260 lines
11 KiB
Groff
260 lines
11 KiB
Groff
LAMMPS (28 Feb 2019)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 2d micelle simulation
|
|
|
|
dimension 2
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 5
|
|
|
|
atom_style bond
|
|
|
|
# Soft potential push-off
|
|
|
|
read_data data.micelle
|
|
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
1200 atoms
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
reading bonds ...
|
|
300 bonds
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
special bonds CPU = 0.000394821 secs
|
|
read_data CPU = 0.00212336 secs
|
|
special_bonds fene
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
special bonds CPU = 0.00018549 secs
|
|
|
|
pair_style soft 1.12246
|
|
pair_coeff * * 0.0 1.12246
|
|
|
|
bond_style harmonic
|
|
bond_coeff 1 50.0 0.75
|
|
|
|
velocity all create 0.45 2349852
|
|
|
|
variable prefactor equal ramp(1.0,20.0)
|
|
|
|
fix 1 all nve
|
|
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
|
fix 3 all adapt 1 pair soft a * * v_prefactor
|
|
fix 4 all enforce2d
|
|
|
|
thermo 50
|
|
run 1000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 5 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 1.42246
|
|
ghost atom cutoff = 1.42246
|
|
binsize = 0.71123, bins = 51 51 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair soft, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
|
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
|
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
|
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
|
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
|
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
|
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
|
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
|
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
|
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
|
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
|
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
|
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
|
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
|
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
|
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
|
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
|
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
|
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
|
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
|
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
|
Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms
|
|
|
|
Performance: 3792167.464 tau/day, 8778.165 timesteps/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44
|
|
Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67
|
|
Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98
|
|
Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67
|
|
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15
|
|
Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85
|
|
Other | | 0.002551 | | | 2.24
|
|
|
|
Nlocal: 1200 ave 1200 max 1200 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 195 ave 195 max 195 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3136 ave 3136 max 3136 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3136
|
|
Ave neighs/atom = 2.61333
|
|
Ave special neighs/atom = 0.5
|
|
Neighbor list builds = 92
|
|
Dangerous builds = 0
|
|
|
|
unfix 3
|
|
|
|
# Main run
|
|
|
|
pair_style lj/cut 2.5
|
|
|
|
# solvent/head - full-size and long-range
|
|
|
|
pair_coeff 1 1 1.0 1.0 2.5
|
|
pair_coeff 2 2 1.0 1.0 2.5
|
|
pair_coeff 1 2 1.0 1.0 2.5
|
|
|
|
# tail/tail - size-averaged and long-range
|
|
|
|
pair_coeff 3 3 1.0 0.75 2.5
|
|
pair_coeff 4 4 1.0 0.50 2.5
|
|
pair_coeff 3 4 1.0 0.67 2.5
|
|
|
|
# solvent/tail - full-size and repulsive
|
|
|
|
pair_coeff 1 3 1.0 1.0 1.12246
|
|
pair_coeff 1 4 1.0 1.0 1.12246
|
|
|
|
# head/tail - size-averaged and repulsive
|
|
|
|
pair_coeff 2 3 1.0 0.88 1.12246
|
|
pair_coeff 2 4 1.0 0.75 1.12246
|
|
|
|
thermo 1000
|
|
|
|
#dump 1 all atom 2000 dump.micelle
|
|
|
|
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
|
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
|
|
|
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
|
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
|
|
|
reset_timestep 0
|
|
run 60000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 5 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 2.8
|
|
ghost atom cutoff = 2.8
|
|
binsize = 1.4, bins = 26 26 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
|
1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326
|
|
2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269
|
|
3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618
|
|
4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016
|
|
5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164
|
|
6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891
|
|
7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333
|
|
8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396
|
|
9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554
|
|
10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213
|
|
11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469
|
|
12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225
|
|
13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283
|
|
14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427
|
|
15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836
|
|
16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323
|
|
17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919
|
|
18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638
|
|
19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341
|
|
20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768
|
|
21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935
|
|
22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734
|
|
23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013
|
|
24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789
|
|
25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875
|
|
26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118
|
|
27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415
|
|
28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526
|
|
29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376
|
|
30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113
|
|
31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708
|
|
32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106
|
|
33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458
|
|
34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584
|
|
35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396
|
|
36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939
|
|
37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603
|
|
38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359
|
|
39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385
|
|
40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955
|
|
41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756
|
|
42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561
|
|
43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063
|
|
44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473
|
|
45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054
|
|
46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974
|
|
47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182
|
|
48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142
|
|
49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467
|
|
50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865
|
|
51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859
|
|
52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593
|
|
53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158
|
|
54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814
|
|
55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307
|
|
56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892
|
|
57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988
|
|
58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146
|
|
59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911
|
|
60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471
|
|
Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
|
|
|
|
Performance: 3233199.903 tau/day, 7484.259 timesteps/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39
|
|
Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94
|
|
Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95
|
|
Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80
|
|
Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01
|
|
Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03
|
|
Other | | 0.1508 | | | 1.88
|
|
|
|
Nlocal: 1200 ave 1200 max 1200 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 395 ave 395 max 395 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 9652 ave 9652 max 9652 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 9652
|
|
Ave neighs/atom = 8.04333
|
|
Ave special neighs/atom = 0.5
|
|
Neighbor list builds = 4886
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:08
|