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sjplimp authored
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11548 f3b2605a-c512-4ea7-a41b-209d697bcdaa
sjplimp authoredgit-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11548 f3b2605a-c512-4ea7-a41b-209d697bcdaa
log.gk.2d.1Feb14 19.25 KiB
LAMMPS (1 Feb 2014)
# 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 0.6
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 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 = 2.06394 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 1.0384043 -1.6029205 0 -0.5658142 0.82862869
8000 1.0288194 -1.5760462 0 -0.54851284 1.1299693
10000 0.97521893 -1.5752855 0 -0.60128557 1.0982639
Loop time of 1.72441 on 1 procs for 10000 steps with 800 atoms
Pair time (%) = 0.929897 (53.9255)
Neigh time (%) = 0.203868 (11.8225)
Comm time (%) = 0.0357857 (2.07524)Outpt time (%) = 5.60284e-05 (0.00324913)
Other time (%) = 0.554805 (32.1736)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 261 ave 261 max 261 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5617 ave 5617 max 5617 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5617
Ave neighs/atom = 7.02125
Neighbor list builds = 1101
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])*33.3333333333333
thermo_style custom step temp press pxy v_v11
run 500000
Memory usage per processor = 2.06394 Mbytes
Step Temp Press Pxy v11
0 1 1.1131139 -0.062970733 0.066088554
2000 1.0080895 1.0200888 -0.11243616 -1.2606591
4000 0.99653513 1.0745982 -0.0075361431 -1.2260153
6000 1.015614 1.0288859 -0.045052789 2.2423387
8000 1.0480587 1.0090528 -0.16941968 1.4483022
10000 1.0340413 0.8935734 -0.016265599 1.367264
12000 1.0208142 0.98827028 -0.098494798 0.96391762
14000 1.0063108 1.1900869 0.041555635 0.71920668
16000 1.0104133 1.0341648 -0.08539107 0.87216885
18000 1.0324239 0.78956816 -0.022393354 0.99812938
20000 0.98065939 1.1290253 0.088823616 0.86856675
22000 1.0456522 0.79585972 -0.10649734 1.3811196
24000 1.0120651 1.0552123 0.21725489 1.648588
26000 1.0441983 0.959829 0.0053239549 1.6192642
28000 0.9936521 1.1033308 -0.0013213764 1.4830182
30000 1.0106141 1.0845812 0.048019524 1.3015283
32000 1.0138237 0.96535384 -0.18328359 1.1659494
34000 0.99897229 1.2265577 -0.057168503 1.3064819
36000 0.98508691 1.1289173 -0.18839382 1.5336228
38000 1.0419001 0.79249301 -0.20846158 1.4200528
40000 1.0152017 0.98214979 -0.0067504119 1.3792256
42000 1.0113905 1.0421477 -0.047659129 1.3414456
44000 1.0201365 1.112008 0.01373301 1.3159903
46000 1.018482 0.93142144 -0.10476936 1.3358778
48000 1.0362661 0.77862744 -0.073200405 1.2925615
50000 1.0200063 0.96817572 -0.082635361 1.2477558
52000 1.018602 1.0281262 0.059387055 1.253828
54000 1.0465938 0.78372671 -0.04203004 1.2411918 56000 1.0376258 1.031501 -0.043675881 1.3662686
58000 0.97830162 1.239229 0.033252127 1.2677821
60000 0.99938589 1.2023844 0.05306354 1.191899
62000 1.010291 0.93962979 0.047429505 1.0726624
64000 1.0233048 0.93855809 0.17161686 1.0641676
66000 1.0124208 1.0309115 -0.0040419968 1.0550472
68000 0.98507874 1.0281731 -0.090367158 1.070317
70000 1.0012103 1.0065752 0.11646809 1.2306811
72000 1.0257593 0.94487824 0.047164906 1.2402116
74000 0.99773444 1.0006634 -0.16947105 1.3458531
76000 0.99053502 1.1802621 -0.011315672 1.4050256
78000 1.0266873 0.92896952 0.053862201 1.4183056
80000 1.0181396 1.0028774 -0.1669873 1.3918642
82000 1.0183891 1.0045513 0.12750581 1.3598925
84000 1.0054008 1.1361355 0.11127961 1.3235664
86000 1.0153982 1.0270658 0.032996007 1.244148
88000 1.0089441 0.94065248 -0.14958385 1.2504534
90000 1.0090826 0.96386446 0.04002849 1.19906
92000 0.98701529 1.0170739 0.048669738 1.230085
94000 1.0271895 0.90965645 0.16524668 1.2111807
96000 1.0588564 0.64666046 -0.012052311 1.1865422
98000 1.01362 1.02233 0.015426298 1.198456
100000 0.99253832 1.1498855 -0.11430916 1.1821222
102000 1.0260594 0.8604477 -0.038050842 1.1482599
104000 1.0248424 1.0639555 -0.08295859 1.1390154
106000 1.0069076 1.2491555 0.010334731 1.1352025
108000 1.0350323 0.9938777 0.028015622 1.1395354
110000 1.0090965 1.0811591 -0.069761835 1.1641264
112000 0.98126774 1.2677506 0.03105149 1.1417489
114000 1.0053548 1.05943 -0.053492802 1.1435347
116000 1.0116531 1.1377687 0.08984011 1.1290702
118000 1.0441155 0.94024004 0.069880409 1.1352496
120000 0.99682009 1.1603848 -0.09404725 1.2100588
122000 1.0155742 1.0078645 -0.027651839 1.173532
124000 0.99222072 1.1821546 -0.0308041 1.2037919
126000 1.0405098 1.155637 0.030664374 1.1715576
128000 1.0187941 0.98070733 0.0059064696 1.2064639
130000 1.0399447 0.99686501 0.14875158 1.26474
132000 1.0409005 1.0086593 0.021338889 1.2817848
134000 1.0476219 0.8026445 0.036028195 1.269031
136000 1.0361278 0.82017002 0.12410098 1.2516208
138000 1.0118377 1.017853 -0.051473869 1.2497683
140000 1.0150827 1.0187598 -0.021626098 1.2422255
142000 1.0299632 0.85581133 0.0020789713 1.3028929
144000 1.0299864 0.75409682 0.067708051 1.2807235
146000 1.0300343 0.95486967 -0.12805174 1.2639701
148000 0.99833371 1.0636801 -0.012957113 1.2450247
150000 1.0218031 1.0345594 -0.0076210772 1.238176
152000 1.0166582 1.000406 0.048913573 1.2350809
154000 1.0200436 0.9620376 0.016990704 1.2277908
156000 1.0174714 0.97523697 -0.089095058 1.2333756
158000 1.0057212 0.98373273 0.10571489 1.2207665
160000 1.0116139 1.0531268 0.040970831 1.1908489
162000 1.0141586 0.97503702 -0.12255418 1.1835675
164000 0.96779259 1.1194358 0.17756759 1.1540165
166000 1.0009628 1.1253418 0.050763812 1.141318
168000 0.99014049 1.1155831 -0.14569673 1.1317473
170000 1.0298577 0.98702864 -0.00084160851 1.1904372
172000 1.0202995 0.96163813 0.0045819305 1.1873872
174000 1.0359389 0.89018321 0.011677378 1.1807412
176000 1.0256185 1.0300041 0.02536302 1.1857003
178000 1.0271101 1.0152692 -0.13910986 1.2068771
180000 1.0194759 0.87873048 -0.12169124 1.1850476
182000 1.0319658 1.0033092 -0.095869229 1.1660609
184000 1.0078723 1.2412606 -0.049703306 1.1654829
186000 1.0442603 0.79824994 -0.093218879 1.1463494
188000 1.0004515 0.90810497 -0.048680818 1.1105332
190000 1.000942 0.94373473 0.10613178 1.1009497
192000 1.048449 0.97658358 -0.17712897 1.1263395
194000 1.0290391 0.98531851 -0.012106089 1.0921536 196000 1.0315571 1.1564407 0.057141413 1.0858253
198000 1.0142691 1.0606813 0.029671093 1.0716634
200000 1.0456713 0.84981128 0.11494717 1.0676611
202000 1.0260155 1.0217822 -0.040530429 1.0674862
204000 0.99472169 1.1602851 0.0051321303 1.0579412
206000 1.0014916 1.0461488 0.0060656173 1.0549157
208000 1.0022353 1.0846052 -0.11185825 1.0596996
210000 1.015275 1.0276323 -0.030737448 1.0550317
212000 1.0039546 1.1104646 0.10845813 1.0540841
214000 1.007432 1.024032 -0.11046904 1.0455342
216000 0.99740694 1.140278 -0.065900867 1.048484
218000 1.0237293 0.94527063 -0.20653618 1.0406664
220000 1.0069562 1.1273839 -0.0067054642 1.0387632
222000 1.0342064 1.0131146 0.035157231 1.0296557
224000 1.003096 1.0550729 0.03305911 1.0335
226000 1.0144191 1.0049718 0.042900611 1.0650019
228000 1.0268793 0.90872396 -0.17661877 1.0602896
230000 1.0237908 0.98063448 -0.029475684 1.0685714
232000 1.0069934 1.1044794 0.13426396 1.0662281
234000 0.98863378 0.95248555 -0.024211245 1.0765215
236000 1.0134171 1.0478432 -0.17292923 1.0525098
238000 1.0120921 0.99042234 0.025333354 1.0420108
240000 1.0042316 1.1071855 -0.02061948 1.0468243
242000 1.0086548 1.0773029 -0.10892118 1.0462304
244000 1.0016487 1.0120587 -0.11220572 1.0530018
246000 1.0206702 0.96270397 0.076386758 1.0399964
248000 1.0106322 0.97979007 -0.056885564 1.0285937
250000 1.0521704 0.90240063 -0.098004463 1.0680676
252000 1.0031792 1.1298376 -0.12700293 1.0572962
254000 1.0023361 1.0397687 -0.042138767 1.055246
256000 1.0207399 0.99843942 -0.067694614 1.0678481
258000 0.98874431 1.228494 0.040793426 1.0558317
260000 1.0183455 1.0188006 -0.17725132 1.0629806
262000 1.0018425 0.94317435 0.10076842 1.0548939
264000 1.0166318 0.8436724 -0.056681878 1.0488651
266000 1.0091103 1.0775158 0.028771667 1.0371622
268000 1.0013292 0.95251758 -0.050343862 1.0496861
270000 0.99674492 1.1472622 -0.11346408 1.1092918
272000 1.0049198 1.0673533 -0.064343803 1.0881727
274000 1.0303169 0.97093144 -0.010278759 1.0846913
276000 1.0273615 0.84473644 -0.017151036 1.0688783
278000 1.0127363 1.2089228 -0.039397817 1.0875618
280000 0.98505511 1.1212088 -0.04261016 1.0843387
282000 1.0210332 0.93982023 -0.11219324 1.0790461
284000 1.0157606 1.0203143 0.0002164565 1.0721431
286000 1.0062366 1.0025507 -0.16786234 1.0720064
288000 0.98467873 1.2326624 -0.081203997 1.0660396
290000 1.0099975 0.88882236 -0.031064103 1.0590327
292000 1.0122416 1.0611548 -0.022475529 1.0519549
294000 1.0104116 1.0266518 -0.10512697 1.0414083
296000 1.0034132 1.0427754 -0.014337433 1.0415291
298000 1.0171588 0.92899734 0.10623709 1.0432266
300000 1.0280222 1.0524269 0.079178549 1.0534846
302000 1.035771 0.87031074 0.029223556 1.0548035
304000 0.99817826 0.96586889 -0.092577945 1.051271
306000 0.99961879 1.1082249 -0.079054344 1.0495721
308000 1.0136108 1.0992365 -0.11696242 1.0384906
310000 0.99316114 1.0758087 0.067733542 1.0276102
312000 1.0106481 0.99751609 0.096323719 1.0260196
314000 1.0069421 1.0474061 -0.0071188531 1.0257001
316000 1.0401836 0.81939716 -0.088499972 1.0302389
318000 1.0095707 1.1018438 -0.0069997734 1.0318989
320000 1.0316135 1.003588 0.010687649 1.0262453
322000 1.009186 0.93116391 0.02270494 1.0207195
324000 1.0186856 1.0207355 -0.049273034 1.0315045
326000 1.0496148 0.9479271 -0.019377803 1.0186608
328000 1.0280164 0.83246382 -0.067199824 1.0121899
330000 1.0292958 0.96946051 -0.0067323294 1.0106087
332000 1.0118055 0.94580297 -0.1158678 0.99982007
334000 1.0090884 1.1414243 -0.082638749 0.98931612 336000 0.96668553 1.2041384 0.0042176058 0.98213644
338000 1.0292409 0.91712359 -0.10674714 1.0014886
340000 1.0056353 1.0054878 -0.067790602 0.97639404
342000 1.0105034 1.1000009 -0.065106486 0.98781851
344000 1.0296097 0.97446628 -0.11031518 0.98121512
346000 1.022878 1.0302285 -0.092796664 1.0040982
348000 1.0200294 0.84461432 0.001340607 1.0143357
350000 0.9942428 1.0974217 0.032976965 1.0066948
352000 1.0038173 1.1777572 -0.02105487 0.99841101
354000 1.0363725 1.0742789 -0.068095272 0.99311679
356000 1.0142211 0.93380261 0.011873553 0.98531527
358000 0.99346289 1.2559305 -0.1027067 0.98126142
360000 0.99957906 1.0307272 -0.052751638 1.0043971
362000 1.0196151 1.1349776 -0.09260849 1.0011441
364000 1.0371154 0.88342615 0.12450793 0.99706262
366000 1.014625 1.0304514 -0.027977229 0.9921965
368000 1.0584324 0.83998131 -0.07933342 0.99525213
370000 1.0480268 0.83980605 -0.089536871 0.99539504
372000 1.0124627 1.060244 0.14069432 0.99714731
374000 1.0319035 0.80898054 0.13773298 0.99196179
376000 1.0175987 0.86095756 -0.022196463 0.99034665
378000 1.024277 0.96855584 -0.082372168 0.98711506
380000 1.0309973 0.91266594 -0.0038718874 1.0004437
382000 1.0195474 0.84949163 -0.090011652 0.97877658
384000 1.0127199 0.92573997 -0.047436984 0.99568293
386000 1.0155482 1.0260345 0.058825776 1.0032397
388000 1.0341266 1.0684283 0.042324727 0.9962933
390000 1.015419 1.2043476 -0.065809399 0.98978792
392000 0.99510423 1.0679104 0.1194931 0.98198405
394000 0.99275686 1.1827413 0.064956819 1.0203304
396000 1.0004565 1.1524019 -0.12851079 1.0328568
398000 1.0230487 1.1653679 0.066552948 1.0356753
400000 1.0246668 1.0378562 -0.014987589 1.0388305
402000 0.99713302 0.98996019 -0.12440697 1.0369703
404000 1.0078626 1.0678616 -0.0361031 1.0292353
406000 1.0264278 0.91482461 0.1001659 1.0269674
408000 0.99866487 1.1801482 -0.062540579 1.021615
410000 0.97734309 1.1861242 0.05416943 1.014162
412000 1.0157071 0.9442541 0.22262556 1.0141824
414000 0.98254015 1.2581149 0.015246929 1.0085563
416000 1.0325598 0.90098178 0.041081387 1.0044668
418000 1.0285532 0.82679005 -0.10105529 1.0017654
420000 1.0324223 0.95868597 0.024808094 0.99789922
422000 1.0056928 1.0690554 -0.024850455 1.0197904
424000 0.99482351 1.1228662 0.049501791 1.0272213
426000 1.0222594 0.97941801 -0.11968536 1.0186344
428000 1.0111263 1.1141009 0.1437415 1.0130656
430000 0.98139004 1.0366378 0.067956814 1.0108714
432000 0.98613642 1.0119979 0.041509654 1.0033766
434000 1.0230324 0.86869314 0.055734923 1.0020727
436000 1.0212417 0.8436869 -0.022905431 0.9985587
438000 1.0093302 0.97821341 0.023100883 0.99687144
440000 1.0419272 0.87856473 -0.020071536 0.99762884
442000 1.0172555 0.90164932 0.19704935 0.99904268
444000 1.0399087 1.0051297 -0.022213498 0.99616218
446000 1.0281756 1.0867446 -0.048363674 0.99230925
448000 0.98980118 1.1266212 0.16193455 0.99381525
450000 1.0397066 1.0216642 -0.017946472 1.0119634
452000 1.0148816 1.0709423 -0.072255226 1.0011103
454000 0.97505657 1.1553955 -0.019747328 0.9952685
456000 1.0423127 0.93927199 0.1031593 1.0160711
458000 1.0185738 0.9317795 -0.14238875 1.0212947
460000 1.0254941 0.94237321 0.17279884 1.0176267
462000 1.0331624 0.90556647 -0.17064389 1.0197747
464000 1.0170281 0.98452898 -0.17212408 1.006159
466000 1.0201836 1.0477978 0.0063101913 0.99741201
468000 0.99055758 1.19768 -0.04304958 0.99395064
470000 1.0140337 1.1042576 0.06483947 1.0006513
472000 1.0369845 0.82562513 -0.06621037 1.0320218
474000 1.0149565 0.86550007 0.060011486 1.0723558 476000 1.0056806 0.99384495 -0.069441814 1.0623019
478000 1.0333144 0.91193908 0.0045431056 1.0625281
480000 1.0176402 0.90416174 -0.065787627 1.0534142
482000 0.99406615 1.1281258 0.15969853 1.0526461
484000 1.0119737 1.0284268 -0.020359549 1.0710582
486000 0.98481179 1.08347 0.049797547 1.0738962
488000 1.0444857 0.87660853 0.0011127729 1.0730464
490000 1.0253141 0.92405109 0.070770655 1.0712017
492000 1.0167975 0.88249423 0.12097353 1.0689941
494000 0.96051412 1.3166559 -0.034841104 1.0721439
496000 1.0284614 1.0149666 -0.0055275607 1.0641449
498000 1.0107367 1.0406533 -0.030980028 1.0623882
500000 0.9902026 1.2232023 -0.038731213 1.0606073
Loop time of 70.5579 on 1 procs for 500000 steps with 800 atoms
Pair time (%) = 47.4863 (67.3012)
Neigh time (%) = 11.1177 (15.7568)
Comm time (%) = 1.90226 (2.69603)
Outpt time (%) = 0.00377345 (0.00534802)
Other time (%) = 10.0479 (14.2406)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 260 ave 260 max 260 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5611 ave 5611 max 5611 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5611
Ave neighs/atom = 7.01375
Neighbor list builds = 59311
Dangerous builds = 0
variable eta equal v_v11
print "running average viscosity: ${eta}"
running average viscosity: 1.06060731864499