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update micelle example with corrected data file and rigid body input

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Axel Kohlmeyer 2019-03-26 16:35:35 -04:00
parent 6e7f13e6f9
commit dbd458e9e3
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8 changed files with 2707 additions and 2038 deletions
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examples/micelle/data.micelle
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examples/micelle/in.micelle-rigid Normal file
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# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
special_bonds fene
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
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
group solvent molecule 0
group solute subtract all solvent
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000

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examples/micelle/log.27Nov18.micelle.g++.1
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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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examples/micelle/log.27Nov18.micelle.g++.4
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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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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 0.108068 on 1 procs for 1000 steps with 1200 atoms
Performance: 3997492.279 tau/day, 9253.454 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.071711 | 0.071711 | 0.071711 | 0.0 | 66.36
Bond | 0.0039465 | 0.0039465 | 0.0039465 | 0.0 | 3.65
Neigh | 0.01743 | 0.01743 | 0.01743 | 0.0 | 16.13
Comm | 0.0018625 | 0.0018625 | 0.0018625 | 0.0 | 1.72
Output | 0.00015855 | 0.00015855 | 0.00015855 | 0.0 | 0.15
Modify | 0.01058 | 0.01058 | 0.01058 | 0.0 | 9.79
Other | | 0.00238 | | | 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
group solvent molecule 0
0 atoms in group solvent
group solute subtract all solvent
1200 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms
fix 4 all enforce2d
run 20000
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) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.43824398 -1.7061976 0.094144249 -1.5297 35.328657
1000 0.44980495 -1.7618752 0.094144249 -1.5832051 -0.78239121
2000 0.4080548 -1.7592744 0.094144249 -1.5884498 3.7941359
3000 0.43543409 -1.7704837 0.094144249 -1.5945142 2.0801732
4000 0.43624218 -1.7752975 0.094144249 -1.5991761 5.3401997
5000 0.44526204 -1.7627039 0.094144249 -1.5848875 1.8074242
6000 0.45601171 -1.7578409 0.094144249 -1.5780044 3.6999235
7000 0.45000311 -1.7707158 0.094144249 -1.5920085 14.198063
8000 0.49199853 -1.7647643 0.094144249 -1.5781653 1.1767602
9000 0.42662498 -1.7719397 0.094144249 -1.5976255 1.8316615
10000 0.44225069 -1.7704012 0.094144249 -1.5931507 4.2515329
11000 0.54415369 -1.7634927 0.094144249 -1.5670929 7.626065
12000 0.42501235 -1.7698463 0.094144249 -1.5958351 1.4118043
13000 0.48382538 -1.7497323 0.094144249 -1.5646692 2.2441707
14000 0.4376704 -1.7658795 0.094144249 -1.5894897 2.7170856
15000 0.42644426 -1.758103 0.094144249 -1.5838228 5.6129465
16000 0.37371943 -1.7881668 0.094144249 -1.6237944 4.0731922
17000 0.42320956 -1.7831129 0.094144249 -1.6094406 -4.2042077
18000 0.47319029 -1.7642512 0.094144249 -1.5811866 1.8859862
19000 0.45117547 -1.7736983 0.094144249 -1.5947706 -1.3566752
20000 0.48993295 -1.7820573 0.094144249 -1.5958465 -0.63347623
Loop time of 3.56168 on 1 procs for 20000 steps with 1200 atoms
Performance: 2425823.418 tau/day, 5615.332 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 | 1.7048 | 1.7048 | 1.7048 | 0.0 | 47.86
Bond | 0.079658 | 0.079658 | 0.079658 | 0.0 | 2.24
Neigh | 0.36319 | 0.36319 | 0.36319 | 0.0 | 10.20
Comm | 0.042085 | 0.042085 | 0.042085 | 0.0 | 1.18
Output | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.01
Modify | 1.3169 | 1.3169 | 1.3169 | 0.0 | 36.97
Other | | 0.05485 | | | 1.54
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 414 ave 414 max 414 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8824 ave 8824 max 8824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8824
Ave neighs/atom = 7.35333
Ave special neighs/atom = 0.5
Neighbor list builds = 1148
Dangerous builds = 0
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms
25.2208 = max distance from body owner to body atom
fix 4 all enforce2d
run 20000
Per MPI rank memory allocation (min/avg/max) = 8.642 | 8.642 | 8.642 Mbytes
Step Temp E_pair E_mol TotEng Press
20000 0.48993295 -1.7820573 0.094144249 -1.5958465 3.267595
21000 0.42136691 -1.7767171 0.094144249 -1.6033909 1.1186996
22000 0.42456205 -1.7606471 0.094144249 -1.5867205 2.8866506
23000 0.48026533 -1.7693864 0.094144249 -1.5849923 7.3708907
24000 0.51908347 -1.7748052 0.094144249 -1.5831165 -0.88177558
25000 0.46033763 -1.7615973 0.094144249 -1.580948 7.0803034
26000 0.48667124 -1.7625783 0.094144249 -1.5769804 -11.557404
27000 0.45085745 -1.7833193 0.094144249 -1.6044514 6.5390499
28000 0.47333185 -1.7561049 0.094144249 -1.5730137 -3.2587604
29000 0.46380712 -1.7830962 0.094144249 -1.6017949 7.1120026
30000 0.41845082 -1.7808054 0.094144249 -1.6080272 3.6435588
31000 0.510966 -1.7649896 0.094144249 -1.5748263 1.4979844
32000 0.42169482 -1.7623593 0.094144249 -1.5889716 2.6130718
33000 0.43724881 -1.769415 0.094144249 -1.5931044 1.1205627
34000 0.43753147 -1.7878022 0.094144249 -1.6114385 9.0463054
35000 0.44230686 -1.7554417 0.094144249 -1.5781806 3.776513
36000 0.39564972 -1.7614398 0.094144249 -1.5929464 4.6243057
37000 0.39176208 -1.7586072 0.094144249 -1.5908443 -2.1444581
38000 0.4601972 -1.7727349 0.094144249 -1.5921119 9.513042
39000 0.42107042 -1.7703643 0.094144249 -1.5970939 5.3409161
40000 0.45100889 -1.7794839 0.094144249 -1.6005876 -8.2877164
Loop time of 3.5613 on 1 procs for 20000 steps with 1200 atoms
Performance: 2426077.738 tau/day, 5615.921 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7113 | 1.7113 | 1.7113 | 0.0 | 48.05
Bond | 0.079594 | 0.079594 | 0.079594 | 0.0 | 2.23
Neigh | 0.36249 | 0.36249 | 0.36249 | 0.0 | 10.18
Comm | 0.042057 | 0.042057 | 0.042057 | 0.0 | 1.18
Output | 0.00020933 | 0.00020933 | 0.00020933 | 0.0 | 0.01
Modify | 1.3102 | 1.3102 | 1.3102 | 0.0 | 36.79
Other | | 0.05553 | | | 1.56
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: 8806 ave 8806 max 8806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8806
Ave neighs/atom = 7.33833
Ave special neighs/atom = 0.5
Neighbor list builds = 1149
Dangerous builds = 0
Total wall time: 0:00:07

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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)
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 | 3.758 | 3.758 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 0.0372003 on 4 procs for 1000 steps with 1200 atoms
Performance: 11612799.682 tau/day, 26881.481 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016521 | 0.017472 | 0.018793 | 0.6 | 46.97
Bond | 0.00099087 | 0.0011039 | 0.0012043 | 0.2 | 2.97
Neigh | 0.004885 | 0.0049515 | 0.0050163 | 0.1 | 13.31
Comm | 0.0060358 | 0.007614 | 0.0085688 | 1.1 | 20.47
Output | 0.00021625 | 0.00048053 | 0.0012674 | 0.0 | 1.29
Modify | 0.0035112 | 0.0037069 | 0.0038922 | 0.2 | 9.96
Other | | 0.001872 | | | 5.03
Nlocal: 300 ave 305 max 295 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 105.5 ave 109 max 102 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 797.75 ave 810 max 792 min
Histogram: 2 0 1 0 0 0 0 0 0 1
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
group solvent molecule 0
0 atoms in group solvent
group solute subtract all solvent
1200 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms
fix 4 all enforce2d
run 20000
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) = 5.251 | 5.251 | 5.251 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.43824398 -1.7061976 0.094144249 -1.5297 35.328657
1000 0.44980495 -1.7618752 0.094144249 -1.5832051 -0.78239121
2000 0.40805491 -1.7592744 0.094144249 -1.5884498 3.794136
3000 0.43543405 -1.770484 0.094144249 -1.5945145 2.0801519
4000 0.43643917 -1.7753492 0.094144249 -1.5991908 5.3403198
5000 0.45205579 -1.7629096 0.094144249 -1.5838165 1.9144765
6000 0.44220306 -1.7576322 0.094144249 -1.5803906 3.6971068
7000 0.4462785 -1.7647165 0.094144249 -1.586709 14.683449
8000 0.50268339 -1.7617766 0.094144249 -1.5731698 0.60117188
9000 0.4185915 -1.7725393 0.094144249 -1.5997347 1.5667222
10000 0.41970397 -1.7644115 0.094144249 -1.5913979 3.8986052
11000 0.51816323 -1.766257 0.094144249 -1.5747412 7.1402513
12000 0.42512195 -1.7744735 0.094144249 -1.6004418 1.4082461
13000 0.47476574 -1.7409224 0.094144249 -1.5575618 2.340655
14000 0.42835873 -1.7615597 0.094144249 -1.5869197 2.3617147
15000 0.44020572 -1.7540214 0.094144249 -1.5771552 6.6780537
16000 0.40238891 -1.795345 0.094144249 -1.6255852 3.9488478
17000 0.45191638 -1.7874875 0.094144249 -1.6084206 -4.6290962
18000 0.49064485 -1.7647644 0.094144249 -1.5784198 1.7453052
19000 0.46160705 -1.7769365 0.094144249 -1.5960486 -1.1662864
20000 0.47959574 -1.7800673 0.094144249 -1.595799 -0.98697816
Loop time of 1.7116 on 4 procs for 20000 steps with 1200 atoms
Performance: 5047917.690 tau/day, 11684.995 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.37681 | 0.38516 | 0.39458 | 1.0 | 22.50
Bond | 0.020415 | 0.021627 | 0.022797 | 0.7 | 1.26
Neigh | 0.10577 | 0.10609 | 0.10629 | 0.1 | 6.20
Comm | 0.13426 | 0.14677 | 0.15824 | 2.6 | 8.58
Output | 0.0002625 | 0.00055283 | 0.0014203 | 0.0 | 0.03
Modify | 0.98032 | 0.99445 | 1.0072 | 1.0 | 58.10
Other | | 0.05693 | | | 3.33
Nlocal: 300 ave 303 max 297 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 218.25 ave 220 max 216 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 2200 ave 2256 max 2100 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 8800
Ave neighs/atom = 7.33333
Ave special neighs/atom = 0.5
Neighbor list builds = 1151
Dangerous builds = 0
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms
25.2208 = max distance from body owner to body atom
fix 4 all enforce2d
run 20000
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.566 | 8.567 Mbytes
Step Temp E_pair E_mol TotEng Press
20000 0.47959574 -1.7800673 0.094144249 -1.595799 2.1834568
21000 0.45192649 -1.7677564 0.094144249 -1.5886876 5.0300353
22000 0.48175977 -1.7671661 0.094144249 -1.5824911 2.3411062
23000 0.46753063 -1.7602689 0.094144249 -1.5782678 5.8757813
24000 0.45718166 -1.7635844 0.094144249 -1.5835281 -1.1327974
25000 0.45674572 -1.7712591 0.094144249 -1.5912847 -6.0018365
26000 0.44622761 -1.7601243 0.094144249 -1.5821264 5.1254356
27000 0.41586479 -1.7807035 0.094144249 -1.6084114 -5.3810671
28000 0.41308577 -1.7679534 0.094144249 -1.5961835 0.71052669
29000 0.43702439 -1.7690454 0.094144249 -1.592777 1.9213508
30000 0.43066072 -1.7724511 0.094144249 -1.5973785 2.4355851
31000 0.48969168 -1.7625278 0.094144249 -1.5763624 5.7700505
32000 0.39884729 -1.7714506 0.094144249 -1.6023563 11.053577
33000 0.4347186 -1.7737143 0.094144249 -1.5978792 -2.6480619
34000 0.44709286 -1.7661896 0.094144249 -1.5880292 6.5468593
35000 0.45546222 -1.7718546 0.094144249 -1.5921214 0.52103696
36000 0.48138774 -1.770575 0.094144249 -1.58597 1.1512536
37000 0.42613993 -1.7639698 0.094144249 -1.5897468 1.9532262
38000 0.45269407 -1.7624131 0.094144249 -1.5832001 4.9018622
39000 0.47640838 -1.7756583 0.094144249 -1.591989 0.3741248
40000 0.50397124 -1.7866289 0.094144249 -1.59778 1.704803
Loop time of 1.21517 on 4 procs for 20000 steps with 1200 atoms
Performance: 7110090.321 tau/day, 16458.542 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38099 | 0.38923 | 0.40336 | 1.4 | 32.03
Bond | 0.020087 | 0.021536 | 0.022812 | 0.7 | 1.77
Neigh | 0.10813 | 0.10901 | 0.10931 | 0.2 | 8.97
Comm | 0.12643 | 0.14414 | 0.15438 | 3.0 | 11.86
Output | 0.00025606 | 0.00054097 | 0.0013928 | 0.0 | 0.04
Modify | 0.50525 | 0.50958 | 0.52151 | 1.0 | 41.93
Other | | 0.04114 | | | 3.39
Nlocal: 300 ave 303 max 296 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 216 ave 221 max 212 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2205 ave 2277 max 2105 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 8820
Ave neighs/atom = 7.35
Ave special neighs/atom = 0.5
Neighbor list builds = 1150
Dangerous builds = 0
Total wall time: 0:00:02

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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

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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)
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 | 3.758 | 3.758 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 0.038061 on 4 procs for 1000 steps with 1200 atoms
Performance: 11350211.981 tau/day, 26273.639 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016952 | 0.017563 | 0.018236 | 0.3 | 46.14
Bond | 0.00098968 | 0.0010636 | 0.0011351 | 0.2 | 2.79
Neigh | 0.0048919 | 0.0049396 | 0.0049865 | 0.1 | 12.98
Comm | 0.0075874 | 0.0083745 | 0.0094497 | 0.7 | 22.00
Output | 0.00021791 | 0.00024784 | 0.00033474 | 0.0 | 0.65
Modify | 0.0035474 | 0.0036926 | 0.0038188 | 0.2 | 9.70
Other | | 0.00218 | | | 5.73
Nlocal: 300 ave 305 max 295 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 105.5 ave 109 max 102 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 797.75 ave 810 max 792 min
Histogram: 2 0 1 0 0 0 0 0 0 1
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) = 4.001 | 4.001 | 4.001 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7061976 0.094144249 -1.1624283 3.8015113
1000 0.45 -1.9656272 0.065737702 -1.4502645 1.8869504
2000 0.45643021 -1.9804979 0.06069692 -1.4637511 1.7840488
3000 0.45 -2.0069774 0.063273903 -1.4940785 1.5344808
4000 0.46877185 -2.0118089 0.063511162 -1.4799165 1.5112039
5000 0.45037477 -2.0202928 0.064675812 -1.5056176 1.5614253
6000 0.46516417 -2.041891 0.0633751 -1.5137393 1.302917
7000 0.43402321 -2.0309525 0.080389027 -1.5169019 1.2526669
8000 0.44698877 -2.0438825 0.056384491 -1.5408818 1.2320847
9000 0.46716896 -2.0490995 0.055185945 -1.5271339 1.1323067
10000 0.45585592 -2.0534599 0.059172717 -1.5388112 1.2103699
11000 0.44678446 -2.0702287 0.064814108 -1.5590025 0.93753889
12000 0.46238947 -2.0533635 0.061899722 -1.5294596 1.039375
13000 0.44497125 -2.0582622 0.055753243 -1.5579085 1.105247
14000 0.46197842 -2.0700459 0.061177996 -1.5472745 1.0365751
15000 0.45391975 -2.0698433 0.071128012 -1.5451738 0.94060338
16000 0.44617128 -2.0921643 0.064669811 -1.5816951 0.96199988
17000 0.45205591 -2.0892946 0.073532323 -1.5640831 0.72042835
18000 0.44742647 -2.0667234 0.066469731 -1.5532 1.0881956
19000 0.45154441 -2.0603669 0.0589846 -1.5502142 1.1682254
20000 0.44930673 -2.0699762 0.060197 -1.5608469 0.93709988
21000 0.44952144 -2.0787365 0.054909176 -1.5746805 0.91906714
22000 0.45094085 -2.1027668 0.05970659 -1.5924952 0.76875966
23000 0.45653288 -2.0752194 0.057879405 -1.5611875 0.90288603
24000 0.45659718 -2.1051589 0.061071012 -1.5878712 0.67941553
25000 0.44943892 -2.0785434 0.063137757 -1.5663412 0.91848225
26000 0.46662896 -2.0912992 0.060997699 -1.5640614 0.84321344
27000 0.45990587 -2.0872861 0.062249833 -1.5655136 0.7970408
28000 0.44904041 -2.0887241 0.067592763 -1.5724651 0.83063368
29000 0.44840621 -2.082931 0.063504343 -1.5713941 0.85259731
30000 0.45 -2.1005553 0.061020694 -1.5899096 0.85076517
31000 0.43293607 -2.0834216 0.062211326 -1.588635 0.87798767
32000 0.45 -2.1041864 0.056583773 -1.5979776 0.74721991
33000 0.45483731 -2.0843819 0.064702707 -1.5652209 0.72878185
34000 0.45 -2.0946388 0.056465271 -1.5885485 0.81958535
35000 0.45561477 -2.0962413 0.058642378 -1.5823639 0.86190757
36000 0.46372156 -2.0819766 0.061679429 -1.556962 0.92734228
37000 0.46602014 -2.0978422 0.05861007 -1.5736003 0.87514767
38000 0.45496066 -2.0993783 0.054914099 -1.5898827 0.7885952
39000 0.45215206 -2.0997742 0.061140603 -1.5868584 0.83434324
40000 0.43961538 -2.095479 0.061779306 -1.5944507 0.79151814
41000 0.45065436 -2.0992641 0.058334617 -1.5906507 0.84329542
42000 0.44063989 -2.0911919 0.058682846 -1.5922364 0.83653642
43000 0.45090762 -2.1109187 0.056792395 -1.6035945 0.66699616
44000 0.43620597 -2.1163977 0.068503171 -1.6120521 0.72985642
45000 0.4536995 -2.1169236 0.06222035 -1.6013818 0.6724514
46000 0.44961963 -2.0949168 0.056381135 -1.5892907 0.85934269
47000 0.45429621 -2.0982372 0.05977093 -1.5845486 0.78798948
48000 0.45889422 -2.1042317 0.062692038 -1.5830278 0.80652424
49000 0.44973607 -2.1107622 0.05251269 -1.6088882 0.80305097
50000 0.45422606 -2.1083846 0.05061301 -1.603924 0.81750837
51000 0.45545299 -2.1154627 0.053581638 -1.6068076 0.77970255
52000 0.46382715 -2.1001689 0.053408569 -1.5833197 0.77034515
53000 0.44707619 -2.1134818 0.055878089 -1.6109001 0.63749083
54000 0.45951971 -2.1155704 0.05958078 -1.5968529 0.81426779
55000 0.45588645 -2.1128869 0.060361673 -1.5970187 0.70242718
56000 0.44752186 -2.0917439 0.058352116 -1.5862429 0.89773952
57000 0.44921415 -2.115356 0.05318821 -1.613328 0.81456406
58000 0.44046295 -2.1119294 0.063384551 -1.6084489 0.59683679
59000 0.4349702 -2.0981796 0.059156694 -1.6044152 0.71438644
60000 0.4568814 -2.1060323 0.06038074 -1.5891509 0.70442841
Loop time of 2.49332 on 4 procs for 60000 steps with 1200 atoms
Performance: 10395764.892 tau/day, 24064.271 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1638 | 1.2432 | 1.3093 | 4.7 | 49.86
Bond | 0.055561 | 0.063918 | 0.072427 | 2.4 | 2.56
Neigh | 0.45107 | 0.45366 | 0.45616 | 0.3 | 18.20
Comm | 0.40982 | 0.48044 | 0.56933 | 8.4 | 19.27
Output | 0.00072122 | 0.0013784 | 0.0033441 | 3.1 | 0.06
Modify | 0.14899 | 0.15204 | 0.15837 | 1.0 | 6.10
Other | | 0.09871 | | | 3.96
Nlocal: 300 ave 307 max 288 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 216 ave 222 max 212 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 2391.75 ave 2543 max 2194 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 9567
Ave neighs/atom = 7.9725
Ave special neighs/atom = 0.5
Neighbor list builds = 4889
Dangerous builds = 0
Total wall time: 0:00:02