257 lines
11 KiB
Groff
257 lines
11 KiB
Groff
LAMMPS (28 Feb 2019)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
|
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 = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 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 fene
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
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 0.40179153 0.017198847 0.86861538 0.75625658
|
|
50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879
|
|
100 0.45 0.73189198 0.056737309 1.2382543 2.321972
|
|
150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146
|
|
200 0.45 0.78767975 0.079977445 1.3172822 3.0463605
|
|
250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758
|
|
300 0.45 0.76847924 0.069944127 1.2880484 3.7420091
|
|
350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161
|
|
400 0.45 0.69469019 0.094115526 1.2384307 4.4786122
|
|
450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436
|
|
500 0.45 0.64066675 0.080351857 1.1706436 4.7965076
|
|
550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662
|
|
600 0.45 0.58371075 0.088545932 1.1218817 5.0963739
|
|
650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897
|
|
700 0.45 0.5394553 0.10365542 1.0927357 5.3370157
|
|
750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553
|
|
800 0.45 0.51563293 0.1030928 1.0683507 5.5156219
|
|
850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809
|
|
900 0.45 0.4758065 0.098479812 1.0239113 5.6783722
|
|
950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261
|
|
1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623
|
|
Loop time of 0.10837 on 1 procs for 1000 steps with 1200 atoms
|
|
|
|
Performance: 3986358.208 tau/day, 9227.681 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.071949 | 0.071949 | 0.071949 | 0.0 | 66.39
|
|
Bond | 0.0039806 | 0.0039806 | 0.0039806 | 0.0 | 3.67
|
|
Neigh | 0.01737 | 0.01737 | 0.01737 | 0.0 | 16.03
|
|
Comm | 0.0019217 | 0.0019217 | 0.0019217 | 0.0 | 1.77
|
|
Output | 0.00016022 | 0.00016022 | 0.00016022 | 0.0 | 0.15
|
|
Modify | 0.010607 | 0.010607 | 0.010607 | 0.0 | 9.79
|
|
Other | | 0.002382 | | | 2.20
|
|
|
|
Nlocal: 1200 ave 1200 max 1200 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 206 ave 206 max 206 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3191 ave 3191 max 3191 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3191
|
|
Ave neighs/atom = 2.65917
|
|
Ave special neighs/atom = 0.5
|
|
Neighbor list builds = 99
|
|
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 -1.7061976 0.094144249 -1.1624283 3.8015113
|
|
1000 0.45 -1.9656133 0.065736052 -1.4502522 1.8870315
|
|
2000 0.45917162 -1.9677772 0.06512989 -1.4438584 1.6197525
|
|
3000 0.45029543 -1.9993287 0.060436068 -1.4889724 1.6749521
|
|
4000 0.44658614 -2.0150793 0.070735372 -1.49813 1.4982834
|
|
5000 0.45 -2.0317981 0.06873808 -1.513435 1.375846
|
|
6000 0.46323984 -2.0135007 0.067698691 -1.4829482 1.3342928
|
|
7000 0.46154055 -2.0268144 0.064313941 -1.5013445 1.2936811
|
|
8000 0.45911863 -2.032873 0.058832094 -1.5153049 1.1717652
|
|
9000 0.46126695 -2.0435575 0.060645049 -1.5220299 1.1810833
|
|
10000 0.44212317 -2.0552317 0.066386857 -1.5470901 1.1217265
|
|
11000 0.46455191 -2.0852383 0.064035544 -1.557038 1.0722284
|
|
12000 0.45647983 -2.0711846 0.058592351 -1.5564929 1.1487056
|
|
13000 0.44296686 -2.0532457 0.059554979 -1.551093 1.1665292
|
|
14000 0.44154216 -2.045874 0.059814984 -1.5448848 1.1231544
|
|
15000 0.43921469 -2.0642415 0.057245543 -1.5681472 1.1342333
|
|
16000 0.44278133 -2.0696899 0.053114875 -1.5741627 1.0881442
|
|
17000 0.45 -2.0847259 0.060756733 -1.5743441 0.94801701
|
|
18000 0.45115973 -2.0899292 0.061273297 -1.5778721 0.86251832
|
|
19000 0.45210059 -2.0822877 0.061618471 -1.5689454 0.80428644
|
|
20000 0.44516679 -2.0789966 0.060221274 -1.5739795 0.98113308
|
|
21000 0.44850103 -2.0920747 0.060514536 -1.5834329 0.92324
|
|
22000 0.44679652 -2.0669569 0.067895097 -1.5526376 1.106608
|
|
23000 0.45651863 -2.0904722 0.06387795 -1.5704561 0.850672
|
|
24000 0.4584402 -2.0845866 0.062994228 -1.5635342 0.78607061
|
|
25000 0.45668297 -2.0867185 0.057694285 -1.5727218 0.85872516
|
|
26000 0.45509931 -2.0887933 0.057944017 -1.5761293 0.97591479
|
|
27000 0.44666043 -2.1050106 0.056793397 -1.601929 0.86053641
|
|
28000 0.44305811 -2.0986076 0.06061175 -1.595307 0.8337899
|
|
29000 0.43309506 -2.0797769 0.057836836 -1.5892059 0.781554
|
|
30000 0.45295672 -2.1062574 0.059985016 -1.5936931 0.82009912
|
|
31000 0.44732019 -2.097185 0.050654563 -1.599583 0.85301217
|
|
32000 0.44266582 -2.0953191 0.054789729 -1.5982324 0.71512496
|
|
33000 0.4453828 -2.0994714 0.060417004 -1.5940427 0.72747171
|
|
34000 0.46294819 -2.1152896 0.057702794 -1.5950244 0.76689535
|
|
35000 0.45151588 -2.1057688 0.067282487 -1.5873467 0.58239461
|
|
36000 0.43762794 -2.110522 0.064864579 -1.6083942 0.67640246
|
|
37000 0.45 -2.1238558 0.055080557 -1.6191502 0.66264135
|
|
38000 0.45242633 -2.090514 0.052892245 -1.5855725 0.82462117
|
|
39000 0.46220707 -2.1171223 0.066563814 -1.5887366 0.61579423
|
|
40000 0.46129497 -2.1127774 0.052158545 -1.5997083 0.7450628
|
|
41000 0.44910025 -2.1105051 0.055407892 -1.6063712 0.63060789
|
|
42000 0.43949477 -2.1111359 0.053274048 -1.6187333 0.7589387
|
|
43000 0.44780419 -2.1131157 0.064089346 -1.6015953 0.66207693
|
|
44000 0.45601736 -2.103811 0.05661822 -1.5915554 0.82031717
|
|
45000 0.4444893 -2.1288758 0.064280408 -1.6204765 0.63115787
|
|
46000 0.4412452 -2.126527 0.069196255 -1.6164532 0.5245319
|
|
47000 0.46558295 -2.1302034 0.061017021 -1.6039914 0.47795265
|
|
48000 0.4447318 -2.10327 0.051780625 -1.6071281 0.56768661
|
|
49000 0.45152907 -2.1159427 0.052803985 -1.6119859 0.79924946
|
|
50000 0.43009519 -2.1080874 0.067204222 -1.6111465 0.85332392
|
|
51000 0.46317379 -2.1123268 0.058408991 -1.59113 0.72230777
|
|
52000 0.45417978 -2.1200771 0.065575223 -1.6007006 0.7742118
|
|
53000 0.43662759 -2.0916043 0.061621629 -1.593719 0.80656554
|
|
54000 0.44985568 -2.1167148 0.063414372 -1.6038197 0.63989449
|
|
55000 0.44499083 -2.1104573 0.056857917 -1.6089794 0.73153307
|
|
56000 0.44760788 -2.1162558 0.061556514 -1.6074644 0.62340704
|
|
57000 0.43753788 -2.1127115 0.05633761 -1.6192006 0.7012971
|
|
58000 0.46476788 -2.121983 0.057525001 -1.6000774 0.64993478
|
|
59000 0.45 -2.1329625 0.069789212 -1.6135483 0.63819024
|
|
60000 0.44526017 -2.1213789 0.071976974 -1.6045128 0.71055045
|
|
Loop time of 7.83001 on 1 procs for 60000 steps with 1200 atoms
|
|
|
|
Performance: 3310339.921 tau/day, 7662.824 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 5.2292 | 5.2292 | 5.2292 | 0.0 | 66.78
|
|
Bond | 0.23627 | 0.23627 | 0.23627 | 0.0 | 3.02
|
|
Neigh | 1.5068 | 1.5068 | 1.5068 | 0.0 | 19.24
|
|
Comm | 0.14386 | 0.14386 | 0.14386 | 0.0 | 1.84
|
|
Output | 0.00068521 | 0.00068521 | 0.00068521 | 0.0 | 0.01
|
|
Modify | 0.56151 | 0.56151 | 0.56151 | 0.0 | 7.17
|
|
Other | | 0.1516 | | | 1.94
|
|
|
|
Nlocal: 1200 ave 1200 max 1200 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 374 ave 374 max 374 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 9604 ave 9604 max 9604 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 9604
|
|
Ave neighs/atom = 8.00333
|
|
Ave special neighs/atom = 0.5
|
|
Neighbor list builds = 4881
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:07
|