256 lines
14 KiB
Groff
256 lines
14 KiB
Groff
LAMMPS (20 Nov 2019)
|
|
|
|
WARNING-WARNING-WARNING-WARNING-WARNING
|
|
This LAMMPS executable was compiled using C++98 compatibility.
|
|
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
|
|
GNU C++ 4.8.5
|
|
WARNING-WARNING-WARNING-WARNING-WARNING
|
|
|
|
Reading data file ...
|
|
orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
320 atoms
|
|
reading velocities ...
|
|
320 velocities
|
|
scanning bonds ...
|
|
8 = max bonds/atom
|
|
scanning angles ...
|
|
18 = max angles/atom
|
|
scanning dihedrals ...
|
|
22 = max dihedrals/atom
|
|
scanning impropers ...
|
|
26 = max impropers/atom
|
|
reading bonds ...
|
|
320 bonds
|
|
reading angles ...
|
|
480 angles
|
|
reading dihedrals ...
|
|
640 dihedrals
|
|
reading impropers ...
|
|
160 impropers
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
3 = max # of 1-2 neighbors
|
|
6 = max # of 1-3 neighbors
|
|
12 = max # of 1-4 neighbors
|
|
39 = max # of special neighbors
|
|
special bonds CPU = 0.000751222 secs
|
|
read_data CPU = 0.0268223 secs
|
|
Read molecule mol1:
|
|
32 atoms with max type 4
|
|
32 bonds with max type 6
|
|
48 angles with max type 8
|
|
64 dihedrals with max type 9
|
|
16 impropers with max type 4
|
|
Read molecule mol2:
|
|
32 atoms with max type 6
|
|
33 bonds with max type 10
|
|
54 angles with max type 16
|
|
79 dihedrals with max type 19
|
|
22 impropers with max type 7
|
|
Read molecule mol3:
|
|
46 atoms with max type 6
|
|
47 bonds with max type 10
|
|
75 angles with max type 16
|
|
105 dihedrals with max type 19
|
|
29 impropers with max type 7
|
|
Read molecule mol4:
|
|
46 atoms with max type 6
|
|
48 bonds with max type 13
|
|
81 angles with max type 22
|
|
121 dihedrals with max type 36
|
|
35 impropers with max type 9
|
|
Read molecule mol5:
|
|
50 atoms with max type 6
|
|
51 bonds with max type 10
|
|
84 angles with max type 16
|
|
118 dihedrals with max type 19
|
|
36 impropers with max type 7
|
|
Read molecule mol6:
|
|
50 atoms with max type 6
|
|
52 bonds with max type 10
|
|
90 angles with max type 16
|
|
135 dihedrals with max type 19
|
|
42 impropers with max type 5
|
|
dynamic group bond_react_MASTER_group defined
|
|
dynamic group statted_grp_REACT defined
|
|
PPPM initialization ...
|
|
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
|
|
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
|
|
G vector (1/distance) = 0.255611
|
|
grid = 6 6 6
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.00974692
|
|
estimated relative force accuracy = 2.93525e-05
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 704 72
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 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 = 4 4 4
|
|
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
|
(1) pair lj/class2/coul/long, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d/newton
|
|
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
|
|
Per MPI rank memory allocation (min/avg/max) = 30.66 | 30.68 | 30.69 Mbytes
|
|
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
|
|
0 320.13638 -376.0844 0.76796752 0 0 0
|
|
100 522.71544 6623.0579 0.76796752 8 0 0
|
|
200 500.86716 -9439.5519 0.76796752 8 3 2
|
|
300 594.60588 6714.1323 0.76796752 8 3 3
|
|
400 598.68768 683.70457 0.76796752 8 3 3
|
|
500 563.1011 3576.6857 0.76796752 8 3 4
|
|
600 510.29713 -196148.37 0.76796752 8 3 5
|
|
700 494.14346 -118517.45 0.76796752 8 3 6
|
|
800 565.62849 7678.1235 0.76796752 8 3 6
|
|
900 515.74468 554.84571 0.76796752 8 3 6
|
|
1000 500.64636 450.15932 0.76796752 8 3 6
|
|
1100 463.34973 6023.8346 0.76796752 8 3 6
|
|
1200 529.88483 2748.185 0.76796752 8 3 6
|
|
1300 546.84049 1353.4891 0.76796752 8 3 6
|
|
1400 552.27356 1446.5807 0.76796752 8 3 6
|
|
1500 557.70874 -2745.1523 0.76796752 8 3 6
|
|
1600 572.0005 629.36722 0.76796752 8 3 6
|
|
1700 503.96569 5937.0231 0.76796752 8 3 6
|
|
1800 491.34262 -1175.8104 0.76796752 8 3 6
|
|
1900 538.24798 -81.197397 0.76796752 8 3 6
|
|
2000 523.89324 2857.2466 0.76796752 8 3 6
|
|
2100 515.1424 2288.2405 0.76796752 8 3 6
|
|
2200 546.80854 3807.1038 0.76796752 8 3 6
|
|
2300 500.31231 -135.33933 0.76796752 8 4 6
|
|
2400 497.16354 5516.857 0.76796752 8 4 6
|
|
2500 545.34187 3485.5645 0.76796752 8 4 6
|
|
2600 522.70122 3114.1284 0.76796752 8 4 6
|
|
2700 531.76604 6633.5518 0.76796752 8 4 6
|
|
2800 521.97643 -279.83682 0.76796752 8 4 6
|
|
2900 497.29575 7052.9409 0.76796752 8 4 6
|
|
3000 524.5942 2284.8918 0.76796752 8 4 6
|
|
3100 567.61329 -3667.4557 0.76796752 8 4 6
|
|
3200 506.82452 -2934.4936 0.76796752 8 4 6
|
|
3300 510.8521 313.36263 0.76796752 8 4 6
|
|
3400 516.70206 3671.1899 0.76796752 8 4 6
|
|
3500 535.12788 2645.2564 0.76796752 8 4 6
|
|
3600 580.14214 2604.3079 0.76796752 8 4 6
|
|
3700 529.77869 2684.0812 0.76796752 8 4 6
|
|
3800 502.93191 2838.6698 0.76796752 8 4 6
|
|
3900 585.91492 5308.0828 0.76796752 8 4 6
|
|
4000 548.89917 5262.5775 0.76796752 8 4 6
|
|
4100 550.7662 -1066.6807 0.76796752 8 4 6
|
|
4200 519.19198 2777.5276 0.76796752 8 4 6
|
|
4300 521.46332 -3429.7171 0.76796752 8 4 6
|
|
4400 532.64173 2301.3135 0.76796752 8 4 6
|
|
4500 528.96107 1369.0991 0.76796752 8 4 6
|
|
4600 564.66443 9687.2531 0.76796752 8 4 6
|
|
4700 558.49446 2322.6085 0.76796752 8 4 6
|
|
4800 497.78614 -442.45053 0.76796752 8 4 6
|
|
4900 511.09435 -10251.159 0.76796752 8 4 6
|
|
5000 525.6642 -1202.0584 0.76796752 8 4 6
|
|
5100 521.76974 1821.7811 0.76796752 8 4 6
|
|
5200 555.9859 7256.9632 0.76796752 8 4 6
|
|
5300 551.51971 -122893.16 0.76796752 8 4 7
|
|
5400 524.34705 2905.1033 0.76796752 8 4 7
|
|
5500 567.09396 2896.4824 0.76796752 8 4 7
|
|
5600 487.57746 1417.1715 0.76796752 8 4 7
|
|
5700 547.37304 3900.8734 0.76796752 8 4 7
|
|
5800 536.17647 -4048.7522 0.76796752 8 4 7
|
|
5900 536.85051 4497.9847 0.76796752 8 4 7
|
|
6000 548.58212 -4880.4979 0.76796752 8 4 7
|
|
6100 500.94692 6004.2105 0.76796752 8 4 7
|
|
6200 486.82494 402.5875 0.76796752 8 4 7
|
|
6300 478.09381 6600.767 0.76796752 8 4 7
|
|
6400 559.90398 2868.0805 0.76796752 8 4 7
|
|
6500 526.01866 -3398.4788 0.76796752 8 4 7
|
|
6600 539.68471 -1202.0012 0.76796752 8 4 7
|
|
6700 507.51217 -378.71164 0.76796752 8 4 7
|
|
6800 526.15958 -4536.9888 0.76796752 8 4 7
|
|
6900 511.37134 -2522.3553 0.76796752 8 4 7
|
|
7000 538.86918 -2028.0323 0.76796752 8 4 7
|
|
7100 523.25566 2911.9962 0.76796752 8 4 7
|
|
7200 513.28464 -1000.4758 0.76796752 8 4 7
|
|
7300 510.19826 5181.7976 0.76796752 8 4 7
|
|
7400 493.46528 -1166.3996 0.76796752 8 4 7
|
|
7500 491.51305 5669.2213 0.76796752 8 4 7
|
|
7600 506.72032 -2840.301 0.76796752 8 4 7
|
|
7700 513.4319 2802.1719 0.76796752 8 4 7
|
|
7800 543.7658 -7477.3623 0.76796752 8 4 7
|
|
7900 527.35619 -3182.3155 0.76796752 8 4 7
|
|
8000 533.50993 613.16561 0.76796752 8 4 7
|
|
8100 512.44958 -5037.3414 0.76796752 8 4 7
|
|
8200 494.88981 1799.3513 0.76796752 8 4 7
|
|
8300 554.81474 -2436.0507 0.76796752 8 4 7
|
|
8400 523.22917 364.30593 0.76796752 8 4 7
|
|
8500 515.12395 525.24581 0.76796752 8 4 7
|
|
8600 511.6321 -1679.8669 0.76796752 8 4 7
|
|
8700 531.6327 -1168.1215 0.76796752 8 4 7
|
|
8800 548.14438 -5222.7573 0.76796752 8 4 7
|
|
8900 517.72579 2073.9695 0.76796752 8 4 7
|
|
9000 543.11894 -5307.0759 0.76796752 8 4 7
|
|
9100 521.13747 -5546.8552 0.76796752 8 4 7
|
|
9200 509.66142 -1584.019 0.76796752 8 4 7
|
|
9300 488.73821 -277.85847 0.76796752 8 4 7
|
|
9400 513.67282 989.60653 0.76796752 8 4 7
|
|
9500 509.98833 -1754.8786 0.76796752 8 4 7
|
|
9600 558.72497 5616.6969 0.76796752 8 4 7
|
|
9700 533.74988 811.48871 0.76796752 8 4 7
|
|
9800 510.94641 -3136.5876 0.76796752 8 4 7
|
|
9900 517.80127 -1962.0837 0.76796752 8 4 7
|
|
10000 477.50428 -3768.1653 0.76796752 8 4 7
|
|
Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms
|
|
|
|
Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s
|
|
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.4968 | 3.0329 | 3.3607 | 18.6 | 14.45
|
|
Bond | 2.3164 | 2.8835 | 3.456 | 26.0 | 13.73
|
|
Kspace | 1.3332 | 2.2082 | 3.285 | 48.0 | 10.52
|
|
Neigh | 7.4831 | 7.4922 | 7.5012 | 0.3 | 35.68
|
|
Comm | 1.2809 | 1.3121 | 1.3297 | 1.6 | 6.25
|
|
Output | 0.0012138 | 0.0013506 | 0.0017552 | 0.6 | 0.01
|
|
Modify | 4.0269 | 4.0301 | 4.0335 | 0.1 | 19.19
|
|
Other | | 0.03583 | | | 0.17
|
|
|
|
Nlocal: 80 ave 94 max 66 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 2243.75 ave 2260 max 2221 min
|
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
Neighs: 13658.5 ave 17096 max 9421 min
|
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
|
|
|
Total # of neighbors = 54634
|
|
Ave neighs/atom = 170.731
|
|
Ave special neighs/atom = 11.3063
|
|
Neighbor list builds = 10000
|
|
Dangerous builds = 0
|
|
System init for write_data ...
|
|
PPPM initialization ...
|
|
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
|
|
G vector (1/distance) = 0.255611
|
|
grid = 6 6 6
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.00974692
|
|
estimated relative force accuracy = 2.93525e-05
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 704 72
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:00:21
|