 0.96273739 -0.06423689 0.91302568
154000 0.99242128 1.0133692 0.054121583 0.90943966
156000 0.9565225 1.1188086 0.14095454 0.90748691
158000 0.98447114 1.0678162 0.029354999 0.95922918
160000 0.99401344 0.88196818 0.035219872 0.95995359
162000 0.99157731 0.98581187 0.092655892 1.0460888
164000 0.98700844 1.0628065 -0.097600946 1.0021877
166000 0.99653656 1.0967715 -0.13363058 1.0272155
168000 0.97631159 1.0234334 -0.085606659 1.0452207
170000 1.0037365 0.87168897 -0.05818739 1.1534091
172000 0.99599564 0.9223394 -0.021708101 1.1079595
174000 0.95487975 1.1632417 0.07399437 1.0992262
176000 0.99699032 1.0259118 -0.069297394 1.086451
178000 0.99794248 0.92978817 -0.036423033 1.0850363
180000 0.97147417 1.0886532 -0.10560093 1.0831337
182000 0.9875809 1.1116588 0.074972498 1.1130653
184000 0.97900449 0.93659533 -0.039279882 1.1189945
186000 0.9679462 1.2538405 -0.015579462 1.099796
188000 1.0074452 0.87991578 -0.20476294 1.1007234
190000 0.97473004 0.98106665 -0.072522838 1.0894785
192000 0.98717919 0.9718274 0.059062062 1.086273
194000 1.0030985 0.94066352 0.15646304 1.1914576
196000 0.98500284 0.96429266 0.11204948 1.1594863
198000 0.9840631 0.90903459 -0.0053663326 1.1502972
200000 0.97458345 1.0019506 0.00027337741 1.1410582
202000 0.98772368 1.0082562 0.0069097265 1.2104792
204000 0.99875662 0.90609936 -0.024992308 1.2337143
206000 0.98028117 0.92135146 0.015407324 1.2200096
208000 0.98909505 0.89346463 -0.13505415 1.2282618
210000 0.99264762 1.0637228 0.15772329 1.2298716
212000 1.001344 0.92015447 -0.022356905 1.2175726
214000 1.0199747 0.92259571 0.012763156 1.2046812
216000 0.95599898 1.0739248 -0.075513344 1.1935807
218000 0.99797077 1.0673568 0.049840078 1.1801809
220000 0.9905579 0.97950128 0.058186552 1.2027082
222000 0.99177609 1.028659 -0.076396538 1.1782589
224000 1.0105632 1.0136738 0.039008755 1.1848006
226000 1.0023731 0.8427875 -0.10734019 1.177471
228000 0.98752126 0.90957923 -0.050531743 1.3182698
230000 0.9810267 1.0784386 0.08508881 1.3092904
232000 1.0021266 0.93921109 -0.18635777 1.2973489
234000 0.99533025 0.91807335 0.16664865 1.2848923
236000 0.98011149 0.92896398 0.020234263 1.2941781
238000 1.0080589 1.0422206 0.080342493 1.2756861
240000 1.013769 0.91271642 0.10024033 1.2720643
242000 1.0084395 0.8645878 -0.014896263 1.2473047
244000 0.96637824 1.0817071 -0.16165169 1.2490751
246000 0.97629725 1.0768466 0.062453669 1.2348816
248000 0.97081168 0.95332682 0.09584424 1.2232201
250000 1.001316 0.90207588 -0.045980098 1.2179401
252000 1.0107243 0.97832107 -0.14601722 1.2134106
254000 0.98659744 1.0943909 -0.088294528 1.2333875
256000 1.0123386 0.99162386 -0.039344985 1.2164364
258000 0.95762302 1.0676734 0.012199759 1.2076414
260000 0.99842463 0.99944454 -0.060917216 1.1988621
262000 0.97766994 1.0286325 -0.10141058 1.2395609
264000 0.97615582 0.90531751 0.18512981 1.2044769
266000 0.96241019 1.0566036 0.078113491 1.2005364
268000 1.0168176 0.81665569 -0.030349244 1.2025997
270000 0.99827104 1.0749573 -0.056801916 1.1962529
272000 0.9968558 0.94529972 0.028725191 1.1828897
274000 0.97566641 0.91457261 0.015049168 1.1902579
276000 0.99070015 0.94576384 0.025755724 1.1896323
278000 0.96895102 1.0397797 0.080651494 1.1763571
280000 1.0072996 0.89570696 -0.15542961 1.1652696
282000 1.0144016 0.77288242 -0.029784437 1.1582708
284000 1.0181351 0.7694665 -0.054640099 1.1544617
286000 0.98291392 0.9938831 -0.0062479011 1.1596522
288000 0.97279582 1.0358224 -0.13401081 1.1505486
290000 0.99909636 1.0213079 -0.0012162009 1.1399725
292000 0.98460352 0.94742548 -0.031343507 1.1581955
294000 0.99038521 0.98665849 0.051955637 1.1524198
296000 0.99556533 0.86180797 0.055142099 1.1523058
298000 0.97636077 0.98781403 0.013204553 1.129189
300000 0.97032776 1.0678134 0.11879155 1.1176141
302000 1.0003067 0.87686391 0.023979249 1.1210971
304000 1.0209877 0.82384059 -0.019162225 1.1201332
306000 0.98495148 0.97853853 0.0067884582 1.1146556
308000 1.0080456 0.89962394 -0.039014939 1.1072495
310000 0.98760314 1.0580182 -0.0084950963 1.1128641
312000 1.0163132 0.743878 -0.13381063 1.1072529
314000 0.97482482 0.93981262 0.1188583 1.1113744
316000 0.99642196 0.92559157 -0.076386258 1.1180406
318000 0.98668334 0.9960588 0.051851225 1.1282305
320000 1.018361 0.82279734 -0.033370883 1.1306313
322000 1.0101361 0.79697655 -0.0097104031 1.1269227
324000 0.98374012 0.89538164 0.072387631 1.1184602
326000 1.0005728 0.81698596 -0.097827025 1.1067008
328000 0.98296796 1.0888354 -0.00019150727 1.1026196
330000 0.97244323 1.1015085 0.047308269 1.0967215
332000 0.99301221 1.0908167 -0.12434045 1.0911357
334000 0.99279827 1.0192878 -0.030977699 1.0804029
336000 0.98580679 1.055276 0.11288823 1.0750277
338000 0.98757346 1.0072102 0.10201237 1.0933627
340000 1.0067327 0.87701361 0.067382458 1.0850067
342000 1.0154351 0.94291159 0.070059816 1.0801363
344000 0.9743083 1.1059353 0.066961003 1.1524185
346000 0.99814584 1.0356474 -0.016510209 1.1432772
348000 0.97641572 1.1686199 0.046528576 1.1496039
350000 0.99518846 1.0517486 0.13448583 1.1381818
352000 0.98588655 0.98536282 -0.060862396 1.1294455
354000 0.96615995 1.1110151 0.083719861 1.1256268
356000 1.0078606 0.78439358 -0.10603102 1.1362455
358000 0.99367549 1.0489552 0.07500459 1.1427616
360000 0.98811261 1.0329632 0.02037644 1.1456498
362000 0.99543973 0.89319851 0.071618522 1.1516636
364000 0.98165417 0.88412777 0.01496297 1.1479466
366000 0.97321522 1.1989343 0.12226461 1.1407247
368000 0.98226259 0.98513508 -0.032773905 1.145514
370000 0.98523554 0.99191598 0.048321875 1.1454723
372000 0.99757543 1.0704533 -0.044499362 1.1397563
374000 0.96826544 1.0155716 0.10537727 1.1380956
376000 0.97764036 0.91461704 -0.0071326471 1.1311759
378000 0.96197183 1.2654546 0.063772824 1.1342523
380000 0.9563135 0.92013089 0.14946354 1.122797
382000 0.99157671 1.1416454 -0.0020281283 1.1146792
384000 0.99439496 1.0461009 -0.095485509 1.1101174
386000 0.9964491 0.96726205 -0.096570092 1.1043801
388000 0.98660387 0.92002862 -0.050238768 1.1028544
390000 0.97619357 0.95568771 -0.0093958893 1.0994103
392000 0.97043698 1.1278757 0.078765507 1.1095933
394000 0.97478556 0.93908482 0.010033169 1.0896552
396000 0.98483138 0.88172231 -0.0092943479 1.0731932
398000 0.99224177 0.84195437 -0.0059744644 1.0682901
400000 1.0140238 0.88969569 -0.14294787 1.0626823
402000 0.98939257 0.91691411 0.0064466276 1.0892164
404000 0.9930004 0.91196344 -0.15724573 1.0852194
406000 0.98184881 0.93556127 -0.030604809 1.0779626
408000 1.0097979 0.97009028 -0.011737511 1.0779471
410000 0.9913927 0.9406984 0.00091540813 1.0902918
412000 0.95799086 1.1298786 -0.03512312 1.1138864
414000 1.0089501 0.84475916 0.13645298 1.1142398
416000 0.9897256 0.98316262 0.010485716 1.1164657
418000 1.0133333 0.86050241 0.055260598 1.1048567
420000 0.97407581 0.97216618 0.098782939 1.1125666
422000 1.0009494 0.88470049 0.038139624 1.1163397
424000 0.97321563 1.1466493 -0.086272829 1.1173945
426000 0.96442304 1.0810966 -0.061944411 1.1068751
428000 0.9982547 0.87602547 0.081196445 1.1070854
430000 0.97915448 1.1485682 -0.065531916 1.1259179
432000 0.96422041 1.1298461 -0.0082763069 1.1175144
434000 0.99510123 1.0224406 -0.11423626 1.1160931
436000 1.0240236 0.88695443 0.0075708194 1.1085978
438000 0.99001944 1.0244717 0.075879487 1.1212094
440000 1.0116423 0.89412767 -0.11768379 1.1190682
442000 0.98993631 0.92631483 0.067324168 1.111235
444000 0.95107091 1.1508927 0.0019160629 1.1098578
446000 0.98621381 0.91043895 -0.061521131 1.1148618
448000 0.97695569 1.177126 -0.05322695 1.1104409
450000 0.99066051 0.99745105 0.080431605 1.1058023
452000 1.0146071 0.95227428 0.007801217 1.1249178
454000 0.99162513 0.96925579 -0.036153968 1.1100001
456000 1.0215781 0.88427275 -0.050979723 1.1071667
458000 0.98021089 0.84902388 0.08620799 1.1003492
460000 0.98981752 1.0990911 0.047765387 1.1091971
462000 0.97418524 1.023144 -0.11243577 1.101482
464000 0.98172755 1.0676962 0.065603574 1.0966983
466000 0.99352242 0.88377489 0.11849997 1.0934089
468000 0.9916114 0.9404547 0.041191002 1.0843991
470000 0.9675487 1.0416201 0.038992075 1.0909162
472000 0.97960188 1.0249638 0.1102279 1.087763
474000 0.97114134 1.1160983 0.046857123 1.0919439
476000 0.99567674 0.93675154 -0.06832563 1.0879316
478000 0.9784867 1.0660872 0.0030176417 1.0834439
480000 0.99936399 0.97607692 0.096835801 1.0780983
482000 1.0274496 0.87081314 0.054818419 1.0724507
484000 0.97139265 1.0730706 -0.12345378 1.0754362
486000 0.97408298 0.99765268 -0.0064488819 1.0691212
488000 0.9873109 1.0488011 0.001679366 1.0680362
490000 1.0289514 0.77625996 -0.090952895 1.0799008
492000 0.98122494 0.97560083 0.068756789 1.0746541
494000 1.0009648 1.0046735 0.013556863 1.074882
496000 0.96262432 0.94043431 -0.1359217 1.078487
498000 1.00248 1.1101056 -0.065062628 1.0774483
500000 0.964375 1.1119972 0.062483884 1.0744491
Loop time of 78.4755 on 1 procs for 500000 steps with 800 atoms
Pair time (%) = 54.1325 (68.9801)
Neigh time (%) = 12.1352 (15.4637)
Comm time (%) = 1.85499 (2.36378)
Outpt time (%) = 0.00424814 (0.00541334)
Other time (%) = 10.3486 (13.1871)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 267 ave 267 max 267 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 58699
Dangerous builds = 0
variable eta equal v_v11
print "running average viscosity: ${eta}"
running average viscosity: 1.0744491378557243788
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