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lammps/examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1
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LAMMPS (13 Oct 2016)
# 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 # velocity of top edge
# 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 $x 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 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 -0.651099 0.9201564
Loop time of 0.896852 on 1 procs for 5000 steps with 800 atoms
Performance: 2408424.088 tau/day, 5575.056 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47349 | 0.47349 | 0.47349 | 0.0 | 52.79
Neigh | 0.15355 | 0.15355 | 0.15355 | 0.0 | 17.12
Comm | 0.017267 | 0.017267 | 0.017267 | 0.0 | 1.93
Output | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00
Modify | 0.2278 | 0.2278 | 0.2278 | 0.0 | 25.40
Other | | 0.0247 | | | 2.75
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
# shear rate defined relative to perpendicular dimension
variable xyrate equal ${srate}/ly
variable xyrate equal 2.7/ly
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
compute layers all chunk/atom bin/1d y center 0.05 units reduced
fix 4 all ave/chunk 20 250 5000 layers vx 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 = 2.74501 Mbytes
Step Temp c_usual E_pair TotEng Press Pxy
5000 2.2074694 1 -1.6087309 0.59597914 1.6684033 -0.13173628
6000 0.93152386 1.0817401 -1.6660819 -0.73572242 0.68318536 -0.028129339
7000 1.0014344 1.1738041 -1.7011099 -0.70092725 0.6084685 -0.14709751
8000 1.025345 1.29299 -1.7011316 -0.67706829 0.58584918 -0.13492866
9000 0.98439625 1.3014301 -1.6432929 -0.66012715 0.78568164 0.03166088
10000 0.94167448 1.304837 -1.6809777 -0.74048031 0.6767415 0.004807405
11000 0.98264458 1.3309352 -1.6681636 -0.68674728 0.74844384 -0.043997826
12000 0.99403655 1.3580131 -1.6369662 -0.6441722 0.86251493 -0.05441449
13000 1.0396869 1.4466214 -1.6285376 -0.59015033 0.85584533 -0.077842666
14000 1.0356564 1.4337041 -1.6284938 -0.59413198 0.86325196 0.021727401
15000 0.97016374 1.4146903 -1.6551162 -0.68616512 0.78678055 -0.067107584
16000 0.94805836 1.4367742 -1.6338511 -0.68697777 0.8447822 -0.11723973
17000 0.9784648 1.4621496 -1.6203417 -0.64309998 0.93704401 -0.070556149
18000 1.0180917 1.5223337 -1.6393062 -0.62248714 0.81117394 -0.21773149
19000 1.0186815 1.5716289 -1.6471996 -0.62979147 0.71667451 -0.091605896
20000 0.9743659 1.5914706 -1.6150957 -0.64194775 0.94267754 -0.034378699
21000 1.0482265 1.5882157 -1.6319486 -0.58503242 0.86464563 -0.30608617
22000 1.0372488 1.6614229 -1.618808 -0.58285576 0.9619593 0.030218471
23000 1.02322 1.605947 -1.6128071 -0.5908661 0.89153388 -0.054926254
24000 0.99202826 1.6263761 -1.6309182 -0.64013 0.82035209 -0.15760707
25000 0.96842077 1.6079837 -1.6514188 -0.6842086 0.74289154 -0.15054022
26000 1.0131182 1.6599526 -1.6282941 -0.61644236 0.79717592 -0.17392393
27000 0.99274208 1.6992131 -1.6141775 -0.6226763 0.87559226 -0.025698533
28000 1.0124353 1.682322 -1.6350699 -0.62390012 0.81863458 -0.10578616
29000 1.0159913 1.7444965 -1.670694 -0.65597278 0.77422638 -0.074417391
30000 0.95757504 1.6770477 -1.6100645 -0.65368638 0.84900509 -0.13811335
31000 0.9882106 1.7024812 -1.6135646 -0.62658928 0.8819342 -0.0083109839
32000 0.94243022 1.665312 -1.6173333 -0.67608112 1.0312796 -0.087350514
33000 0.97629132 1.804652 -1.6148954 -0.63982441 0.73933894 -0.010842321
34000 0.96053868 1.768861 -1.6201954 -0.66085743 0.80440002 -0.0098573375
35000 0.96192532 1.7951878 -1.5904258 -0.62970292 0.98930679 0.061382767
36000 1.034984 1.835204 -1.5872923 -0.55360202 1.1673704 -0.086610164
37000 1.0109946 1.8695414 -1.5899371 -0.58020627 1.0247304 -0.081320896
38000 1.0189063 1.9299754 -1.591087 -0.57345437 1.0238951 -0.12903934
39000 0.96964269 1.8518181 -1.5939152 -0.62548456 1.064667 -0.12625393
40000 0.93813023 1.8601846 -1.5808497 -0.64389211 1.0739269 -0.21342957
41000 1.01992 1.9192923 -1.6087202 -0.59007511 0.96050424 -0.3264004
42000 1.0243282 1.9429183 -1.5918401 -0.56879229 1.1845661 -0.062971629
43000 1.0696065 2.0074757 -1.5973264 -0.52905692 0.90524954 -0.12923233
44000 1.0338542 1.9624549 -1.6079246 -0.57536268 1.0536815 0.070524993
45000 0.95583069 1.945773 -1.6279372 -0.67330128 0.74985796 -0.17325375
46000 0.99732695 1.966957 -1.631205 -0.6351247 0.77350616 -0.1852725
47000 1.0135329 2.0107676 -1.6049852 -0.59271924 0.87782961 -0.20632054
48000 0.98735917 1.9771245 -1.6053591 -0.61923413 0.92710662 -0.0002501296
49000 0.99618418 1.9493979 -1.6066882 -0.61174922 0.89595133 -0.20337142
50000 1.0651949 2.0467535 -1.6074294 -0.54356601 0.99645561 -0.099150393
51000 1.0559004 2.0710034 -1.5978367 -0.54325617 0.99030671 -0.1841017
52000 1.0083619 2.0399634 -1.5973313 -0.5902299 1.1130916 -0.0079150985
53000 1.0118925 2.0439094 -1.5896233 -0.57899564 1.1640067 -0.053482574
54000 1.0162238 2.0117062 -1.6173202 -0.60236666 0.92299331 -0.13080758
55000 1.0101742 2.0023882 -1.5870609 -0.57814937 1.0166974 -0.2462163
Loop time of 12.3385 on 1 procs for 50000 steps with 800 atoms
Performance: 1750615.444 tau/day, 4052.351 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0133 | 5.0133 | 5.0133 | 0.0 | 40.63
Neigh | 3.262 | 3.262 | 3.262 | 0.0 | 26.44
Comm | 0.29422 | 0.29422 | 0.29422 | 0.0 | 2.38
Output | 0.0017447 | 0.0017447 | 0.0017447 | 0.0 | 0.01
Modify | 3.4226 | 3.4226 | 3.4226 | 0.0 | 27.74
Other | | 0.3447 | | | 2.79
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 282 ave 282 max 282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5602 ave 5602 max 5602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5602
Ave neighs/atom = 7.0025
Neighbor list builds = 11232
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:690)
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 2 all image 50 image.*.jpg vx type zoom 1.2 adiam 1.2
#dump_modify 2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
run 50000
Memory usage per processor = 2.75392 Mbytes
Step Temp Press Pxy v_visc f_vave
55000 1.0101742 1.0168023 -0.24961054 3.3757364 0
56000 0.95430669 0.99109494 -0.11503816 1.5557777 0.73512854
57000 0.96493583 0.77019161 0.032071381 -0.4337338 0.69832329
58000 1.043882 1.190321 -0.1948503 2.6351582 0.7662455
59000 0.99522262 0.71653967 -0.056810457 0.7683054 0.87054399
60000 1.0147329 1.0803743 -0.13097761 1.7713431 0.8832817
61000 0.93812211 1.0627199 -0.044643317 0.60375683 0.96513251
62000 1.0107288 0.93643991 -0.07289428 0.98582325 0.99515995
63000 1.0516762 1.206755 -0.12107833 1.637465 1.0476529
64000 0.96288473 0.99015782 -0.040632073 0.54950872 1.0857708
65000 0.96981457 1.1393466 0.081769326 -1.1058495 1.0598383
66000 1.0549734 0.9862292 -0.038519333 0.52093599 1.0631279
67000 1.0597179 1.0849355 0.026292892 -0.35558543 1.0560538
68000 1.0260974 0.95293785 0.049285149 -0.66653304 1.0367987
69000 1.0075299 1.0303201 0.041539329 -0.56177846 1.0467854
70000 1.0622593 1.2021547 -0.20731618 2.8037469 1.0667574
71000 0.99847432 1.0509829 -0.15346894 2.075516 1.0655178
72000 0.97453232 0.97670205 -0.22406814 3.0303006 1.0503175
73000 0.9641619 0.89104495 -0.12889334 1.7431553 1.0532335
74000 0.99089222 1.0444418 0.18074575 -2.444408 1.0546561
75000 0.99756998 0.91703128 -0.21829649 2.9522447 1.065423
76000 0.93605182 0.98651769 -0.20794378 2.8122346 1.0798472
77000 0.94258356 0.95471193 -0.14211735 1.9219969 1.0819944
78000 0.9798062 1.2187257 -0.063527885 0.85915199 1.1001509
79000 0.96451401 0.84225692 -0.025071518 0.33906755 1.0969807
80000 0.95011391 1.0570755 -0.11124947 1.5045394 1.1031908
81000 0.99774906 0.96668849 -0.0053084468 0.071791507 1.1312113
82000 0.98889022 0.8762984 0.071585243 -0.96811981 1.1334001
83000 0.93610495 1.0660717 -0.047681336 0.64484304 1.1299719
84000 1.0072593 1.0286446 -0.21827159 2.951908 1.1400137
85000 1.0128434 1.0894592 -0.094017511 1.2714941 1.1421825
86000 1.0193552 0.99088304 -0.057046347 0.77149558 1.1372979
87000 0.92702641 0.88034638 -0.012355342 0.16709381 1.1311508
88000 0.98946493 0.81515436 0.016806513 -0.22729152 1.1379472
89000 0.99799875 1.0151454 -0.084127501 1.1377415 1.1352016
90000 0.99133716 0.86655201 -0.056333485 0.76185483 1.1447978
91000 0.94330916 0.93345911 -0.12219086 1.6525109 1.1417404
92000 0.94909987 1.0726222 -0.26976121 3.6482544 1.1573797
93000 0.99526745 1.0680147 -0.1142234 1.5447588 1.1646702
94000 1.0018217 1.1512259 -0.19659509 2.6587547 1.1604884
95000 0.9686519 1.0577224 -0.055162686 0.74602092 1.1618973
96000 0.97493046 0.96044751 0.050456814 -0.68237864 1.1574483
97000 0.97351913 1.0981546 -0.16357534 2.2121952 1.1677946
98000 1.0157509 0.97339707 -0.13441353 1.8178105 1.1778369
99000 1.0414889 1.0103719 -0.10696881 1.4466477 1.1823616
100000 1.0249428 1.0036886 -0.27447626 3.7120207 1.1792453
101000 0.96960692 0.94692891 -0.053860891 0.72841544 1.1752286
102000 1.0371247 1.0840917 -0.040114754 0.54251249 1.1644228
103000 0.96769028 1.0471324 -0.07971043 1.0780049 1.1657168
104000 0.96896685 1.0326732 -0.23873693 3.2286815 1.162545
105000 1.0122807 0.97927614 -0.068569604 0.92733627 1.1684457
Loop time of 12.8562 on 1 procs for 50000 steps with 800 atoms
Performance: 1680117.354 tau/day, 3889.161 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0725 | 5.0725 | 5.0725 | 0.0 | 39.46
Neigh | 3.5621 | 3.5621 | 3.5621 | 0.0 | 27.71
Comm | 0.31528 | 0.31528 | 0.31528 | 0.0 | 2.45
Output | 0.00097895 | 0.00097895 | 0.00097895 | 0.0 | 0.01
Modify | 3.5411 | 3.5411 | 3.5411 | 0.0 | 27.54
Other | | 0.3643 | | | 2.83
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 283 ave 283 max 283 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5585 ave 5585 max 5585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5585
Ave neighs/atom = 6.98125
Neighbor list builds = 12225
Dangerous builds = 0
Total wall time: 0:00:26
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