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mixing.log
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using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading data file ...
orthogonal box = (-2.3164529 -60 -60) to (13.21044 60 60)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
192 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
3 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (-2.3164529 -60 -60) to (13.21044 60 60)
1 by 1 by 1 MPI processor grid
reading bonds ...
288 bonds
reading angles ...
576 angles
reading dihedrals ...
1152 dihedrals
reading impropers ...
192 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
29 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
192 atoms in group CNT
Read molecule template styrene:
styrene_molecule
1 molecules
0 fragments
16 atoms with max type 4
16 bonds with max type 11
24 angles with max type 19
32 dihedrals with max type 21
8 impropers with max type 9
Created 3200 atoms
using lattice units in orthogonal box = (-2.3164529 -60 -60) to (13.21044 60 60)
create_atoms CPU = 0.085 seconds
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 ...
WARNING: System is not charge neutral, net charge = -0.04 (src/kspace.cpp:327)
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26305894
grid = 9 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0032149548
estimated relative force accuracy = 9.6817409e-06
using double precision KISS FFT
3d grid and FFT values/proc = 32400 14400
Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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 = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 3 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long/omp, perpetual
attributes: half, newton on, omp
pair build: half/bin/newton/omp
stencil: half/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : real
Current step : 0
WARNING: Inconsistent image flags (src/domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 24.1 | 24.1 | 24.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 2481.7682 33059.224 35540.992 -460.38193
90 0 1559.4952 10442.031 12001.526 -2206.5445
Loop time of 0.421362 on 8 procs for 90 steps with 3392 atoms
807.7% CPU use with 1 MPI tasks x 8 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
35540.9920717563 12002.4859236628 12001.5257186809
Force two-norm initial, final = 13128.037 37.531878
Force max component initial, final = 659.35639 4.856523
Final line search alpha, max atom move = 0.010159839 0.049341491
Iterations, force evaluations = 90 179
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.062837 | 0.062837 | 0.062837 | 0.0 | 14.91
Bond | 0.11054 | 0.11054 | 0.11054 | 0.0 | 26.23
Kspace | 0.23303 | 0.23303 | 0.23303 | 0.0 | 55.30
Neigh | 0.0013631 | 0.0013631 | 0.0013631 | 0.0 | 0.32
Comm | 0.0037799 | 0.0037799 | 0.0037799 | 0.0 | 0.90
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.0046924 | 0.0046924 | 0.0046924 | 0.0 | 1.11
Other | | 0.005123 | | | 1.22
Nlocal: 3392 ave 3392 max 3392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7635 ave 7635 max 7635 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 134397 ave 134397 max 134397 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 134397
Ave neighs/atom = 39.621757
Ave special neighs/atom = 8.6462264
Neighbor list builds = 1
Dangerous builds = 0
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26305894
grid = 9 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0032149548
estimated relative force accuracy = 9.6817409e-06
using double precision KISS FFT
3d grid and FFT values/proc = 32400 14400
Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Last active /omp style is kspace_style pppm/omp
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (src/domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 22.97 | 22.97 | 22.97 Mbytes
Step Temp PotEng TotEng Press Density
0 530 12001.526 17358.727 -1111.268 0.17183267
200 344.37856 14955.999 18436.952 -2258.7261 0.17891781
400 452.33463 15375.804 19947.969 -2053.1404 0.18645038
600 528.04542 15898.773 21236.218 -1770.5563 0.19446884
800 546.25264 15850.536 21372.018 -2333.4947 0.20301591
1000 501.69294 15802.579 20873.654 -2837.4245 0.2121391
1200 532.37031 15938.323 21319.483 -2739.94 0.22189136
1400 538.68411 15797.04 21242.02 -2166.7639 0.23233189
1600 521.19507 15722.719 20990.921 -2785.8389 0.24352702
1800 541.13306 15861.945 21331.678 -2496.8492 0.25555126
2000 531.51291 15752.119 21124.613 -3025.0053 0.26848854
2200 523.73756 15739.601 21033.502 -3473.258 0.28243371
2400 541.52776 15756.968 21230.691 -2815.7256 0.29749423
2600 521.51688 15719.399 20990.854 -3332.3815 0.31379231
2800 523.1514 15749.785 21037.762 -3771.9919 0.33146734
3000 539.43837 15679.002 21131.605 -3597.702 0.35067891
3200 522.49072 15643.224 20924.522 -4593.3804 0.37161044
3400 525.33369 15709.878 21019.912 -4006.3495 0.39447353
3600 529.15934 15552.443 20901.147 -4543.4537 0.41951335
3800 524.83845 15489.668 20794.697 -4768.5679 0.44701526
4000 543.71109 15451.151 20946.943 -4970.2427 0.47731297
4200 524.46894 15403.064 20704.358 -5540.443 0.51079866
4400 519.39515 15310.847 20560.855 -5286.2145 0.5479358
4600 526.04522 15425.783 20743.009 -5551.7038 0.58927527
4800 524.08494 15169.497 20466.909 -7136.7311 0.63547584
5000 533.40053 15037.567 20429.141 -5017.8275 0.68733067
5200 532.76716 15080.897 20466.069 -5553.7445 0.74580151
5400 516.12182 14932.638 20149.56 -6430.7854 0.81206365
5600 533.62595 14966.081 20359.933 -5475.6042 0.88756543
Fix halt condition for fix-id myhal met on step 5640 with value 0.9039257417441506 (src/fix_halt.cpp:240)
Loop time of 16.6889 on 8 procs for 5640 steps with 3392 atoms
Performance: 29.199 ns/day, 0.822 hours/ns, 337.949 timesteps/s, 1.146 Matom-step/s
806.3% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6447 | 2.6447 | 2.6447 | 0.0 | 15.85
Bond | 3.1127 | 3.1127 | 3.1127 | 0.0 | 18.65
Kspace | 7.9123 | 7.9123 | 7.9123 | 0.0 | 47.41
Neigh | 0.87544 | 0.87544 | 0.87544 | 0.0 | 5.25
Comm | 0.21073 | 0.21073 | 0.21073 | 0.0 | 1.26
Output | 0.00075901 | 0.00075901 | 0.00075901 | 0.0 | 0.00
Modify | 1.8953 | 1.8953 | 1.8953 | 0.0 | 11.36
Other | | 0.03691 | | | 0.22
Nlocal: 3392 ave 3392 max 3392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12121 ave 12121 max 12121 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 653217 ave 653217 max 653217 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 653217
Ave neighs/atom = 192.57577
Ave special neighs/atom = 8.6462264
Neighbor list builds = 413
Dangerous builds = 0
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.28904869
grid = 9 24 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0026123692
estimated relative force accuracy = 7.8670722e-06
using double precision KISS FFT
3d grid and FFT values/proc = 13456 5184
Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Last active /omp style is kspace_style pppm/omp
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (src/domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes
Step Temp PotEng TotEng Press Density
0 536.62729 14947.209 20371.399 -5285.3567 0.90392574
200 529.11909 14848.913 20197.21 -4566.2423 0.90392574
400 525.22966 15000.54 20309.523 -8075.117 0.90392574
600 548.51677 15006.587 20550.954 -4756.2674 0.90392574
800 535.16532 14893.4 20302.812 -6517.8281 0.90392574
1000 533.38762 15042.329 20433.772 -8497.147 0.90392574
1200 535.60188 15168.872 20582.697 -6046.4604 0.90392574
1400 519.70727 15199.109 20452.272 -7347.3438 0.90392574
1600 527.39368 15121.09 20451.947 -8141.5518 0.90392574
1800 535.23215 15142.926 20553.014 -7458.6276 0.90392574
2000 527.93996 15272.943 20609.322 -5849.4797 0.90392574
2200 518.26777 15151.34 20389.953 -10476.344 0.90392574
2400 520.53374 15313.473 20574.99 -4750.1519 0.90392574
2600 527.25172 15254.527 20583.949 -9160.7418 0.90392574
2800 524.4647 15192.693 20493.944 -9296.1648 0.90392574
3000 537.55928 15110.527 20544.137 -7986.6699 0.90392574
3200 532.93492 15276.067 20662.934 -7518.2997 0.90392574
3400 515.74271 15166.526 20379.616 -8675.0081 0.90392574
3600 529.67022 15205.166 20559.034 -9775.2692 0.90392574
3800 529.83827 15344.574 20700.14 -7497.1202 0.90392574
4000 522.0196 15279.106 20555.642 -7461.6093 0.90392574
4200 519.99509 15454.553 20710.625 -6337.7515 0.90392574
4400 534.52654 15277.672 20680.628 -9417.8508 0.90392574
4600 525.06143 15237.042 20544.324 -9491.4381 0.90392574
4800 544.28479 15264.782 20766.372 -7656.9885 0.90392574
5000 530.79729 15265.576 20630.836 -8284.5616 0.90392574
5200 520.27626 15361.542 20620.456 -10454.122 0.90392574
5400 546.85519 15366.377 20893.949 -5684.7533 0.90392574
5600 525.20162 15275.479 20584.179 -8896.5015 0.90392574
5800 522.47231 15374.155 20655.267 -9012.6377 0.90392574
6000 537.07345 15361.391 20790.09 -8009.9807 0.90392574
6200 522.13355 15252.356 20530.044 -7172.2997 0.90392574
6400 535.48392 15286.45 20699.082 -8341.5477 0.90392574
6600 513.20133 15498.85 20686.251 -9964.089 0.90392574
6800 537.99887 15419.269 20857.322 -7647.1077 0.90392574
7000 528.36102 15367.066 20707.7 -9652.4957 0.90392574
7200 533.40655 15286.58 20678.215 -9706.125 0.90392574
7400 533.94889 15446.263 20843.379 -10718.916 0.90392574
7600 517.19716 15346.658 20574.449 -8282.7167 0.90392574
7800 532.77385 15391.572 20776.812 -8127.3409 0.90392574
8000 524.92851 15416.75 20722.689 -8537.9412 0.90392574
8200 522.98118 15276.159 20562.414 -10441.267 0.90392574
8400 536.91602 15334.372 20761.48 -9651.2216 0.90392574
8600 526.92048 15388.302 20714.375 -6044.1794 0.90392574
8800 519.7603 15270.804 20524.504 -10241.061 0.90392574
9000 535.29683 15366.39 20777.131 -10235.988 0.90392574
9200 530.31817 15350.038 20710.455 -8468.9488 0.90392574
9400 516.02771 15445.78 20661.75 -9228.5508 0.90392574
9600 545.85145 15366.429 20883.855 -7995.0199 0.90392574
9800 524.7683 15379.12 20683.439 -10398.403 0.90392574
10000 522.28375 15411.824 20691.03 -9541.48 0.90392574
Loop time of 31.091 on 8 procs for 10000 steps with 3392 atoms
Performance: 27.789 ns/day, 0.864 hours/ns, 321.637 timesteps/s, 1.091 Matom-step/s
769.7% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.229 | 10.229 | 10.229 | 0.0 | 32.90
Bond | 6.3858 | 6.3858 | 6.3858 | 0.0 | 20.54
Kspace | 8.7779 | 8.7779 | 8.7779 | 0.0 | 28.23
Neigh | 2.6297 | 2.6297 | 2.6297 | 0.0 | 8.46
Comm | 0.5314 | 0.5314 | 0.5314 | 0.0 | 1.71
Output | 1.7903 | 1.7903 | 1.7903 | 0.0 | 5.76
Modify | 0.69063 | 0.69063 | 0.69063 | 0.0 | 2.22
Other | | 0.05617 | | | 0.18
Nlocal: 3392 ave 3392 max 3392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12325 ave 12325 max 12325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 655171 ave 655171 max 655171 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 655171
Ave neighs/atom = 193.15183
Ave special neighs/atom = 8.6462264
Neighbor list builds = 633
Dangerous builds = 1
System init for write_data ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.28904869
grid = 9 24 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0026123692
estimated relative force accuracy = 7.8670722e-06
using double precision KISS FFT
3d grid and FFT values/proc = 13456 5184
Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Last active /omp style is kspace_style pppm/omp
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.28904869
grid = 9 24 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0026123692
estimated relative force accuracy = 7.8670722e-06
using double precision KISS FFT
3d grid and FFT values/proc = 13456 5184
Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Last active /omp style is kspace_style pppm/omp