Skip to content
Snippets Groups Projects
Commit 16d55a7a authored by Adam Fekete's avatar Adam Fekete
Browse files

rerun example for generating main log file

parent eab58171
Branches
Tags
No related merge requests found
Expand all Show whitespace changes
Inline Side-by-side
Showing
with 33305 additions and 33080 deletions
test/examples/methane/.gitkeep 100644 → 100755
+ 0
− 0
View file @ 16d55a7a
File mode changed from 100644 to 100755
test/examples/methane/64xmethane-nvt.lammpstrj
+ 32320
− 32320
View file @ 16d55a7a
This diff is collapsed.
test/examples/methane/64xmethane-nvt.restart 0 → 100644
+ 0
− 0
View file @ 16d55a7a
File added
test/examples/methane/64xmethane-nvt.v 0 → 100644
+ 0
− 0
View file @ 16d55a7a
File added
test/examples/methane/input.methane_nvt_thermo_style_one
+ 2
− 2
View file @ 16d55a7a
......@@ -40,13 +40,13 @@ dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z ix iy iz
#dump_modify 1 unwrap no
# output log
#log log.64xmethane-nvt-thermo_style_one
log log.64xmethane-nvt-thermo_style_one
# 10.0ps
run 40000
# keep a restart of this, too.
write_restart 64xmethane-nvt.restart
write_restart 64xmethane-nvt.v
# this still has not been relaxed for pressure,
# but it should be pretty close.
test/examples/methane/log.64xmethane-nvt-thermo_style_custom
+ 129
− 118
View file @ 16d55a7a
......@@ -4,130 +4,140 @@ run 40000
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
Memory usage per processor = 8.69091 Mbytes
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 8.51606 Mbytes
Step Temp PotEng KinEng Press Volume Density
0 99.699704 -89.822747 94.802296 -2841.6646 3899.6913 0.43720422
400 102.18008 -44.353126 97.16083 1848.4216 3899.6913 0.43720422
800 101.51832 -34.326634 96.531579 -3501.2843 3899.6913 0.43720422
1200 104.85855 -53.591447 99.707728 2415.9461 3899.6913 0.43720422
1600 96.998043 -0.66006397 92.233345 -2292.6491 3899.6913 0.43720422
2000 95.938372 -6.5134449 91.225727 1918.1434 3899.6913 0.43720422
2400 97.295782 -13.331207 92.516458 -2682.637 3899.6913 0.43720422
2800 92.047695 -39.981605 87.526165 1379.9204 3899.6913 0.43720422
3200 104.22842 -66.501436 99.108554 -1878.2391 3899.6913 0.43720422
3600 104.14393 -58.965158 99.028212 6.1760784 3899.6913 0.43720422
4000 97.00878 -48.08041 92.243554 -347.66766 3899.6913 0.43720422
4400 106.6057 -58.226067 101.36905 -276.41202 3899.6913 0.43720422
4800 99.914697 -84.333096 95.006728 -911.67942 3899.6913 0.43720422
5200 100.75587 -41.382726 95.806582 84.474243 3899.6913 0.43720422
5600 101.14823 -22.2367 96.179664 -877.28658 3899.6913 0.43720422
6000 93.955341 -44.134693 89.340105 128.78652 3899.6913 0.43720422
6400 92.628111 -75.104486 88.078071 -1224.4211 3899.6913 0.43720422
6800 99.997558 -47.372085 95.085518 -98.836739 3899.6913 0.43720422
7200 100.9698 -52.077606 96.010004 -1904.4399 3899.6913 0.43720422
7600 102.55287 -44.078106 97.515306 1079.5817 3899.6913 0.43720422
8000 93.677695 -18.848627 89.076097 -2345.9626 3899.6913 0.43720422
8400 94.859755 -58.47051 90.200093 1959.1458 3899.6913 0.43720422
8800 104.04226 -74.762899 98.931538 -3445.9056 3899.6913 0.43720422
9200 105.12357 -49.039036 99.959732 2728.6099 3899.6913 0.43720422
9600 103.85797 -67.71379 98.756305 -2217.6048 3899.6913 0.43720422
10000 102.55478 -37.546236 97.517126 1160.2464 3899.6913 0.43720422
10400 89.532572 -73.093818 85.134589 -1817.1604 3899.6913 0.43720422
10800 91.250686 -36.213651 86.768307 299.67453 3899.6913 0.43720422
11200 95.594096 -25.937584 90.898362 -1134.0614 3899.6913 0.43720422
11600 96.717639 -62.804705 91.966715 -326.87941 3899.6913 0.43720422
12000 104.68771 -72.948368 99.545279 -1024.214 3899.6913 0.43720422
12400 96.705023 -91.93908 91.954718 -1383.566 3899.6913 0.43720422
12800 97.054258 -109.64038 92.286798 -535.80475 3899.6913 0.43720422
13200 98.9447 -52.606252 94.084379 -2006.2046 3899.6913 0.43720422
13600 105.05882 -20.234751 99.898163 782.94479 3899.6913 0.43720422
14000 107.36993 -78.596468 102.09575 -1927.1424 3899.6913 0.43720422
14400 99.755223 -54.189223 94.855087 808.81671 3899.6913 0.43720422
14800 94.041944 -70.021355 89.422454 -1963.5381 3899.6913 0.43720422
15200 99.100319 -70.918255 94.232353 105.21605 3899.6913 0.43720422
15600 102.87938 -16.443248 97.825777 -1168.2347 3899.6913 0.43720422
16000 102.33545 -31.06089 97.308572 444.81666 3899.6913 0.43720422
16400 102.27673 -3.5736671 97.25273 -1662.956 3899.6913 0.43720422
16800 96.547798 -13.8164 91.805216 1123.4637 3899.6913 0.43720422
17200 103.49411 -57.901784 98.410316 -2646.5471 3899.6913 0.43720422
17600 100.13108 -21.284294 95.21248 1006.724 3899.6913 0.43720422
18000 108.38479 -55.630459 103.06076 -1354.5026 3899.6913 0.43720422
18400 113.0929 -15.073939 107.53759 -611.50934 3899.6913 0.43720422
18800 99.133015 -13.488475 94.263443 488.76731 3899.6913 0.43720422
19200 102.30238 -70.026171 97.27712 -2394.376 3899.6913 0.43720422
19600 96.790744 -62.038386 92.036228 1105.6819 3899.6913 0.43720422
20000 105.16683 -52.721659 100.00087 -1647.8289 3899.6913 0.43720422
20400 105.70698 -19.926224 100.51448 410.2422 3899.6913 0.43720422
20800 103.53984 -52.962407 98.453797 -977.97868 3899.6913 0.43720422
21200 101.43154 -35.041222 96.449066 -160.46637 3899.6913 0.43720422
21600 98.670006 -57.474199 93.823178 -326.73021 3899.6913 0.43720422
22000 97.953943 -30.312348 93.142289 -615.34146 3899.6913 0.43720422
22400 96.011555 -53.914655 91.295315 -193.22166 3899.6913 0.43720422
22800 102.39627 -70.929479 97.366404 -884.32994 3899.6913 0.43720422
23200 107.82018 -58.310762 102.52388 -1300.4477 3899.6913 0.43720422
23600 102.73695 -69.932904 97.690351 641.48035 3899.6913 0.43720422
24000 96.460847 -67.562244 91.722537 -1791.2607 3899.6913 0.43720422
24400 93.796128 -61.744989 89.188712 873.89034 3899.6913 0.43720422
24800 97.353953 -23.030472 92.571771 -1871.9361 3899.6913 0.43720422
25200 97.091705 -3.0955371 92.322405 1280.3854 3899.6913 0.43720422
25600 98.648844 -32.406075 93.803055 -1381.2537 3899.6913 0.43720422
26000 100.18179 -42.205042 95.260697 322.01702 3899.6913 0.43720422
26400 100.74179 -38.727721 95.793193 -862.08064 3899.6913 0.43720422
26800 90.111333 -76.364269 85.68492 -1640.9138 3899.6913 0.43720422
27200 93.312795 -14.435862 88.729122 1708.28 3899.6913 0.43720422
27600 102.23172 -42.249845 97.209935 -2880.6641 3899.6913 0.43720422
28000 104.37293 -65.260309 99.245961 2121.8475 3899.6913 0.43720422
28400 104.29906 -36.495584 99.175724 -3296.3716 3899.6913 0.43720422
28800 94.003175 -57.580857 89.385589 2161.5287 3899.6913 0.43720422
29200 94.690933 -47.458231 90.039563 -3090.7786 3899.6913 0.43720422
29600 100.45435 -40.849141 95.51987 1118.3437 3899.6913 0.43720422
30000 95.933737 -33.06947 91.221319 -2084.8456 3899.6913 0.43720422
30400 103.68687 -78.310292 98.593609 501.20335 3899.6913 0.43720422
30800 97.692654 -69.858501 92.893835 -1481.6139 3899.6913 0.43720422
31200 93.87282 -3.3878061 89.261637 770.99042 3899.6913 0.43720422
31600 99.300147 -66.68831 94.422366 -708.48547 3899.6913 0.43720422
32000 108.07854 -51.928793 102.76955 63.553384 3899.6913 0.43720422
32400 101.28547 -9.2301269 96.310164 -879.064 3899.6913 0.43720422
32800 101.25503 -77.004404 96.281219 -212.82716 3899.6913 0.43720422
33200 97.691616 -46.698725 92.892848 -1766.6266 3899.6913 0.43720422
33600 98.92508 -13.178514 94.065722 556.92298 3899.6913 0.43720422
34000 100.03798 -40.957651 95.123956 -1814.8718 3899.6913 0.43720422
34400 99.722709 -11.917666 94.82417 1165.8056 3899.6913 0.43720422
34800 103.63061 -32.987362 98.540111 -1107.3729 3899.6913 0.43720422
35200 101.8862 -34.492921 96.881385 -302.68667 3899.6913 0.43720422
35600 100.13402 -63.516759 95.215281 82.545283 3899.6913 0.43720422
36000 95.371028 -77.653394 90.686251 -2067.3795 3899.6913 0.43720422
36400 94.414731 7.3396958 89.776929 1175.4557 3899.6913 0.43720422
36800 98.210629 -10.242483 93.386367 -2768.3386 3899.6913 0.43720422
37200 104.41074 -8.231639 99.281915 2618.9021 3899.6913 0.43720422
37600 102.60834 -50.497971 97.568053 -3807.4432 3899.6913 0.43720422
38000 98.134676 -51.628077 93.314144 3065.6292 3899.6913 0.43720422
38400 94.150428 -42.606959 89.525609 -3758.2934 3899.6913 0.43720422
38800 98.217332 -66.058112 93.392741 2640.2861 3899.6913 0.43720422
39200 98.074978 -16.484175 93.257379 -3198.9899 3899.6913 0.43720422
39600 102.11461 -68.070886 97.098573 1515.9944 3899.6913 0.43720422
40000 97.92377 -63.290956 93.113598 -2705.14 3899.6913 0.43720422
Loop time of 132.433 on 1 procs for 40000 steps with 320 atoms
0 0 236.82259 0 23932.721 3899.6913 0.43720426
400 42.170619 310.33602 40.099131 -19954.362 3899.6913 0.43720426
800 80.98602 233.92794 77.007857 22799.821 3899.6913 0.43720426
1200 63.638898 205.85696 60.512854 -22688.205 3899.6913 0.43720426
1600 125.03824 80.977464 118.89617 24872.686 3899.6913 0.43720426
2000 132.65412 179.21176 126.13794 -25280.813 3899.6913 0.43720426
2400 68.74818 204.52813 65.37116 25404.029 3899.6913 0.43720426
2800 106.62011 -30.495921 101.38276 -23779.763 3899.6913 0.43720426
3200 81.924583 196.14283 77.900317 20030.528 3899.6913 0.43720426
3600 38.776859 141.93606 36.872078 -16121.888 3899.6913 0.43720426
4000 73.251026 91.314034 69.652819 14829.442 3899.6913 0.43720426
4400 95.448747 177.16847 90.760152 -10754.85 3899.6913 0.43720426
4800 74.531106 134.80221 70.870019 11443.604 3899.6913 0.43720426
5200 113.23379 58.345589 107.67157 -6850.2391 3899.6913 0.43720426
5600 161.66144 24.558493 153.72037 6950.5199 3899.6913 0.43720426
6000 109.12102 115.79324 103.76082 -5079.5277 3899.6913 0.43720426
6400 114.18323 114.91907 108.57437 6952.5685 3899.6913 0.43720426
6800 140.09315 19.733937 133.21155 -5687.3146 3899.6913 0.43720426
7200 77.017167 15.296254 73.233961 1809.3423 3899.6913 0.43720426
7600 82.146728 -49.821313 78.11155 -620.8975 3899.6913 0.43720426
8000 91.620752 -83.6084 87.120194 -6791.187 3899.6913 0.43720426
8400 61.279764 -38.913655 58.269604 4329.6396 3899.6913 0.43720426
8800 77.861735 -75.554354 74.037043 -9227.9846 3899.6913 0.43720426
9200 109.16809 -67.884475 103.80558 5352.4797 3899.6913 0.43720426
9600 103.33272 -52.232644 98.256848 -8911.3128 3899.6913 0.43720426
10000 118.40703 -61.011796 112.59068 5698.6657 3899.6913 0.43720426
10400 132.17421 -89.945318 125.68161 -6128.8722 3899.6913 0.43720426
10800 127.5984 -57.588305 121.33056 2473.2672 3899.6913 0.43720426
11200 93.995587 -54.224199 89.378374 -3784.5778 3899.6913 0.43720426
11600 121.42086 -75.070286 115.45647 1712.8154 3899.6913 0.43720426
12000 93.06677 -51.087486 88.495182 -7078.2331 3899.6913 0.43720426
12400 79.472363 -58.521917 75.568554 4849.9737 3899.6913 0.43720426
12800 87.350598 -18.396516 83.059797 -9548.9665 3899.6913 0.43720426
13200 84.19161 -22.491981 80.055984 5135.448 3899.6913 0.43720426
13600 73.330517 -26.181368 69.728405 -8476.4457 3899.6913 0.43720426
14000 94.614208 -48.590677 89.966607 4085.6464 3899.6913 0.43720426
14400 104.31288 -44.717118 99.188867 -6404.7229 3899.6913 0.43720426
14800 112.42709 -38.912166 106.90449 2615.2737 3899.6913 0.43720426
15200 116.98429 -76.48999 111.23783 -3956.669 3899.6913 0.43720426
15600 116.24293 -53.847135 110.53289 949.57325 3899.6913 0.43720426
16000 102.35486 -60.164875 97.327022 -3245.2489 3899.6913 0.43720426
16400 98.509731 -83.058086 93.670776 523.13227 3899.6913 0.43720426
16800 93.856029 -77.228566 89.245671 -4534.967 3899.6913 0.43720426
17200 82.862943 -31.407353 78.792583 512.05326 3899.6913 0.43720426
17600 92.246236 -42.460851 87.714954 -3386.955 3899.6913 0.43720426
18000 90.573763 -2.4536027 86.124635 -985.73563 3899.6913 0.43720426
18400 86.448307 -22.589448 82.201828 -1417.9972 3899.6913 0.43720426
18800 92.694425 -72.654401 88.141128 -2257.4645 3899.6913 0.43720426
19200 103.78071 -43.10104 98.682832 -500.31491 3899.6913 0.43720426
19600 110.51425 -46.55707 105.08561 -2286.4077 3899.6913 0.43720426
20000 111.55761 -54.121178 106.07772 -83.271072 3899.6913 0.43720426
20400 106.25254 -66.641039 101.03324 -2087.2331 3899.6913 0.43720426
20800 102.1888 -84.27007 97.169119 -1028.9644 3899.6913 0.43720426
21200 91.989317 -68.662556 87.470655 -1853.9654 3899.6913 0.43720426
21600 96.670417 -17.753249 91.921812 -939.46553 3899.6913 0.43720426
22000 92.76359 -34.624773 88.206895 -1947.4447 3899.6913 0.43720426
22400 96.854286 -46.385068 92.096649 -314.41148 3899.6913 0.43720426
22800 91.031169 -5.1749597 86.559573 -2572.0254 3899.6913 0.43720426
23200 93.765382 -4.4879523 89.159477 461.1709 3899.6913 0.43720426
23600 101.04845 -41.586196 96.084793 -3044.2266 3899.6913 0.43720426
24000 109.09352 -33.941039 103.73468 242.67198 3899.6913 0.43720426
24400 106.83291 -16.436016 101.58511 -1855.3463 3899.6913 0.43720426
24800 107.5377 -8.7004463 102.25528 -475.74819 3899.6913 0.43720426
25200 102.22146 -90.159261 97.200184 -2155.4347 3899.6913 0.43720426
25600 100.9791 -56.300469 96.018844 -832.78753 3899.6913 0.43720426
26000 100.58994 -34.515481 95.648797 -2079.9828 3899.6913 0.43720426
26400 102.13829 17.684663 97.121093 -184.33268 3899.6913 0.43720426
26800 97.913385 -29.164711 93.103723 -1626.8641 3899.6913 0.43720426
27200 98.830635 -35.138487 93.975917 -1527.2921 3899.6913 0.43720426
27600 99.046289 8.7541206 94.180978 -911.00352 3899.6913 0.43720426
28000 99.111014 -49.203539 94.242523 -2332.2739 3899.6913 0.43720426
28400 100.29043 -39.929201 95.364007 -271.61864 3899.6913 0.43720426
28800 115.41288 -29.72555 109.74361 -2742.9954 3899.6913 0.43720426
29200 107.94994 -54.623643 102.64726 -735.3395 3899.6913 0.43720426
29600 95.529576 -15.134643 90.837011 -1532.0223 3899.6913 0.43720426
30000 106.93724 -48.638255 101.68431 -1392.6149 3899.6913 0.43720426
30400 99.565043 -60.164838 94.674249 -1872.7857 3899.6913 0.43720426
30800 99.790003 -71.675461 94.888159 -877.71444 3899.6913 0.43720426
31200 101.96558 -34.883198 96.956871 -2666.5694 3899.6913 0.43720426
31600 95.019312 -21.982862 90.351812 -70.18726 3899.6913 0.43720426
32000 91.13249 -32.011781 86.655917 -3190.2712 3899.6913 0.43720426
32400 97.508653 -57.268621 92.718872 14.171425 3899.6913 0.43720426
32800 103.83682 -14.681429 98.736192 -2525.3295 3899.6913 0.43720426
33200 102.40394 -21.284543 97.373698 -970.42186 3899.6913 0.43720426
33600 106.5316 -64.167964 101.2986 -869.90896 3899.6913 0.43720426
34000 102.34467 -11.608225 97.317337 -2639.3492 3899.6913 0.43720426
34400 99.331541 -26.892683 94.452217 236.07704 3899.6913 0.43720426
34800 98.333341 -29.446047 93.503051 -2796.481 3899.6913 0.43720426
35200 104.46624 -46.82507 99.334694 -312.30562 3899.6913 0.43720426
35600 103.958 -43.622667 98.851416 -2295.0989 3899.6913 0.43720426
36000 101.72744 -38.42648 96.730428 -636.3713 3899.6913 0.43720426
36400 95.274738 -31.677875 90.594691 -2103.3573 3899.6913 0.43720426
36800 95.394514 -13.350899 90.708583 -392.04941 3899.6913 0.43720426
37200 99.204759 -22.6491 94.331663 -2369.0031 3899.6913 0.43720426
37600 100.00616 -3.0463463 95.093702 -326.97652 3899.6913 0.43720426
38000 109.08255 -53.073441 103.72425 -2170.681 3899.6913 0.43720426
38400 105.1299 15.336043 99.965749 -245.37205 3899.6913 0.43720426
38800 103.76901 -17.770275 98.671713 -1396.4733 3899.6913 0.43720426
39200 106.80306 -35.522794 101.55673 -2080.199 3899.6913 0.43720426
39600 93.75398 -37.739319 89.148635 -598.53989 3899.6913 0.43720426
40000 103.97395 -19.846971 98.866588 -1236.6744 3899.6913 0.43720426
Loop time of 34.648 on 6 procs for 40000 steps with 320 atoms
Pair time (%) = 125.964 (95.1151)
Bond time (%) = 2.09382 (1.58104)
Neigh time (%) = 1.81563 (1.37098)
Comm time (%) = 1.70091 (1.28435)
Outpt time (%) = 0.124259 (0.0938276)
Other time (%) = 0.734602 (0.554696)
Performance: 24.936 ns/day, 0.962 hours/ns, 1154.466 timesteps/s
86.0% CPU use with 6 MPI tasks x no OpenMP threads
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6149 ave 6149 max 6149 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 134624 ave 134624 max 134624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.886 | 22.224 | 24.054 | 22.8 | 64.14
Bond | 0.27925 | 0.32386 | 0.36312 | 5.0 | 0.93
Neigh | 0.23306 | 0.23509 | 0.23746 | 0.3 | 0.68
Comm | 9.3003 | 11.104 | 12.46 | 32.3 | 32.05
Output | 0.031933 | 0.032164 | 0.033211 | 0.3 | 0.09
Modify | 0.40567 | 0.46847 | 0.52303 | 5.8 | 1.35
Other | | 0.261 | | | 0.75
Total # of neighbors = 134624
Ave neighs/atom = 420.7
Nlocal: 53.3333 ave 64 max 48 min
Histogram: 2 0 2 0 0 1 0 0 0 1
Nghost: 3871 ave 3909 max 3824 min
Histogram: 1 0 1 0 1 1 0 0 0 2
Neighs: 22383 ave 25722 max 19207 min
Histogram: 1 0 1 0 1 1 1 0 0 1
Total # of neighbors = 134298
Ave neighs/atom = 419.681
Ave special neighs/atom = 4
Neighbor list builds = 267
Neighbor list builds = 182
Dangerous builds = 0
# keep a restart of this, too.
......@@ -135,3 +145,4 @@ write_restart 64xmethane-nvt.restart
# this still has not been relaxed for pressure,
# but it should be pretty close.
Total wall time: 0:00:34
test/examples/methane/log.64xmethane-nvt-thermo_style_multi
+ 532
− 521
View file @ 16d55a7a
This diff is collapsed.
test/examples/methane/log.64xmethane-nvt-thermo_style_one
+ 130
− 119
View file @ 16d55a7a
......@@ -4,134 +4,145 @@ run 40000
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
Memory usage per processor = 8.69091 Mbytes
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 8.51606 Mbytes
Step Temp E_pair E_mol TotEng Press
0 99.699704 -154.31804 64.495298 4.9795486 -2841.6646
400 102.18008 -108.61436 64.261231 52.807704 1848.4216
800 101.51832 -105.12539 70.798761 62.204945 -3501.2843
1200 104.85855 -125.10775 71.516302 46.116281 2415.9461
1600 96.998043 -72.911294 72.25123 91.573281 -2292.6491
2000 95.938372 -76.6826 70.169155 84.712282 1918.1434
2400 97.295782 -78.576027 65.24482 79.185251 -2682.637
2800 92.047695 -110.74159 70.759982 47.544561 1379.9204
3200 104.22842 -133.99502 67.493589 32.607118 -1878.2391
3600 104.14393 -123.51587 64.550715 40.063054 6.1760784
4000 97.00878 -116.56418 68.483775 44.163144 -347.66766
4400 106.6057 -120.26843 62.04236 43.142988 -276.41202
4800 99.914697 -150.32594 65.992843 10.673632 -911.67942
5200 100.75587 -106.88989 65.507164 54.423857 84.474243
5600 101.14823 -90.82177 68.58507 73.942964 -877.28658
6000 93.955341 -110.74374 66.609048 45.205412 128.78652
6400 92.628111 -142.48014 67.375654 12.973585 -1224.4211
6800 99.997558 -118.38321 71.011129 47.713433 -98.836739
7200 100.9698 -122.71741 70.639805 43.932398 -1904.4399
7600 102.55287 -110.72499 66.646883 53.4372 1079.5817
8000 93.677695 -83.872187 65.02356 70.22747 -2345.9626
8400 94.859755 -120.29717 61.826658 31.729583 1959.1458
8800 104.04226 -139.26191 64.499009 24.16864 -3445.9056
9200 105.12357 -112.93962 63.900579 50.920695 2728.6099
9600 103.85797 -131.40842 63.694627 31.042516 -2217.6048
10000 102.55478 -100.44134 62.895104 59.97089 1160.2464
10400 89.532572 -137.32443 64.230612 12.040771 -1817.1604
10800 91.250686 -99.573248 63.359597 50.554656 299.67453
11200 95.594096 -94.748602 68.811018 64.960778 -1134.0614
11600 96.717639 -132.79416 69.989453 29.16201 -326.87941
12000 104.68771 -140.9818 68.033429 26.596911 -1024.214
12400 96.705023 -159.66143 67.722352 0.01563768 -1383.566
12800 97.054258 -172.894 63.253619 -17.353581 -535.80475
13200 98.9447 -113.16096 60.55471 41.478127 -2006.2046
13600 105.05882 -88.317811 68.08306 79.663412 782.94479
14000 107.36993 -142.64294 64.046473 23.499277 -1927.1424
14400 99.755223 -119.3447 65.15548 40.665865 808.81671
14800 94.041944 -137.23279 67.211431 19.401099 -1963.5381
15200 99.100319 -131.61121 60.692958 23.314099 105.21605
15600 102.87938 -86.855016 70.411768 81.38253 -1168.2347
16000 102.33545 -103.12103 72.060137 66.247682 444.81666
16400 102.27673 -70.938622 67.364955 93.679063 -1662.956
16800 96.547798 -81.196617 67.380217 77.988816 1123.4637
17200 103.49411 -121.40354 63.501753 40.508532 -2646.5471
17600 100.13108 -87.846155 66.561861 73.928186 1006.724
18000 108.38479 -121.03553 65.405074 47.430298 -1354.5026
18400 113.0929 -80.527038 65.453099 92.463656 -611.50934
18800 99.133015 -80.010975 66.5225 80.774968 488.76731
19200 102.30238 -130.38354 60.357367 27.250949 -2394.376
19600 96.790744 -129.10804 67.069653 29.997842 1105.6819
20000 105.16683 -118.17687 65.455216 47.279209 -1647.8289
20400 105.70698 -90.625193 70.698969 80.58826 410.2422
20800 103.53984 -120.79658 67.834178 45.49139 -977.97868
21200 101.43154 -101.56922 66.527999 61.407843 -160.46637
21600 98.670006 -126.5834 69.109206 36.348979 -326.73021
22000 97.953943 -94.391435 64.079088 62.829942 -615.34146
22400 96.011555 -120.61994 66.705285 37.38066 -193.22166
22800 102.39627 -136.39615 65.466675 26.436925 -884.32994
23200 107.82018 -125.42796 67.117198 44.213115 -1300.4477
23600 102.73695 -137.18586 67.252953 27.757447 641.48035
24000 96.460847 -130.94495 63.38271 24.160292 -1791.2607
24400 93.796128 -128.00562 66.260634 27.443723 873.89034
24800 97.353953 -88.444384 65.413912 69.541299 -1871.9361
25200 97.091705 -72.044164 68.948627 89.226868 1280.3854
25600 98.648844 -101.58799 69.181915 61.39698 -1381.2537
26000 100.18179 -113.04929 70.844246 53.055655 322.01702
26400 100.74179 -104.51281 65.785089 57.065472 -862.08064
26800 90.111333 -140.38641 64.022143 9.3206518 -1640.9138
27200 93.312795 -79.845805 65.409942 74.293259 1708.28
27600 102.23172 -106.33538 64.085536 54.960091 -2880.6641
28000 104.37293 -132.5739 67.313593 33.985652 2121.8475
28400 104.29906 -100.21983 63.724249 62.680139 -3296.3716
28800 94.003175 -122.52092 64.940063 31.804732 2161.5287
29200 94.690933 -107.85189 60.393659 42.581332 -3090.7786
29600 100.45435 -106.02294 65.173795 54.670729 1118.3437
30000 95.933737 -106.07038 73.00091 58.151849 -2084.8456
30400 103.68687 -143.55908 65.248786 20.283316 501.20335
30800 97.692654 -138.68435 68.825851 23.035334 -1481.6139
31200 93.87282 -67.819013 64.431207 85.873831 770.99042
31600 99.300147 -131.38177 64.693462 27.734055 -708.48547
32000 108.07854 -118.32754 66.398747 50.840756 63.553384
32400 101.28547 -80.220498 70.990371 87.080037 -879.064
32800 101.25503 -142.74593 65.741528 19.276815 -212.82716
33200 97.691616 -112.33942 65.6407 46.194124 -1766.6266
33600 98.92508 -80.130148 66.951634 80.887209 556.92298
34000 100.03798 -108.23665 67.279003 54.166304 -1814.8718
34400 99.722709 -78.827618 66.909952 82.906505 1165.8056
34800 103.63061 -96.346199 63.358837 65.552749 -1107.3729
35200 101.8862 -102.27943 67.786509 62.388464 -302.68667
35600 100.13402 -127.74167 64.224915 31.698523 82.545283
36000 95.371028 -140.54681 62.893418 13.032857 -2067.3795
36400 94.414731 -55.311766 62.651462 97.116625 1175.4557
36800 98.210629 -78.11667 67.874187 83.143884 -2768.3386
37200 104.41074 -74.965133 66.733494 91.050276 2618.9021
37600 102.60834 -118.49539 67.997417 47.070082 -3807.4432
38000 98.134676 -119.73954 68.111463 41.686068 3065.6292
38400 94.150428 -106.43544 63.828484 46.91865 -3758.2934
38800 98.217332 -128.75227 62.694161 27.334629 2640.2861
39200 98.074978 -84.579023 68.094849 76.773204 -3198.9899
39600 102.11461 -132.45673 64.385846 29.027687 1515.9944
40000 97.92377 -130.67506 67.384102 29.822642 -2705.14
Loop time of 122.595 on 1 procs for 40000 steps with 320 atoms
0 0 100.26402 136.55858 236.82259 23932.721
400 42.170619 211.50173 98.834284 350.43515 -19954.362
800 80.98602 137.51745 96.410487 310.93579 22799.821
1200 63.638898 79.147382 126.70958 266.36981 -22688.205
1600 125.03824 8.3936932 72.58377 199.87363 24872.686
2000 132.65412 100.54512 78.666633 305.3497 -25280.813
2400 68.74818 86.737691 117.79044 269.89929 25404.029
2800 106.62011 -124.51222 94.016299 70.886839 -23779.763
3200 81.924583 101.55636 94.586469 274.04315 20030.528
3600 38.776859 -18.457174 160.39324 178.80814 -16121.888
4000 73.251026 -25.261953 116.57599 160.96685 14829.442
4400 95.448747 78.798674 98.369795 267.92862 -10754.85
4800 74.531106 9.1821255 125.62008 205.67223 11443.604
5200 113.23379 -18.137598 76.483186 166.01716 -6850.2391
5600 161.66144 -9.9936109 34.552103 178.27887 6950.5199
6000 109.12102 42.411255 73.381982 219.55406 -5079.5277
6400 114.18323 45.006738 69.912331 223.49344 6952.5685
6800 140.09315 -29.36111 49.095048 152.94549 -5687.3146
7200 77.017167 -100.03116 115.32741 88.530215 1809.3423
7600 82.146728 -157.61424 107.79292 28.290237 -620.8975
8000 91.620752 -170.47805 86.869654 3.5117938 -6791.187
8400 61.279764 -157.82824 118.91458 19.355949 4329.6396
8800 77.861735 -182.60601 107.05166 -1.5173115 -9227.9846
9200 109.16809 -146.58439 78.69991 35.921106 5352.4797
9600 103.33272 -143.43481 91.202163 46.024204 -8911.3128
10000 118.40703 -143.86319 82.85139 51.578888 5698.6657
10400 132.17421 -150.23934 60.294023 35.736287 -6128.8722
10800 127.5984 -115.4874 57.899096 63.742256 2473.2672
11200 93.995587 -142.30798 88.083786 35.154175 -3784.5778
11600 121.42086 -138.93143 63.861143 40.386186 1712.8154
12000 93.06677 -144.55776 93.470278 37.407696 -7078.2331
12400 79.472363 -167.47298 108.95107 17.046637 4849.9737
12800 87.350598 -120.68912 102.29261 64.663281 -9548.9665
13200 84.19161 -122.38986 99.897876 57.564003 5135.448
13600 73.330517 -127.91434 101.73297 43.547036 -8476.4457
14000 94.614208 -132.05384 83.463163 41.37593 4085.6464
14400 104.31288 -127.27279 82.555669 54.471749 -6404.7229
14800 112.42709 -112.99643 74.084263 67.992321 2615.2737
15200 116.98429 -146.23566 69.745666 34.747844 -3956.669
15600 116.24293 -120.51434 66.6672 56.685759 949.57325
16000 102.35486 -136.23785 76.072977 37.162147 -3245.2489
16400 98.509731 -156.63733 73.579249 10.61269 523.13227
16800 93.856029 -159.24119 82.012624 12.017105 -4534.967
17200 82.862943 -131.62209 100.21474 47.385231 512.05326
17600 92.246236 -136.92101 94.460159 45.254103 -3386.955
18000 90.573763 -96.47122 94.017617 83.671033 -985.73563
18400 86.448307 -113.2457 90.656253 59.61238 -1417.9972
18800 92.694425 -151.22451 78.570107 15.486727 -2257.4645
19200 103.78071 -118.63515 75.534113 55.581792 -500.31491
19600 110.51425 -123.76062 77.203548 58.528543 -2286.4077
20000 111.55761 -129.60212 75.480943 51.956546 -83.271072
20400 106.25254 -142.60405 75.963011 34.392203 -2087.2331
20800 102.1888 -162.02928 77.759214 12.89905 -1028.9644
21200 91.989317 -151.75523 83.09267 18.808099 -1853.9654
21600 96.670417 -104.90533 87.152082 74.168563 -939.46553
22000 92.76359 -131.7315 97.106726 53.582122 -1947.4447
22400 96.854286 -135.75059 89.36552 45.711581 -314.41148
22800 91.031169 -95.119068 89.944109 81.384613 -2572.0254
23200 93.765382 -87.627677 83.139724 84.671524 461.1709
23600 101.04845 -120.63195 79.045752 54.498597 -3044.2266
24000 109.09352 -118.88925 84.948215 69.793637 242.67198
24400 106.83291 -100.70414 84.268121 85.149091 -1855.3463
24800 107.5377 -82.89201 74.191564 93.554831 -475.74819
25200 102.22146 -167.17661 77.017351 7.0409222 -2155.4347
25600 100.9791 -136.50673 80.20626 39.718375 -832.78753
26000 100.58994 -120.80191 86.286429 61.133316 -2079.9828
26400 102.13829 -71.989798 89.674461 114.80576 -184.33268
26800 97.913385 -118.72923 89.564515 63.939012 -1626.8641
27200 98.830635 -122.14552 87.007035 58.837429 -1527.2921
27600 99.046289 -74.100659 82.85478 102.9351 -911.00352
28000 99.111014 -131.8402 82.636664 45.038984 -2332.2739
28400 100.29043 -127.24531 87.316114 55.434806 -271.61864
28800 115.41288 -110.09863 80.37308 80.018063 -2742.9954
29200 107.94994 -139.32629 84.702647 48.023621 -735.3395
29600 95.529576 -99.478489 84.343846 75.702368 -1532.0223
30000 106.93724 -124.64127 76.003017 53.046055 -1392.6149
30400 99.565043 -145.67079 85.505953 34.509412 -1872.7857
30800 99.790003 -159.79104 88.115581 23.212698 -877.71444
31200 101.96558 -121.75414 86.870947 62.073673 -2666.5694
31600 95.019312 -108.28189 86.299029 68.36895 -70.18726
32000 91.13249 -117.30325 85.291466 54.644136 -3190.2712
32400 97.508653 -141.36983 84.101207 35.450251 14.171425
32800 103.83682 -102.52016 87.838726 84.054763 -2525.3295
33200 102.40394 -109.46532 88.180777 76.089156 -970.42186
33600 106.5316 -144.73685 80.568884 37.130638 -869.90896
34000 102.34467 -94.122594 82.514369 85.709112 -2639.3492
34400 99.331541 -109.01027 82.117582 67.559534 236.07704
34800 98.333341 -110.65061 81.20456 64.057003 -2796.481
35200 104.46624 -131.23807 84.413001 52.509624 -312.30562
35600 103.958 -133.89181 90.269143 55.228749 -2295.0989
36000 101.72744 -123.93254 85.506062 58.303947 -636.3713
36400 95.274738 -116.0478 84.369922 58.916816 -2103.3573
36800 95.394514 -98.317329 84.96643 77.357685 -392.04941
37200 99.204759 -107.78707 85.13797 71.682563 -2369.0031
37600 100.00616 -90.025874 86.979528 92.047356 -326.97652
38000 109.08255 -141.81089 88.737444 50.650804 -2170.681
38400 105.1299 -73.818057 89.1541 115.30179 -245.37205
38800 103.76901 -100.29692 82.526647 80.901438 -1396.4733
39200 106.80306 -111.9981 76.475305 66.033932 -2080.199
39600 93.75398 -124.35702 86.617701 51.409316 -598.53989
40000 103.97395 -106.27012 86.423153 79.019616 -1236.6744
Loop time of 33.0377 on 6 procs for 40000 steps with 320 atoms
Pair time (%) = 116.941 (95.3878)
Bond time (%) = 1.93531 (1.57862)
Neigh time (%) = 1.5429 (1.25853)
Comm time (%) = 1.45484 (1.1867)
Outpt time (%) = 0.0928471 (0.0757348)
Other time (%) = 0.628479 (0.512647)
Performance: 26.152 ns/day, 0.918 hours/ns, 1210.740 timesteps/s
89.3% CPU use with 6 MPI tasks x no OpenMP threads
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6149 ave 6149 max 6149 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 134624 ave 134624 max 134624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.495 | 21.705 | 23.407 | 25.9 | 65.70
Bond | 0.27524 | 0.32203 | 0.36941 | 5.9 | 0.97
Neigh | 0.2328 | 0.23425 | 0.23531 | 0.2 | 0.71
Comm | 8.379 | 10.127 | 11.36 | 38.6 | 30.65
Output | 0.028365 | 0.02857 | 0.029573 | 0.3 | 0.09
Modify | 0.33563 | 0.37283 | 0.40583 | 3.7 | 1.13
Other | | 0.2478 | | | 0.75
Total # of neighbors = 134624
Ave neighs/atom = 420.7
Nlocal: 53.3333 ave 64 max 48 min
Histogram: 2 0 2 0 0 1 0 0 0 1
Nghost: 3871 ave 3909 max 3824 min
Histogram: 1 0 1 0 1 1 0 0 0 2
Neighs: 22383 ave 25722 max 19207 min
Histogram: 1 0 1 0 1 1 1 0 0 1
Total # of neighbors = 134298
Ave neighs/atom = 419.681
Ave special neighs/atom = 4
Neighbor list builds = 267
Neighbor list builds = 182
Dangerous builds = 0
# keep a restart of this, too.
write_restart 64xmethane-nvt.restart
write_restart 64xmethane-nvt.v
# this still has not been relaxed for pressure,
# but it should be pretty close.
Total wall time: 0:00:33
test/examples/methane/mainlog.64xmethane-nvt-thermo_style_custom 0 → 100644
+ 64
− 0
View file @ 16d55a7a
LAMMPS (14 May 2016)
# input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.methane
orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735)
3 by 2 by 1 MPI processor grid
reading atoms ...
320 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
256 bonds
reading angles ...
384 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
#dihedral_style opls
pair_modify mix geometric tail yes
# OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# force field parameters
pair_coeff 1 1 0.066 3.5 # CT
pair_coeff 2 2 0.03 2.5 # HC
# the remaining parameters are inferred from mixing.
bond_coeff 1 340.0 1.09 # CT-HC
angle_coeff 1 33.0 107.8 # HC-CT-HC
# equilibration. real methane freezes at 91K and boils at 112K
# so we hope the force field has it as a liquid at 100K.
timestep 0.25
reset_timestep 0
neighbor 1.5 bin
neigh_modify every 10 delay 20 check yes
thermo 400
thermo_style custom step temp pe ke press vol density
fix 2 all nvt temp 100.0 100.0 100.0
# equilibration trajectory
# dump 1 all dcd 400 64xmethane-nvt.dcd
dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z ix iy iz
#dump_modify 1 unwrap no
# output log
log log.64xmethane-nvt-thermo_style_custom
test/examples/methane/mainlog.64xmethane-nvt-thermo_style_multi 0 → 100644
+ 64
− 0
View file @ 16d55a7a
LAMMPS (14 May 2016)
# input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.methane
orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735)
3 by 2 by 1 MPI processor grid
reading atoms ...
320 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
256 bonds
reading angles ...
384 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
#dihedral_style opls
pair_modify mix geometric tail yes
# OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# force field parameters
pair_coeff 1 1 0.066 3.5 # CT
pair_coeff 2 2 0.03 2.5 # HC
# the remaining parameters are inferred from mixing.
bond_coeff 1 340.0 1.09 # CT-HC
angle_coeff 1 33.0 107.8 # HC-CT-HC
# equilibration. real methane freezes at 91K and boils at 112K
# so we hope the force field has it as a liquid at 100K.
timestep 0.25
reset_timestep 0
neighbor 1.5 bin
neigh_modify every 10 delay 20 check yes
thermo 400
thermo_style multi
fix 2 all nvt temp 100.0 100.0 100.0
# equilibration trajectory
# dump 1 all dcd 400 64xmethane-nvt.dcd
dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z ix iy iz
#dump_modify 1 unwrap no
# output log
log log.64xmethane-nvt-thermo_style_multi
test/examples/methane/mainlog.64xmethane-nvt-thermo_style_one 0 → 100644
+ 64
− 0
View file @ 16d55a7a
LAMMPS (14 May 2016)
# input script for topotools tutorial step 2a
units real
boundary p p p
atom_style full
read_data data.methane
orthogonal box = (-8.297 -8.1455 -7.2013) to (8.3174 8.1829 7.1735)
3 by 2 by 1 MPI processor grid
reading atoms ...
320 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
256 bonds
reading angles ...
384 angles
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# interaction styles
pair_style lj/cut/coul/cut 12.0
bond_style harmonic
angle_style harmonic
#dihedral_style opls
pair_modify mix geometric tail yes
# OPLS considers 1-4 interactions with 50%.
special_bonds lj/coul 0.0 0.0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
# force field parameters
pair_coeff 1 1 0.066 3.5 # CT
pair_coeff 2 2 0.03 2.5 # HC
# the remaining parameters are inferred from mixing.
bond_coeff 1 340.0 1.09 # CT-HC
angle_coeff 1 33.0 107.8 # HC-CT-HC
# equilibration. real methane freezes at 91K and boils at 112K
# so we hope the force field has it as a liquid at 100K.
timestep 0.25
reset_timestep 0
neighbor 1.5 bin
neigh_modify every 10 delay 20 check yes
thermo 400
thermo_style one
fix 2 all nvt temp 100.0 100.0 100.0
# equilibration trajectory
# dump 1 all dcd 400 64xmethane-nvt.dcd
dump 1 all custom 400 64xmethane-nvt.lammpstrj id type x y z ix iy iz
#dump_modify 1 unwrap no
# output log
log log.64xmethane-nvt-thermo_style_one
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please to comment