Homec4science
Diffusion lammps (runner) Browse

lammps/examples/VISCOSITY/log.nemd.2d.1Feb14
03c5ce601babrunner

Last Change
Raw File

log.nemd.2d.1Feb14
View Options

LAMMPS (1 Feb 2014)
# 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 0.6
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 = 2.06394 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 0.92015627
Loop time of 0.897984 on 1 procs for 5000 steps with 800 atoms
Pair time (%) = 0.464335 (51.7087)
Neigh time (%) = 0.13359 (14.8767)
Comm time (%) = 0.0208902 (2.32635)
Outpt time (%) = 5.31673e-05 (0.00592074)
Other time (%) = 0.279115 (31.0824)
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 2.7/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 0.0739425452631974 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 = 2.06486 Mbytes
Step Temp usual E_pair TotEng Press Pxy
5000 2.2074694 1 -1.6087309 0.59597912 1.6684032 -0.13173614
6000 0.92758142 1.0829648 -1.6587109 -0.732289 0.69434408 -0.040395721
7000 0.95692582 1.2000988 -1.7242343 -0.76850461 0.58119159 -0.078038652
8000 1.0214774 1.223802 -1.6519928 -0.63179227 0.74285068 -0.10278761
9000 1.0293091 1.3122841 -1.6684363 -0.64041383 0.90722071 -0.19178365
10000 1.0445241 1.3788798 -1.6688897 -0.62567124 0.71535783 -0.086951926
11000 1.0023372 1.362187 -1.6622117 -0.66112741 0.71746537 -0.18121663
12000 0.95256804 1.379025 -1.6574208 -0.70604349 0.57745775 -0.040719788
13000 1.0318148 1.4597155 -1.6433202 -0.61279515 0.65027764 -0.093427737
14000 1.0332344 1.4031097 -1.6290961 -0.59715319 0.90536763 0.0020682054
15000 1.0277172 1.5207267 -1.6221988 -0.59576627 0.84609392 -0.0074794989
16000 0.99207101 1.5017016 -1.6247974 -0.63396649 0.92606954 -0.10188984
17000 0.96488503 1.4793873 -1.600228 -0.63654911 0.89923523 -0.14261301
18000 0.99547475 1.5236224 -1.635473 -0.64124255 0.68307708 -0.25098795
19000 1.0323664 1.5855445 -1.6227003 -0.59162439 0.94072356 -0.09360683
20000 1.0180092 1.5842966 -1.6143642 -0.59762743 0.93103828 0.040342848
21000 1.0254077 1.6283785 -1.6301278 -0.60600186 0.87479869 0.044804621
22000 0.97172908 1.5990643 -1.6486056 -0.67809118 0.76887644 0.037405021
23000 0.97049676 1.6076804 -1.6058839 -0.63660024 0.93367017 -0.024871417
24000 1.0026729 1.6776495 -1.622805 -0.62138548 0.8635542 -0.038997148
25000 0.9633361 1.6349825 -1.6404336 -0.67830169 0.76001017 -0.1311218
26000 1.0001388 1.6907443 -1.6004823 -0.60159366 0.81806855 -0.18349721
27000 0.94191819 1.6384271 -1.5965443 -0.65580352 0.95785507 -0.086102432
28000 1.0108584 1.731468 -1.6463325 -0.63673767 0.74516073 -0.19911341
29000 1.0138048 1.7289581 -1.6000006 -0.58746311 0.94740326 0.016609077
30000 1.0050557 1.7572204 -1.599182 -0.59538264 0.8223186 -0.24136602
31000 1.0344558 1.7783254 -1.6122236 -0.57906086 1.1734714 -0.23484979
32000 1.0174318 1.8509241 -1.5854329 -0.56927295 0.81903748 -0.096360108
33000 1.0052704 1.7954794 -1.6076165 -0.60360266 0.98062712 -0.23179974
34000 1.0138726 1.7784382 -1.6535717 -0.64096651 0.79928063 -0.184148
35000 1.0108265 1.7715149 -1.5944308 -0.58486783 0.999611 -0.11864672
36000 0.98516241 1.7509661 -1.6285996 -0.64466861 0.94523235 -0.13010197
37000 0.971965 1.7638125 -1.5746851 -0.60393507 1.2265617 -0.077584507
38000 0.93549343 1.8078749 -1.5840479 -0.64972382 1.0484769 0.031083799
39000 1.0416402 1.8705987 -1.5799828 -0.53964462 0.94816785 -0.0034475262
40000 0.96016973 1.856959 -1.5958952 -0.63692565 0.94610429 -0.18285492
41000 1.0051478 1.8962677 -1.5860155 -0.58212412 1.0946382 -0.068521999
42000 1.0081883 1.8593802 -1.6072469 -0.6003189 0.94320687 -0.041090231
43000 0.98432329 1.8786095 -1.5924866 -0.60939372 1.0486461 -0.12281617
44000 1.0262999 1.9116758 -1.5900042 -0.56498711 1.1223199 0.018952448
45000 0.96577584 1.8870562 -1.6252423 -0.66067367 0.96036779 0.0028994584
46000 1.0245911 1.9444906 -1.613004 -0.58969369 0.99363465 -0.021819492
47000 0.93381748 1.8446233 -1.5772527 -0.64460252 1.0674773 -0.11978723
48000 0.97729437 1.8717878 -1.5711485 -0.59507573 1.1563358 -0.25770589
49000 1.0354354 1.987001 -1.6136701 -0.57952894 0.88244264 0.096378234
50000 1.0094924 1.9808787 -1.612573 -0.60434244 0.94984417 -0.11436064
51000 1.027174 1.9461247 -1.5899623 -0.5640723 1.0198367 0.065037899
52000 1.0281396 2.019881 -1.6005519 -0.57369755 1.0350175 -0.057470252
53000 1.018099 2.0455373 -1.6308565 -0.6140301 0.98344621 -0.095749654
54000 1.0378532 2.0621046 -1.6137201 -0.5771642 0.92484803 -0.20897708
55000 0.94998276 1.9258606 -1.5946282 -0.6458329 1.0304527 -0.061356231
Loop time of 11.8921 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 4.938 (41.5235)
Neigh time (%) = 2.88697 (24.2764)
Comm time (%) = 0.342039 (2.87619)
Outpt time (%) = 0.00175095 (0.0147236)
Other time (%) = 3.72331 (31.3092)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 286 ave 286 max 286 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5610 ave 5610 max 5610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5610
Ave neighs/atom = 7.0125
Neighbor list builds = 11310
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:665)
thermo_modify temp tilt
# only need to run for 5400 steps to make a good 100-frame movie
# set 54K steps above in equil and 5400 here simply to make good movie
# 54K and 5400 are multiples of box-swap periodicity = 2700 steps
#dump 1 all custom 50 dump.nemd.2d id type x y z vx
#dump 1 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
#dump_modify 1 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.10508 Mbytes
Step Temp Press Pxy visc vave
55000 0.94998276 1.0303592 -0.063500962 0.85878789 0
56000 1.0301515 1.0617767 -0.10024411 1.3557027 1.2310718
57000 1.0250473 1.0794382 -0.32669382 4.4182117 1.2359148
58000 0.98594086 1.1283437 0.0380247 -0.51424657 1.30918
59000 1.0164723 1.0980255 -0.069171978 0.93548279 1.3260744
60000 1.0711985 1.1230358 -0.125773 1.7009558 1.3414067
61000 0.98932053 0.9807511 -0.15097335 2.0417657 1.3671221
62000 0.998341 0.81153573 -0.020326294 0.27489307 1.3670784
63000 1.0718254 1.1974744 -0.1580162 2.1370132 1.3213502
64000 1.0057042 1.0230065 0.034014907 -0.46001807 1.3316618
65000 1.0040774 1.0303633 -0.078600273 1.0629912 1.3072524
66000 1.0382782 0.93946231 -0.043423028 0.58725363 1.2837103
67000 1.0226248 0.98900989 -0.054099059 0.73163642 1.253851
68000 0.96605035 1.2060528 0.011937095 -0.16143744 1.2420174
69000 1.0326968 1.0489439 -0.055891469 0.75587699 1.2551535
70000 0.98367121 0.87910603 -0.16249968 2.1976479 1.2607276
71000 1.02139 1.0729641 0.014510511 -0.19624035 1.2555329
72000 0.95586405 0.82121701 0.016186091 -0.21890092 1.2511372
73000 1.0422537 0.8674772 0.029604958 -0.40037786 1.2700259
74000 1.0249336 1.0985439 -0.13831417 1.8705627 1.2656874
75000 0.98213321 0.88865968 0.045972743 -0.62173601 1.2577007
76000 0.9397546 0.71322157 -0.060283057 0.81526889 1.2699146
77000 1.0063205 1.0310471 -0.065558372 0.88661232 1.2675723
78000 0.96815308 1.1257553 0.025044943 -0.33870816 1.258244
79000 1.039923 1.1557001 -0.16485925 2.2295587 1.2397555
80000 1.0203604 0.88432557 -0.096887682 1.3103103 1.2385055
81000 0.9504362 0.98117588 -0.078463955 1.0611476 1.2476425
82000 0.9959177 1.1195113 -0.013058798 0.17660736 1.2360316
83000 1.0001019 0.90295804 -0.26432373 3.5747177 1.2339827
84000 1.0173461 0.84946561 0.12193823 -1.6490943 1.2473019
85000 1.0325527 1.0523874 0.030626506 -0.41419329 1.2440578
86000 0.94990925 1.0851851 -0.28324305 3.8305829 1.2410903
87000 1.0408269 1.2359016 -0.07443383 1.0066441 1.2404526
88000 1.0006532 0.92603737 -0.20524087 2.7756803 1.2439314
89000 0.99846847 0.94779421 -0.047328236 0.64006771 1.2443818
90000 0.98628639 1.0536216 -0.15876739 2.1471724 1.2354671
91000 0.99478876 1.0885053 -0.17485734 2.3647731 1.2249337
92000 1.0423662 0.95712108 -0.13839217 1.8716176 1.2276722
93000 0.99308815 1.1868657 -0.13322814 1.8017792 1.2254173
94000 0.9835718 0.98339544 -0.10768988 1.4563994 1.224888
95000 0.94438219 0.97622034 -0.068799681 0.93044784 1.2204198
96000 1.0142012 0.9210571 -0.14001612 1.8935799 1.217945
97000 0.99678643 1.2773861 -0.091691808 1.2400413 1.2063637
98000 0.96852646 0.89124039 -0.28173744 3.810221 1.203252
99000 0.97030968 1.0148935 -0.11717859 1.5847249 1.2020913
100000 0.97709835 1.0314408 -0.16108012 2.1784497 1.2019234
101000 0.97653875 1.1948328 -0.085456884 1.1557201 1.2026873
102000 0.97469158 1.0508677 -0.062662919 0.84745418 1.2062227
103000 0.99620509 0.96826158 -0.10181244 1.3769128 1.20325
104000 0.98933536 1.0077017 -0.18015152 2.4363717 1.1999909
105000 0.99627299 0.93278548 -0.099781319 1.3494439 1.2018992
Loop time of 12.3598 on 1 procs for 50000 steps with 800 atoms
Pair time (%) = 5.02156 (40.6281)
Neigh time (%) = 3.14134 (25.4158)
Comm time (%) = 0.36303 (2.93718)
Outpt time (%) = 0.00100946 (0.00816731)
Other time (%) = 3.83288 (31.0108)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 256 ave 256 max 256 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 = 12247
Dangerous builds = 0
c4science · Help