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update log files for melt and micelle example

This commit is contained in:
Axel Kohlmeyer 2018-11-29 14:05:28 -05:00
parent d67dad9d67
commit 074a9663cb
6 changed files with 550 additions and 514 deletions
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33
examples/melt/log.5Oct16.melt.g++.1 → examples/melt/log.27Nov18.melt.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
units lj units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000645638 secs
mass 1 1.0 mass 1 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -35,13 +37,18 @@ fix 1 all nve
thermo 50 thermo 50
run 250 run 250
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12 binsize = 1.4, bins = 12 12 12
Memory usage per processor = 2.19271 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064 50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514 150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.724365 on 1 procs for 250 steps with 4000 atoms Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms
Performance: 149096.106 tau/day, 345.130 timesteps/s Performance: 147983.915 tau/day, 342.555 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.61654 | 0.61654 | 0.61654 | 0.0 | 85.11 Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12
Neigh | 0.081313 | 0.081313 | 0.081313 | 0.0 | 11.23 Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63
Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 1.51 Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86
Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.01 Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02
Modify | 0.012401 | 0.012401 | 0.012401 | 0.0 | 1.71 Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97
Other | | 0.003077 | | | 0.42 Other | | 0.002878 | | | 0.39
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

33
examples/melt/log.5Oct16.melt.g++.4 → examples/melt/log.27Nov18.melt.g++.4
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
units lj units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.00041604 secs
mass 1 1.0 mass 1 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -35,13 +37,18 @@ fix 1 all nve
thermo 50 thermo 50
run 250 run 250
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12 binsize = 1.4, bins = 12 12 12
Memory usage per processor = 2.10344 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.210997 on 4 procs for 250 steps with 4000 atoms Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms
Performance: 511855.365 tau/day, 1184.850 timesteps/s Performance: 483592.231 tau/day, 1119.426 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads 97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.15475 | 0.16099 | 0.1682 | 1.2 | 76.30 Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05
Neigh | 0.020829 | 0.021108 | 0.021522 | 0.2 | 10.00 Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29
Comm | 0.01674 | 0.024412 | 0.030987 | 3.3 | 11.57 Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47
Output | 0.00011587 | 0.0001238 | 0.00013185 | 0.1 | 0.06 Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09
Modify | 0.0031242 | 0.0031361 | 0.0031476 | 0.0 | 1.49 Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72
Other | | 0.001227 | | | 0.58 Other | | 0.00085 | | | 0.38
Nlocal: 1000 ave 1010 max 982 min Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 0 0 0 0 1 0 0 2

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examples/micelle/log.27Nov18.micelle.g++.1 Normal file
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LAMMPS (27 Nov 2018)
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 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 0.40003481 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 0.167265 on 1 procs for 1000 steps with 1200 atoms
Performance: 2582728.958 tau/day, 5978.539 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
Other | | 0.006227 | | | 3.72
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 -1.9727655 0.058608715 -1.4645318 1.9982298
2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
Performance: 1859917.639 tau/day, 4305.365 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 | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
Other | | 0.3493 | | | 2.51
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 405 ave 405 max 405 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9565 ave 9565 max 9565 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9565
Ave neighs/atom = 7.97083
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0
Total wall time: 0:00:14

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LAMMPS (27 Nov 2018)
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)
2 by 2 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) = 3.758 | 3.85 | 4.126 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 0.0641922 on 4 procs for 1000 steps with 1200 atoms
Performance: 6729792.131 tau/day, 15578.223 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
Other | | 0.003891 | | | 6.06
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
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) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402
2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
Performance: 5681397.232 tau/day, 13151.382 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
Other | | 0.2346 | | | 5.14
Nlocal: 300 ave 306 max 289 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 227.25 ave 250 max 216 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 2373.25 ave 2489 max 2283 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 9493
Ave neighs/atom = 7.91083
Ave special neighs/atom = 0.5
Neighbor list builds = 4888
Dangerous builds = 0
Total wall time: 0:00:04

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examples/micelle/log.5Oct16.micelle.g++.1
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LAMMPS (5 Oct 2016)
# 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 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 ...
1 neighbor list requests
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
Memory usage per processor = 3.45296 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 0.192637 on 1 procs for 1000 steps with 1200 atoms
Performance: 2242560.228 tau/day, 5191.112 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29
Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44
Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40
Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71
Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10
Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40
Other | | 0.005115 | | | 2.66
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 ...
1 neighbor list requests
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
Memory usage per processor = 3.45296 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299
2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107
3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132
4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127
5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421
6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692
7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802
8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472
9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529
10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481
11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264
12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813
13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127
14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319
15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211
16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991
17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012
18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585
19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228
20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418
21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595
22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955
23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876
24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833
25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274
26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526
27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018
28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478
29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706
30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298
31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692
32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441
33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371
34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708
35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163
36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748
37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072
38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145
39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475
40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301
41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478
42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466
43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235
44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091
45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898
46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901
47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542
48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782
49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201
50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821
51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581
52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576
53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136
54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217
55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948
56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945
57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456
58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379
59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834
60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428
Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms
Performance: 1903978.372 tau/day, 4407.357 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82
Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90
Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24
Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87
Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00
Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95
Other | | 0.3019 | | | 2.22
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 417 ave 417 max 417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9495 ave 9495 max 9495 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9495
Ave neighs/atom = 7.9125
Ave special neighs/atom = 0.5
Neighbor list builds = 4885
Dangerous builds = 0
Total wall time: 0:00:13

244
examples/micelle/log.5Oct16.micelle.g++.4
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LAMMPS (5 Oct 2016)
# 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)
2 by 2 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 ...
1 neighbor list requests
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
Memory usage per processor = 3.55365 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 0.0670803 on 4 procs for 1000 steps with 1200 atoms
Performance: 6440046.660 tau/day, 14907.515 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033971 | 0.034628 | 0.036162 | 0.5 | 51.62
Bond | 0.001687 | 0.0017596 | 0.0018852 | 0.2 | 2.62
Neigh | 0.0068789 | 0.0069902 | 0.0070932 | 0.1 | 10.42
Comm | 0.011152 | 0.012883 | 0.013872 | 0.9 | 19.20
Output | 0.00035501 | 0.00038034 | 0.00044274 | 0.2 | 0.57
Modify | 0.0065997 | 0.0067009 | 0.0068605 | 0.1 | 9.99
Other | | 0.003738 | | | 5.57
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
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 ...
1 neighbor list requests
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
Memory usage per processor = 3.55365 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389
2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222
3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627
4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681
5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201
6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697
7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258
8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483
9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073
10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504
11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919
12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597
13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604
14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118
15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383
16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698
17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709
18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376
19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446
20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174
21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426
22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367
23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975
24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971
25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418
26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166
27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525
28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874
29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766
30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889
31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188
32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981
33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562
34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582
35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438
36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389
37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583
38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974
39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261
40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332
41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574
42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091
43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812
44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595
45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258
46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898
47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032
48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819
49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508
50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822
51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123
52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016
53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287
54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909
55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805
56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345
57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346
58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
Loop time of 4.56204 on 4 procs for 60000 steps with 1200 atoms
Performance: 5681665.051 tau/day, 13152.002 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3705 | 2.4423 | 2.4948 | 2.9 | 53.54
Bond | 0.084795 | 0.10292 | 0.11359 | 3.4 | 2.26
Neigh | 0.63938 | 0.64418 | 0.64857 | 0.4 | 14.12
Comm | 0.81947 | 0.8785 | 0.9618 | 5.7 | 19.26
Output | 0.0012863 | 0.0013551 | 0.0015438 | 0.3 | 0.03
Modify | 0.26717 | 0.27596 | 0.28816 | 1.5 | 6.05
Other | | 0.2168 | | | 4.75
Nlocal: 300 ave 305 max 293 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 211 ave 215 max 205 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 2448.75 ave 2531 max 2414 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 9795
Ave neighs/atom = 8.1625
Ave special neighs/atom = 0.5
Neighbor list builds = 4880
Dangerous builds = 0
Total wall time: 0:00:04