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using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading restart file ...
restart file = 29 Aug 2024, LAMMPS = 29 Aug 2024
restoring atom style full from restart
orthogonal box = (-22.058682 -11.128072 -11.128072) to (22.058682 11.128072 11.128072)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut/coul/long/omp from restart
restoring bond style harmonic/omp from restart
restoring angle style harmonic/omp from restart
restoring dihedral style harmonic/omp from restart
2063 atoms
1394 bonds
772 angles
116 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
15 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.005 seconds
2 atoms in group ends
1 atoms in group topull1
1 atoms in group topull2
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
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.30178312
grid = 32 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0033082643
estimated relative force accuracy = 9.9627396e-06
using double precision KISS FFT
3d grid and FFT values/proc = 28431 12800
Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule
Unused restart file global fix info:
fix style: npt, fix ID: mynpt
Last active /omp style is kspace_style pppm/omp
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 8 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 25000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 21.79 | 21.79 | 21.79 Mbytes
Step Temp TotEng c_rgyr
25000 297.98494 -4381.0186 5.0763714
25250 298.13653 -4484.7843 5.2617127
25500 309.55105 -4374.9698 5.1318643
25750 299.21538 -4425.176 4.8531415
26000 301.95192 -4470.8237 4.9787002
26250 307.80623 -4346.8013 4.9591124
26500 294.029 -4412.4687 4.7787987
26750 305.35148 -4468.516 4.6786241
27000 306.28408 -4497.5245 4.8693313
27250 307.63731 -4409.34 4.7914452
27500 295.07491 -4532.0554 4.7111281
27750 291.87889 -4577.9298 4.7035866
28000 302.46992 -4508.1579 4.7836949
28250 304.1192 -4432.7337 4.7138885
28500 296.78281 -4555.6005 4.6726817
28750 299.00472 -4451.1532 4.7270236
29000 304.89279 -4386.3149 4.7470456
29250 297.07854 -4500.5431 4.9695494
29500 313.14427 -4421.3271 4.8836155
29750 297.9882 -4540.2681 4.9377705
30000 304.00258 -4473.8425 5.2104648
30250 301.93355 -4491.727 5.1850219
30500 299.39586 -4450.0046 5.1565639
30750 295.48895 -4447.359 5.1880439
31000 293.99208 -4539.3238 5.1683024
31250 302.96805 -4514.4894 5.277541
31500 297.60606 -4521.7252 5.4562447
31750 300.2355 -4464.4429 5.6794614
32000 299.45775 -4555.9153 6.0153541
32250 303.955 -4452.7696 6.2692073
32500 308.94908 -4512.5789 6.4165689
32750 305.14906 -4487.5536 6.2000277
33000 305.38719 -4424.4676 6.0475105
33250 295.81692 -4502.4224 5.9427312
33500 303.73291 -4436.8521 5.8979808
33750 292.63726 -4565.2857 5.9160744
34000 303.75193 -4455.2292 5.7177512
34250 299.27428 -4536.6852 5.9805034
34500 294.18261 -4521.3265 6.0298722
34750 300.65387 -4543.6312 6.0066053
35000 305.2171 -4460.6255 5.8670185
35250 296.20749 -4526.6899 5.6874654
35500 305.36493 -4459.6643 5.5602715
35750 291.15806 -4563.3537 5.4044923
36000 299.51368 -4482.3397 5.1734028
36250 307.84128 -4415.744 5.1327907
36500 301.002 -4527.6156 5.3319745
36750 292.1516 -4592.2282 5.3434823
37000 305.47269 -4465.6974 5.3802732
37250 301.77369 -4566.2039 5.2612045
37500 294.38063 -4656.3591 5.1122491
37750 303.8821 -4547.83 5.2060429
38000 308.60691 -4429.9942 5.4315665
38250 296.70856 -4511.606 5.6193565
38500 308.57031 -4377.2706 5.5354327
38750 295.24926 -4512.812 5.7223536
39000 300.23934 -4477.5242 5.7074315
39250 294.74782 -4544.4004 5.5881584
39500 297.83017 -4491.3857 5.7211788
39750 305.36257 -4385.3449 5.8734535
40000 291.19245 -4536.8949 6.0592098
Loop time of 94.3298 on 8 procs for 15000 steps with 2063 atoms
Performance: 13.739 ns/day, 1.747 hours/ns, 159.016 timesteps/s, 328.051 katom-step/s
705.5% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.242 | 31.242 | 31.242 | 0.0 | 33.12
Bond | 0.35119 | 0.35119 | 0.35119 | 0.0 | 0.37
Kspace | 39.538 | 39.538 | 39.538 | 0.0 | 41.91
Neigh | 4.1283 | 4.1283 | 4.1283 | 0.0 | 4.38
Comm | 1.2655 | 1.2655 | 1.2655 | 0.0 | 1.34
Output | 15.914 | 15.914 | 15.914 | 0.0 | 16.87
Modify | 1.7946 | 1.7946 | 1.7946 | 0.0 | 1.90
Other | | 0.09633 | | | 0.10
Nlocal: 2063 ave 2063 max 2063 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11657 ave 11657 max 11657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 703864 ave 703864 max 703864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 703864
Ave neighs/atom = 341.18468
Ave special neighs/atom = 2.2171595
Neighbor list builds = 795
Dangerous builds = 0
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.30178312
grid = 32 20 20
stencil order = 5
estimated absolute RMS force accuracy = 0.0033082643
estimated relative force accuracy = 9.9627396e-06
using double precision KISS FFT
3d grid and FFT values/proc = 28431 12800
Generated 28 of 28 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/omp
Setting up Verlet run ...
Unit style : real
Current step : 40000
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 23.06 | 23.06 | 23.06 Mbytes
Step Temp TotEng c_rgyr
40000 291.19245 -4536.8949 6.0592098
40250 303.94683 -4405.8662 6.6305215
40500 298.72779 -4494.4984 7.3204989
40750 294.58274 -4496.6234 8.2744435
41000 296.34905 -4510.6276 8.7548496
41250 299.74903 -4402.7316 8.5194628
41500 298.66727 -4483.5274 8.6104115
41750 303.73898 -4417.816 8.7371278
42000 302.43391 -4529.6386 8.7590385
42250 295.77226 -4460.9167 8.6939017
42500 296.90346 -4526.7749 8.5715053
42750 304.3456 -4569.8878 8.5042458
43000 302.3154 -4534.1049 8.7926503
43250 302.48504 -4443.5573 8.6740794
43500 299.53289 -4369.5261 8.6560775
43750 303.46229 -4489.3838 8.8428673
44000 306.33302 -4408.4756 8.803004
44250 302.58049 -4516.4758 8.7780158
44500 295.60004 -4444.492 8.6746788
44750 298.35293 -4421.4597 8.6355799
45000 306.5246 -4533.3038 8.8474382
45250 304.42729 -4519.5547 8.6867641
45500 303.58433 -4409.7826 8.7517141
45750 301.57731 -4520.019 8.7870819
46000 300.91149 -4580.7727 8.6853428
46250 308.80186 -4472.2299 8.8409839
46500 293.78825 -4545.8674 8.6747984
46750 295.127 -4540.3845 8.8345397
47000 300.14744 -4444.9903 8.6622747
47250 293.25871 -4553.9178 8.6711485
47500 300.02512 -4494.2806 8.9276743
47750 298.46154 -4552.7699 8.7175094
48000 305.84858 -4524.3553 8.7612334
48250 303.12481 -4545.4718 8.8348217
48500 304.50475 -4458.3142 8.7242477
48750 295.15093 -4519.101 8.8237066
49000 309.33681 -4498.1217 8.7784663
49250 306.78692 -4403.6394 8.828856
49500 305.32823 -4512.1859 8.7680982
49750 307.83792 -4465.3704 8.8291357
50000 299.81306 -4445.8827 8.7244688
50250 295.16198 -4490.3483 8.7523596
50500 303.36383 -4466.4312 8.7129631
50750 302.40653 -4467.7119 8.7887511
51000 311.68179 -4289.7276 8.7794364
51250 301.94935 -4432.0243 8.7455311
51500 298.00531 -4515.5706 8.7222982
51750 298.98198 -4429.1679 8.6697789
52000 298.45831 -4509.5833 8.7949271
52250 303.24965 -4423.8375 8.784284
52500 297.37861 -4494.0321 8.9260683
52750 299.4808 -4527.1428 8.7059698
53000 309.59022 -4390.0524 8.7097334
53250 298.61855 -4497.1804 8.6650088
53500 303.47152 -4471.2721 8.7984831
53750 296.09925 -4517.25 8.6131091
54000 304.27522 -4510.1539 8.7273027
54250 316.81509 -4349.3576 8.7230017
54500 305.34708 -4433.9874 8.9453082
54750 301.16784 -4520.6276 8.6153515
55000 307.05706 -4384.3903 8.7442821
Loop time of 93.2936 on 8 procs for 15000 steps with 2063 atoms
Performance: 13.892 ns/day, 1.728 hours/ns, 160.783 timesteps/s, 331.695 katom-step/s
703.8% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.983 | 31.983 | 31.983 | 0.0 | 34.28
Bond | 0.36076 | 0.36076 | 0.36076 | 0.0 | 0.39
Kspace | 37.778 | 37.778 | 37.778 | 0.0 | 40.49
Neigh | 4.1659 | 4.1659 | 4.1659 | 0.0 | 4.47
Comm | 1.2138 | 1.2138 | 1.2138 | 0.0 | 1.30
Output | 15.822 | 15.822 | 15.822 | 0.0 | 16.96
Modify | 1.8717 | 1.8717 | 1.8717 | 0.0 | 2.01
Other | | 0.09914 | | | 0.11
Nlocal: 2063 ave 2063 max 2063 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11780 ave 11780 max 11780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 704038 ave 704038 max 704038 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 704038
Ave neighs/atom = 341.26903
Ave special neighs/atom = 2.2171595
Neighbor list builds = 780
Dangerous builds = 0