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unbreakable.log
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308 lines (296 loc) · 16.5 KB
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using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading data file ...
orthogonal box = (-60 -40 -40) to (60 40 40)
1 by 1 by 1 MPI processor grid
reading atoms ...
700 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
3 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
orthogonal box = (-60 -40 -40) to (60 40 40)
1 by 1 by 1 MPI processor grid
reading bonds ...
1035 bonds
reading angles ...
2040 angles
reading dihedrals ...
4030 dihedrals
reading impropers ...
670 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.072 seconds
700 atoms in group carbon_atoms
10 atoms in group cnt_top
10 atoms in group cnt_bot
680 atoms in group cnt_mid
Setting atom values ...
10 settings made for mol
Setting atom values ...
10 settings made for mol
Setting atom values ...
680 settings made for mol
630 atoms in group rdel
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141)
Deleted 8 atoms, new total = 692
Deleted 24 bonds, new total = 1011
Deleted 71 angles, new total = 1969
Deleted 187 dihedrals, new total = 3843
Deleted 31 impropers, new total = 639
Resetting atom IDs ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is improper_style harmonic/omp
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 15 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.001 seconds
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is improper_style harmonic/omp
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 19.07 | 19.07 | 19.07 Mbytes
Step Temp TotEng v_Lcnt v_Fcnt
0 300 3412.1698 55.472 -224.39425
100 221.77336 3476.6385 55.472 -318.0386
200 253.58009 3568.4186 55.472 45.52362
300 282.18641 3663.0643 55.472 -165.78662
400 285.65627 3748.1703 55.472 -177.7731
500 304.86932 3808.4606 55.472 34.176067
600 323.82802 3825.9371 55.472 -135.59404
700 311.92686 3791.1429 55.472 36.850716
800 285.86414 3741.4835 55.472 -47.297846
900 275.98484 3723.5714 55.472 -79.853205
1000 291.96328 3749.1369 55.472 -186.60235
1100 295.03869 3788.1693 55.472 155.83122
1200 305.62976 3803.1467 55.472 -197.52455
1300 293.9881 3780.9038 55.472 -73.752162
1400 303.59703 3751.877 55.472 -124.23297
1500 297.2321 3737.1084 55.472 -133.08651
1600 297.65205 3751.2546 55.472 -185.1085
1700 306.38126 3794.2555 55.472 -137.88714
1800 310.96874 3798.7709 55.472 -238.41158
1900 310.12408 3779.1857 55.472 -203.63769
2000 288.90484 3764.4514 55.472 -67.054316
2100 294.54189 3762.7386 55.472 -87.498149
2200 292.97379 3767.6242 55.472 -168.23853
2300 296.45589 3766.1091 55.472 5.2752172
2400 305.59099 3768.5563 55.472 -64.899339
2500 309.09224 3773.6863 55.472 -163.55009
2600 294.82663 3786.3335 55.472 15.651825
2700 300.93872 3779.9101 55.472 -169.74621
2800 295.86726 3749.1023 55.472 -142.22764
2900 294.34747 3735.5243 55.472 -86.122153
3000 295.46019 3769.6605 55.472 -239.81964
3100 301.55838 3805.1205 55.472 -115.46136
3200 302.93251 3791.1756 55.472 -90.210429
3300 300.20578 3767.1222 55.472 -253.67987
3400 308.90327 3751.7048 55.472 -248.11355
3500 287.0456 3755.6305 55.472 -58.452456
3600 312.74571 3814.1721 55.472 -160.32933
3700 306.20479 3829.33 55.472 -216.65501
3800 301.58018 3792.4582 55.472 -93.862881
3900 310.4282 3764.6763 55.472 -133.21933
4000 299.53096 3752.1582 55.472 -316.98373
4100 299.84027 3759.2542 55.472 -56.405048
4200 308.78263 3805.5842 55.472 56.745856
4300 316.76083 3818.9446 55.472 -325.78942
4400 293.79501 3788.3698 55.472 30.45547
4500 303.37188 3771.9381 55.472 -13.146168
4600 296.41389 3763.8326 55.472 -207.08371
4700 297.99767 3756.5491 55.472 -169.21058
4800 291.46054 3757.4635 55.472 -227.74367
4900 285.95195 3784.5062 55.472 -205.64376
5000 304.56243 3805.7189 55.472 -79.853506
Loop time of 8.144 on 8 procs for 5000 steps with 692 atoms
Performance: 53.045 ns/day, 0.452 hours/ns, 613.949 timesteps/s, 424.853 katom-step/s
719.3% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0328 | 3.0328 | 3.0328 | 0.0 | 37.24
Bond | 2.644 | 2.644 | 2.644 | 0.0 | 32.47
Neigh | 0.0068752 | 0.0068752 | 0.0068752 | 0.0 | 0.08
Comm | 0.0027807 | 0.0027807 | 0.0027807 | 0.0 | 0.03
Output | 1.9381 | 1.9381 | 1.9381 | 0.0 | 23.80
Modify | 0.48243 | 0.48243 | 0.48243 | 0.0 | 5.92
Other | | 0.03699 | | | 0.45
Nlocal: 692 ave 692 max 692 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101736 ave 101736 max 101736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 101736
Ave neighs/atom = 147.01734
Ave special neighs/atom = 17.014451
Neighbor list builds = 3
Dangerous builds = 0
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is improper_style harmonic/omp
Setting up Verlet run ...
Unit style : real
Current step : 5000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 19.32 | 19.32 | 19.32 Mbytes
Step Temp TotEng v_Lcnt v_Fcnt
5000 304.56243 3805.7189 55.472 -79.853506
5100 316.94609 3799.6284 55.572 -336.0248
5200 307.58462 3765.6577 55.672 -331.04655
5300 286.95264 3773.2759 55.772 -99.06421
5400 293.12529 3804.7786 55.872 -363.37992
5500 320.42682 3841.5056 55.972 -517.97568
5600 309.79303 3860.804 56.072 -317.96547
5700 286.38394 3825.4266 56.172 -473.15954
5800 300.14054 3837.2556 56.272 -553.09288
5900 302.88878 3894.9877 56.372 -760.60707
6000 304.25973 3952.4255 56.472 -487.01969
6100 310.29809 3995.7924 56.572 -719.11239
6200 292.75477 4013.514 56.672 -658.48529
6300 282.7198 4004.8596 56.772 -642.25955
6400 286.0982 4022.6825 56.872 -850.1449
6500 292.4174 4082.7541 56.972 -808.44173
6600 289.17071 4145.5725 57.072 -950.33601
6700 294.51322 4216.4104 57.172 -990.66783
6800 311.50475 4274.4714 57.272 -1065.2073
6900 307.36405 4316.3928 57.372 -1105.8266
7000 285.99104 4323.1887 57.472 -1034.652
7100 293.67168 4369.2887 57.572 -1122.1656
7200 301.39862 4452.4102 57.672 -1254.8479
7300 319.8264 4539.264 57.772 -1106.4181
7400 298.80532 4601.1101 57.872 -1258.203
7500 301.24396 4649.8954 57.972 -1375.644
7600 312.18665 4709.2761 58.072 -1537.594
7700 307.20002 4767.0487 58.172 -1364.1976
7800 297.94719 4797.1327 58.272 -1519.9583
7900 272.4822 4846.7095 58.372 -1694.0597
8000 293.54961 4955.9972 58.472 -1548.0498
8100 306.61014 5056.3076 58.572 -1565.7628
8200 287.58787 5152.7089 58.672 -1721.0868
8300 316.32008 5241.4153 58.772 -1634.6597
8400 289.07174 5311.7621 58.872 -1757.3465
8500 299.69106 5364.5209 58.972 -1771.389
8600 289.02344 5437.9386 59.072 -1886.5319
8700 293.94081 5559.8881 59.172 -1936.3177
8800 305.31097 5689.0884 59.272 -2047.9707
8900 317.69569 5784.8667 59.372 -2015.7134
9000 300.66894 5855.3999 59.472 -2077.0222
9100 289.91122 5927.7524 59.572 -2077.9773
9200 307.51214 6036.5136 59.672 -2136.7198
9300 305.14804 6156.4513 59.772 -1973.0876
9400 300.03756 6269.9496 59.872 -2171.2338
9500 301.515 6378.5298 59.972 -2357.6478
9600 295.57613 6479.5798 60.072 -2151.0694
9700 288.1921 6586.1883 60.172 -2449.848
9800 285.80456 6701.691 60.272 -2259.0501
9900 317.73765 6837.3947 60.372 -2325.8389
10000 304.64818 6979.3603 60.472 -2334.7796
10100 321.85833 7108.7756 60.572 -2494.1473
10200 295.91106 7191.2733 60.672 -2449.9598
10300 297.48937 7291.3784 60.772 -2577.2125
10400 311.9886 7433.365 60.872 -2618.9504
10500 301.78662 7594.5337 60.972 -2616.071
10600 322.94099 7757.0677 61.072 -2745.1294
10700 293.67248 7879.6043 61.172 -2714.794
10800 288.26444 7949.0232 61.272 -2679.9292
10900 288.3479 8097.8322 61.372 -2864.2182
11000 303.1481 8276.2835 61.472 -2913.5207
11100 318.9141 8443.9207 61.572 -2764.9231
11200 300.01959 8585.9372 61.672 -2831.2821
11300 294.89585 8702.6751 61.772 -2918.86
11400 291.51945 8827.6128 61.872 -3089.7251
11500 290.71254 8990.9818 61.972 -3112.1706
11600 295.69661 9166.7422 62.072 -3062.9155
11700 293.74215 9335.8931 62.172 -3162.3414
11800 303.89407 9502.7835 62.272 -3451.0164
11900 294.80394 9656.3833 62.372 -3393.6917
12000 288.03488 9772.4073 62.472 -3220.6845
12100 284.05766 9935.2738 62.572 -3546.2418
12200 290.5788 10146.703 62.672 -3596.9023
12300 312.41908 10335.894 62.772 -3493.3943
12400 304.26032 10513.89 62.872 -3620.704
12500 300.0626 10689.345 62.972 -3690.8043
12600 300.87588 10836.402 63.072 -3535.823
12700 284.3332 10991.657 63.172 -3623.9498
12800 295.58884 11199.229 63.272 -3716.2194
12900 299.11195 11424.451 63.372 -3566.7161
13000 306.5258 11620.922 63.472 -3791.0592
13100 313.02855 11799.57 63.572 -3910.9016
13200 291.94537 11961.316 63.672 -3740.8289
13300 287.98341 12136.036 63.772 -4200.1948
13400 297.3715 12340.235 63.872 -4125.0622
13500 311.18372 12585.076 63.972 -3855.5959
13600 311.49459 12808.082 64.072 -4270.5575
13700 308.72393 13007.369 64.172 -4077.3628
13800 297.51013 13174.992 64.272 -4082.928
13900 297.14089 13368.139 64.372 -4197.7878
14000 281.56818 13592.474 64.472 -4252.8016
14100 303.66656 13818.505 64.572 -4278.1418
14200 300.75069 14039.016 64.672 -4237.4307
14300 298.35193 14260.322 64.772 -4311.233
14400 295.6975 14469.122 64.872 -4335.777
14500 300.65775 14668.237 64.972 -4469.4045
14600 287.28368 14873.735 65.072 -4570.5033
14700 287.07761 15120.816 65.172 -4617.4744
14800 279.71851 15395.392 65.272 -4570.7173
14900 298.24766 15636.522 65.372 -4725.049
15000 303.29673 15850.789 65.472 -4655.7384
Loop time of 14.8329 on 8 procs for 10000 steps with 692 atoms
Performance: 58.249 ns/day, 0.412 hours/ns, 674.178 timesteps/s, 466.531 katom-step/s
720.4% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3804 | 5.3804 | 5.3804 | 0.0 | 36.27
Bond | 4.8674 | 4.8674 | 4.8674 | 0.0 | 32.81
Neigh | 0.0096903 | 0.0096903 | 0.0096903 | 0.0 | 0.07
Comm | 0.0065843 | 0.0065843 | 0.0065843 | 0.0 | 0.04
Output | 3.5607 | 3.5607 | 3.5607 | 0.0 | 24.01
Modify | 0.93721 | 0.93721 | 0.93721 | 0.0 | 6.32
Other | | 0.07091 | | | 0.48
Nlocal: 692 ave 692 max 692 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 90297 ave 90297 max 90297 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 90297
Ave neighs/atom = 130.48699
Ave special neighs/atom = 17.014451
Neighbor list builds = 5
Dangerous builds = 0