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polymerize.log
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288 lines (284 loc) · 17.8 KB
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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 -26.16 -26.16) to (13.21044 26.16 26.16)
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 ...
3392 atoms
reading velocities ...
3392 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
27 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
orthogonal box = (-2.3164529 -26.16 -26.16) to (13.21044 26.16 26.16)
1 by 1 by 1 MPI processor grid
reading bonds ...
3488 bonds
reading angles ...
5376 angles
reading dihedrals ...
7552 dihedrals
reading impropers ...
1792 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
34 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.043 seconds
Read molecule template mol1:
2styrene_unreacted
1 molecules
0 fragments
32 atoms with max type 4
32 bonds with max type 11
48 angles with max type 19
64 dihedrals with max type 21
16 impropers with max type 9
Read molecule template mol2:
2styrene_reacted
1 molecules
0 fragments
32 atoms with max type 6
33 bonds with max type 13
54 angles with max type 22
79 dihedrals with max type 19
14 impropers with max type 8
Read molecule template mol3:
chain_plus_styrene_unreacted
1 molecules
0 fragments
46 atoms with max type 6
47 bonds with max type 13
75 angles with max type 22
105 dihedrals with max type 21
21 impropers with max type 9
Read molecule template mol4:
chain_plus_styrene_reacted
1 molecules
0 fragments
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 19
19 impropers with max type 8
Read molecule template mol5:
chain_chain_unreacted
1 molecules
0 fragments
50 atoms with max type 6
51 bonds with max type 13
84 angles with max type 22
118 dihedrals with max type 19
20 impropers with max type 8
Read molecule template mol6:
chain_chain_reacted
1 molecules
0 fragments
50 atoms with max type 6
52 bonds with max type 13
90 angles with max type 22
135 dihedrals with max type 19
18 impropers with max type 3
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
192 atoms in group CNT
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) = 0.28904869
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
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 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 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
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
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) = 40.48 | 40.48 | 40.48 Mbytes
Step Temp Press Density f_rxn[1] f_rxn[2] f_rxn[3]
0 522.28375 -9541.48 0.90392574 0 0 0
200 548.89404 -6047.0261 0.90392574 4 0 0
400 528.34026 -9388.0102 0.90392574 11 0 0
600 534.80023 -7971.9718 0.90392574 13 1 0
800 550.52223 -10478.275 0.90392574 13 2 1
1000 537.15357 -8511.6566 0.90392574 15 2 1
1200 530.93955 -14715.249 0.90392574 22 3 1
1400 525.46219 -17550.956 0.90392574 24 3 1
1600 530.34146 -74783.829 0.90392574 30 3 3
1800 537.52127 -30521.584 0.90392574 33 3 4
2000 537.04039 -66670.292 0.90392574 35 3 5
2200 549.04613 -8297.0659 0.90392574 38 3 8
2400 533.75668 -8579.283 0.90392574 40 3 8
2600 548.44233 -7363.7606 0.90392574 42 3 10
2800 549.75956 -8027.7669 0.90392574 43 3 15
3000 524.60241 -9448.2719 0.90392574 44 3 15
3200 536.13443 -6547.2356 0.90392574 47 3 16
3400 539.53067 -7036.717 0.90392574 49 6 17
3600 533.40012 -108044.08 0.90392574 51 6 19
3800 539.71333 -14693.799 0.90392574 53 6 20
4000 534.70631 -7931.769 0.90392574 54 6 22
4200 563.1822 -9610.1184 0.90392574 56 8 26
4400 567.85999 -8895.5749 0.90392574 58 8 31
4600 522.65933 -8666.6644 0.90392574 59 9 31
4800 515.27755 -8512.0343 0.90392574 59 9 33
5000 558.51131 -9671.4191 0.90392574 62 9 35
5200 545.03934 -32148.988 0.90392574 63 9 38
5400 558.18928 -9907.8916 0.90392574 63 9 40
5600 521.74025 -21315.782 0.90392574 64 9 41
5800 540.37206 -8500.8459 0.90392574 64 9 41
6000 528.072 -7776.5747 0.90392574 65 9 41
6200 535.61052 -10640.215 0.90392574 66 10 41
6400 544.75914 -10717.56 0.90392574 66 10 43
6600 542.95809 -7916.1059 0.90392574 66 10 44
6800 519.62862 -10156.77 0.90392574 68 10 45
7000 528.10761 -6727.5517 0.90392574 68 11 45
7200 531.69302 -232445.15 0.90392574 68 11 47
7400 530.80928 -6739.0334 0.90392574 69 11 48
7600 541.26953 -108399.77 0.90392574 70 11 50
7800 548.79007 -5069.4185 0.90392574 70 12 53
8000 522.42895 -9289.5593 0.90392574 70 13 53
8200 530.10639 -7555.6587 0.90392574 70 13 53
8400 524.52973 -9153.6522 0.90392574 71 13 53
8600 550.33526 -6175.4442 0.90392574 71 13 55
8800 547.84598 -10956.544 0.90392574 71 14 57
9000 534.15405 -46247.822 0.90392574 71 14 58
9200 536.83635 -9421.4537 0.90392574 72 14 58
9400 523.6039 -8477.8478 0.90392574 72 14 58
9600 537.72805 -10235.295 0.90392574 72 14 58
9800 516.21896 -11061.079 0.90392574 72 14 58
10000 529.93443 -12635.931 0.90392574 72 14 59
10200 541.50939 -10973.929 0.90392574 72 14 59
10400 524.16278 -9602.6372 0.90392574 72 14 59
10600 540.16629 -8288.024 0.90392574 72 14 59
10800 530.66566 -9782.1523 0.90392574 72 14 59
11000 527.96502 -10588.225 0.90392574 72 15 59
11200 530.63715 -19810.063 0.90392574 72 15 60
11400 533.02088 -9947.762 0.90392574 72 15 60
11600 529.3941 -11068.775 0.90392574 72 15 60
11800 536.00151 -11629.701 0.90392574 72 16 60
12000 536.30137 -11486.566 0.90392574 72 16 60
12200 533.14801 -10713.234 0.90392574 72 16 61
12400 516.40964 -10564.852 0.90392574 72 16 61
12600 527.90965 -10521.483 0.90392574 73 16 61
12800 526.34259 -12497.137 0.90392574 74 16 61
13000 534.18261 -8483.545 0.90392574 74 16 61
13200 535.89384 -11192.901 0.90392574 74 16 61
13400 526.34442 -13106.539 0.90392574 74 16 61
13600 536.31063 -10419.806 0.90392574 74 16 61
13800 521.35707 -9107.9695 0.90392574 74 16 61
14000 538.38656 -14266.2 0.90392574 74 16 61
14200 556.00209 -11484.311 0.90392574 74 16 61
14400 541.37614 -10771.861 0.90392574 74 16 61
14600 519.74952 -11746.169 0.90392574 74 16 61
14800 530.55825 -11621.894 0.90392574 74 16 61
15000 531.99353 -8715.2574 0.90392574 74 16 61
15200 515.79342 -11101.103 0.90392574 75 16 61
15400 546.7363 -11815.64 0.90392574 75 17 61
15600 524.82822 -9808.8083 0.90392574 75 18 61
15800 539.43533 -10876.7 0.90392574 75 18 61
16000 547.12715 -11262.083 0.90392574 75 18 61
16200 519.59804 -10611.36 0.90392574 75 18 61
16400 538.0528 -167762.59 0.90392574 76 19 62
16600 534.6253 -8825.1452 0.90392574 76 19 62
16800 534.46142 -12301.249 0.90392574 77 19 62
17000 531.89541 -12005.079 0.90392574 77 19 63
17200 528.64925 -10210.07 0.90392574 77 19 63
17400 535.37649 -12439.582 0.90392574 77 19 63
17600 523.56778 -12495.187 0.90392574 77 19 63
17800 527.63075 -11816.49 0.90392574 77 19 63
18000 540.1356 -11192.973 0.90392574 77 19 64
18200 529.97148 -9329.2192 0.90392574 77 19 64
18400 527.69083 -9647.7731 0.90392574 77 19 64
18600 547.32863 -11473.915 0.90392574 77 19 64
18800 517.27495 -9670.5679 0.90392574 78 19 64
19000 541.31174 -10369.214 0.90392574 78 19 64
19200 531.36308 -11509.63 0.90392574 79 19 64
19400 522.48223 -10662.614 0.90392574 79 19 64
19600 537.17859 -10736.481 0.90392574 79 19 64
19800 536.16305 -10761.449 0.90392574 79 19 64
20000 528.52344 -10849.428 0.90392574 79 19 64
20200 522.14346 -9741.7651 0.90392574 79 19 64
20400 532.62997 -10037.339 0.90392574 79 19 64
20600 532.64726 -13730.174 0.90392574 79 19 64
20800 521.23886 -11563.726 0.90392574 79 19 64
21000 535.99931 -12561.707 0.90392574 79 19 64
21200 545.99389 -12523.644 0.90392574 79 19 64
21400 529.24877 -12634.771 0.90392574 79 19 64
21600 529.43179 -12949.56 0.90392574 79 19 64
21800 535.87685 -13129.434 0.90392574 80 19 64
22000 521.44105 -11145.24 0.90392574 80 19 66
22200 521.11756 -10549.212 0.90392574 80 19 66
22400 532.84616 -10965.022 0.90392574 80 19 66
22600 524.92043 -11277.756 0.90392574 80 19 66
22800 528.38993 -12565.863 0.90392574 80 19 66
23000 528.29869 -11866.514 0.90392574 80 19 66
23200 536.47787 -11087.902 0.90392574 80 19 66
23400 530.41947 -10336.408 0.90392574 80 19 66
23600 524.40428 -11018.73 0.90392574 80 19 67
23800 521.68591 -11970.372 0.90392574 80 20 67
24000 542.51 -12060.687 0.90392574 80 20 67
24200 534.97257 -11606.798 0.90392574 80 20 67
24400 523.25941 -11884.403 0.90392574 80 20 67
24600 529.56491 -9906.9858 0.90392574 80 20 68
24800 531.09179 -10875.089 0.90392574 80 20 68
25000 534.71351 -13129.427 0.90392574 80 20 68
Loop time of 194.185 on 8 procs for 25000 steps with 3392 atoms
Performance: 11.123 ns/day, 2.158 hours/ns, 128.743 timesteps/s, 436.697 katom-step/s
723.7% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 25.778 | 25.778 | 25.778 | 0.0 | 13.27
Bond | 17.649 | 17.649 | 17.649 | 0.0 | 9.09
Kspace | 21.063 | 21.063 | 21.063 | 0.0 | 10.85
Neigh | 7.7092 | 7.7092 | 7.7092 | 0.0 | 3.97
Comm | 1.3579 | 1.3579 | 1.3579 | 0.0 | 0.70
Output | 24.341 | 24.341 | 24.341 | 0.0 | 12.54
Modify | 96.109 | 96.109 | 96.109 | 0.0 | 49.49
Other | | 0.1777 | | | 0.09
Nlocal: 3392 ave 3392 max 3392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12245 ave 12245 max 12245 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 654340 ave 654340 max 654340 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 654340
Ave neighs/atom = 192.90684
Ave special neighs/atom = 10.575472
Neighbor list builds = 1791
Dangerous builds = 0