ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

correct micelle data file without overwriting the molecule ids

Browse Source
This commit is contained in:
Axel Kohlmeyer
2019-03-26 19:08:58 -04:00
parent dbd458e9e3
commit 1926c95625
5 changed files with 2026 additions and 2021 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3031
examples/micelle/data.micelle
View File

File diff suppressed because it is too large Load Diff

234
examples/micelle/log.28Feb2019.micelle-rigid.g++.1
View File

@ -1,5 +1,5 @@
LAMMPS (28 Feb 2019) LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation # 2d micelle simulation
@ -13,7 +13,7 @@ atom_style bond
# Soft potential push-off # Soft potential push-off
read_data data.micelle read_data data.micelle
orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1) orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
1200 atoms 1200 atoms
@ -25,9 +25,12 @@ read_data data.micelle
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000271559 secs
read_data CPU = 0.00115585 secs
special_bonds fene special_bonds fene
2 = max # of 1-2 neighbors 2 = max # of 1-2 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 8.39233e-05 secs
pair_style soft 1.12246 pair_style soft 1.12246
pair_coeff * * 0.0 1.12246 pair_coeff * * 0.0 1.12246
@ -60,54 +63,54 @@ Neighbor list info ...
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 0.40179153 0.017198847 0.86861538 0.75625658 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73189198 0.056737309 1.2382543 2.321972 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78767975 0.079977445 1.3172822 3.0463605 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76847924 0.069944127 1.2880484 3.7420091 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.69469019 0.094115526 1.2384307 4.4786122 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64066675 0.080351857 1.1706436 4.7965076 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58371075 0.088545932 1.1218817 5.0963739 600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.5394553 0.10365542 1.0927357 5.3370157 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.51563293 0.1030928 1.0683507 5.5156219 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.4758065 0.098479812 1.0239113 5.6783722 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.108068 on 1 procs for 1000 steps with 1200 atoms Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms
Performance: 3997492.279 tau/day, 9253.454 timesteps/s Performance: 4029800.456 tau/day, 9328.242 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% 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 | 0.071711 | 0.071711 | 0.071711 | 0.0 | 66.36 Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20
Bond | 0.0039465 | 0.0039465 | 0.0039465 | 0.0 | 3.65 Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72
Neigh | 0.01743 | 0.01743 | 0.01743 | 0.0 | 16.13 Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00
Comm | 0.0018625 | 0.0018625 | 0.0018625 | 0.0 | 1.72 Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71
Output | 0.00015855 | 0.00015855 | 0.00015855 | 0.0 | 0.15 Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15
Modify | 0.01058 | 0.01058 | 0.01058 | 0.0 | 9.79 Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95
Other | | 0.00238 | | | 2.20 Other | | 0.002429 | | | 2.27
Nlocal: 1200 ave 1200 max 1200 min Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 206 ave 206 max 206 min Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3191 ave 3191 max 3191 min Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3191 Total # of neighbors = 3136
Ave neighs/atom = 2.65917 Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 99 Neighbor list builds = 92
Dangerous builds = 0 Dangerous builds = 0
unfix 3 unfix 3
@ -150,16 +153,16 @@ thermo 1000
reset_timestep 0 reset_timestep 0
group solvent molecule 0 group solvent molecule 0
0 atoms in group solvent 750 atoms in group solvent
group solute subtract all solvent group solute subtract all solvent
1200 atoms in group solute 450 atoms in group solute
unfix 1 unfix 1
unfix 2 unfix 2
unfix 4 unfix 4
fix 1 solvent nve fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 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 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms 150 rigid bodies with 450 atoms
fix 4 all enforce2d fix 4 all enforce2d
run 20000 run 20000
Neighbor list info ... Neighbor list info ...
@ -176,111 +179,112 @@ Neighbor list info ...
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.43824398 -1.7061976 0.094144249 -1.5297 35.328657 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
1000 0.44980495 -1.7618752 0.094144249 -1.5832051 -0.78239121 1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
2000 0.4080548 -1.7592744 0.094144249 -1.5884498 3.7941359 2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
3000 0.43543409 -1.7704837 0.094144249 -1.5945142 2.0801732 3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
4000 0.43624218 -1.7752975 0.094144249 -1.5991761 5.3401997 4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
5000 0.44526204 -1.7627039 0.094144249 -1.5848875 1.8074242 5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
6000 0.45601171 -1.7578409 0.094144249 -1.5780044 3.6999235 6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
7000 0.45000311 -1.7707158 0.094144249 -1.5920085 14.198063 7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
8000 0.49199853 -1.7647643 0.094144249 -1.5781653 1.1767602 8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
9000 0.42662498 -1.7719397 0.094144249 -1.5976255 1.8316615 9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
10000 0.44225069 -1.7704012 0.094144249 -1.5931507 4.2515329 10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
11000 0.54415369 -1.7634927 0.094144249 -1.5670929 7.626065 11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
12000 0.42501235 -1.7698463 0.094144249 -1.5958351 1.4118043 12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
13000 0.48382538 -1.7497323 0.094144249 -1.5646692 2.2441707 13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
14000 0.4376704 -1.7658795 0.094144249 -1.5894897 2.7170856 14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
15000 0.42644426 -1.758103 0.094144249 -1.5838228 5.6129465 15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
16000 0.37371943 -1.7881668 0.094144249 -1.6237944 4.0731922 16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
17000 0.42320956 -1.7831129 0.094144249 -1.6094406 -4.2042077 17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
18000 0.47319029 -1.7642512 0.094144249 -1.5811866 1.8859862 18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
19000 0.45117547 -1.7736983 0.094144249 -1.5947706 -1.3566752 19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
20000 0.48993295 -1.7820573 0.094144249 -1.5958465 -0.63347623 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
Loop time of 3.56168 on 1 procs for 20000 steps with 1200 atoms Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
Performance: 2425823.418 tau/day, 5615.332 timesteps/s Performance: 2347175.802 tau/day, 5433.277 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% 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 | 1.7048 | 1.7048 | 1.7048 | 0.0 | 47.86 Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13
Bond | 0.079658 | 0.079658 | 0.079658 | 0.0 | 2.24 Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16
Neigh | 0.36319 | 0.36319 | 0.36319 | 0.0 | 10.20 Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33
Comm | 0.042085 | 0.042085 | 0.042085 | 0.0 | 1.18 Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33
Output | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.01 Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01
Modify | 1.3169 | 1.3169 | 1.3169 | 0.0 | 36.97 Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58
Other | | 0.05485 | | | 1.54 Other | | 0.05369 | | | 1.46
Nlocal: 1200 ave 1200 max 1200 min Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 414 ave 414 max 414 min Nghost: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8824 ave 8824 max 8824 min Neighs: 8915 ave 8915 max 8915 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8824 Total # of neighbors = 8915
Ave neighs/atom = 7.35333 Ave neighs/atom = 7.42917
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 1148 Neighbor list builds = 1580
Dangerous builds = 0 Dangerous builds = 0
unfix 5 unfix 5
unfix 4 unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms create bodies CPU = 0.00012517 secs
25.2208 = max distance from body owner to body atom 150 rigid bodies with 450 atoms
1.04536 = max distance from body owner to body atom
fix 4 all enforce2d fix 4 all enforce2d
run 20000 run 20000
Per MPI rank memory allocation (min/avg/max) = 8.642 | 8.642 | 8.642 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
20000 0.48993295 -1.7820573 0.094144249 -1.5958465 3.267595 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
21000 0.42136691 -1.7767171 0.094144249 -1.6033909 1.1186996 21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
22000 0.42456205 -1.7606471 0.094144249 -1.5867205 2.8866506 22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
23000 0.48026533 -1.7693864 0.094144249 -1.5849923 7.3708907 23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
24000 0.51908347 -1.7748052 0.094144249 -1.5831165 -0.88177558 24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
25000 0.46033763 -1.7615973 0.094144249 -1.580948 7.0803034 25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
26000 0.48667124 -1.7625783 0.094144249 -1.5769804 -11.557404 26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
27000 0.45085745 -1.7833193 0.094144249 -1.6044514 6.5390499 27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
28000 0.47333185 -1.7561049 0.094144249 -1.5730137 -3.2587604 28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
29000 0.46380712 -1.7830962 0.094144249 -1.6017949 7.1120026 29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
30000 0.41845082 -1.7808054 0.094144249 -1.6080272 3.6435588 30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
31000 0.510966 -1.7649896 0.094144249 -1.5748263 1.4979844 31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
32000 0.42169482 -1.7623593 0.094144249 -1.5889716 2.6130718 32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
33000 0.43724881 -1.769415 0.094144249 -1.5931044 1.1205627 33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
34000 0.43753147 -1.7878022 0.094144249 -1.6114385 9.0463054 34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
35000 0.44230686 -1.7554417 0.094144249 -1.5781806 3.776513 35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
36000 0.39564972 -1.7614398 0.094144249 -1.5929464 4.6243057 36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
37000 0.39176208 -1.7586072 0.094144249 -1.5908443 -2.1444581 37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
38000 0.4601972 -1.7727349 0.094144249 -1.5921119 9.513042 38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
39000 0.42107042 -1.7703643 0.094144249 -1.5970939 5.3409161 39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
40000 0.45100889 -1.7794839 0.094144249 -1.6005876 -8.2877164 40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
Loop time of 3.5613 on 1 procs for 20000 steps with 1200 atoms Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
Performance: 2426077.738 tau/day, 5615.921 timesteps/s Performance: 2341388.948 tau/day, 5419.882 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% 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 | 1.7113 | 1.7113 | 1.7113 | 0.0 | 48.05 Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59
Bond | 0.079594 | 0.079594 | 0.079594 | 0.0 | 2.23 Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15
Neigh | 0.36249 | 0.36249 | 0.36249 | 0.0 | 10.18 Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30
Comm | 0.042057 | 0.042057 | 0.042057 | 0.0 | 1.18 Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31
Output | 0.00020933 | 0.00020933 | 0.00020933 | 0.0 | 0.01 Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01
Modify | 1.3102 | 1.3102 | 1.3102 | 0.0 | 36.79 Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19
Other | | 0.05553 | | | 1.56 Other | | 0.05386 | | | 1.46
Nlocal: 1200 ave 1200 max 1200 min Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 405 ave 405 max 405 min Nghost: 393 ave 393 max 393 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8806 ave 8806 max 8806 min Neighs: 9091 ave 9091 max 9091 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8806 Total # of neighbors = 9091
Ave neighs/atom = 7.33833 Ave neighs/atom = 7.57583
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 1149 Neighbor list builds = 1582
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:07 Total wall time: 0:00:07

264
examples/micelle/log.28Feb2019.micelle-rigid.g++.4
View File

@ -1,5 +1,5 @@
LAMMPS (28 Feb 2019) LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation # 2d micelle simulation
@ -13,7 +13,7 @@ atom_style bond
# Soft potential push-off # Soft potential push-off
read_data data.micelle read_data data.micelle
orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1) orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid 2 by 2 by 1 MPI processor grid
reading atoms ... reading atoms ...
1200 atoms 1200 atoms
@ -25,9 +25,12 @@ read_data data.micelle
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000175714 secs
read_data CPU = 0.00145626 secs
special_bonds fene special_bonds fene
2 = max # of 1-2 neighbors 2 = max # of 1-2 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 7.22408e-05 secs
pair_style soft 1.12246 pair_style soft 1.12246
pair_coeff * * 0.0 1.12246 pair_coeff * * 0.0 1.12246
@ -58,56 +61,56 @@ Neighbor list info ...
pair build: half/bin/newton pair build: half/bin/newton
stencil: half/bin/2d/newton stencil: half/bin/2d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.758 | 3.758 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 0.40179153 0.017198847 0.86861538 0.75625658 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73189198 0.056737309 1.2382543 2.321972 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78767975 0.079977445 1.3172822 3.0463605 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76847924 0.069944127 1.2880484 3.7420091 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.69469019 0.094115526 1.2384307 4.4786122 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64066675 0.080351857 1.1706436 4.7965076 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58371075 0.088545932 1.1218817 5.0963739 600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.5394553 0.10365542 1.0927357 5.3370157 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.51563293 0.1030928 1.0683507 5.5156219 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.4758065 0.098479812 1.0239113 5.6783722 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0372003 on 4 procs for 1000 steps with 1200 atoms Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms
Performance: 11612799.682 tau/day, 26881.481 timesteps/s Performance: 11101855.138 tau/day, 25698.739 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads 95.7% 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 | 0.016521 | 0.017472 | 0.018793 | 0.6 | 46.97 Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73
Bond | 0.00099087 | 0.0011039 | 0.0012043 | 0.2 | 2.97 Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08
Neigh | 0.004885 | 0.0049515 | 0.0050163 | 0.1 | 13.31 Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59
Comm | 0.0060358 | 0.007614 | 0.0085688 | 1.1 | 20.47 Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12
Output | 0.00021625 | 0.00048053 | 0.0012674 | 0.0 | 1.29 Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71
Modify | 0.0035112 | 0.0037069 | 0.0038922 | 0.2 | 9.96 Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34
Other | | 0.001872 | | | 5.03 Other | | 0.002501 | | | 6.43
Nlocal: 300 ave 305 max 295 min Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 105.5 ave 109 max 102 min Nghost: 100.25 ave 108 max 93 min
Histogram: 1 1 0 0 0 0 0 0 1 1 Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 797.75 ave 810 max 792 min Neighs: 784 ave 815 max 739 min
Histogram: 2 0 1 0 0 0 0 0 0 1 Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3191 Total # of neighbors = 3136
Ave neighs/atom = 2.65917 Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 99 Neighbor list builds = 92
Dangerous builds = 0 Dangerous builds = 0
unfix 3 unfix 3
@ -150,16 +153,16 @@ thermo 1000
reset_timestep 0 reset_timestep 0
group solvent molecule 0 group solvent molecule 0
0 atoms in group solvent 750 atoms in group solvent
group solute subtract all solvent group solute subtract all solvent
1200 atoms in group solute 450 atoms in group solute
unfix 1 unfix 1
unfix 2 unfix 2
unfix 4 unfix 4
fix 1 solvent nve fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 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 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms 150 rigid bodies with 450 atoms
fix 4 all enforce2d fix 4 all enforce2d
run 20000 run 20000
Neighbor list info ... Neighbor list info ...
@ -174,113 +177,114 @@ Neighbor list info ...
pair build: half/bin/newton pair build: half/bin/newton
stencil: half/bin/2d/newton stencil: half/bin/2d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.251 | 5.251 Mbytes Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.43824398 -1.7061976 0.094144249 -1.5297 35.328657 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
1000 0.44980495 -1.7618752 0.094144249 -1.5832051 -0.78239121 1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869
2000 0.40805491 -1.7592744 0.094144249 -1.5884498 3.794136 2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671
3000 0.43543405 -1.770484 0.094144249 -1.5945145 2.0801519 3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553
4000 0.43643917 -1.7753492 0.094144249 -1.5991908 5.3403198 4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215
5000 0.45205579 -1.7629096 0.094144249 -1.5838165 1.9144765 5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897
6000 0.44220306 -1.7576322 0.094144249 -1.5803906 3.6971068 6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512
7000 0.4462785 -1.7647165 0.094144249 -1.586709 14.683449 7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309
8000 0.50268339 -1.7617766 0.094144249 -1.5731698 0.60117188 8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852
9000 0.4185915 -1.7725393 0.094144249 -1.5997347 1.5667222 9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071
10000 0.41970397 -1.7644115 0.094144249 -1.5913979 3.8986052 10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464
11000 0.51816323 -1.766257 0.094144249 -1.5747412 7.1402513 11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699
12000 0.42512195 -1.7744735 0.094144249 -1.6004418 1.4082461 12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823
13000 0.47476574 -1.7409224 0.094144249 -1.5575618 2.340655 13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171
14000 0.42835873 -1.7615597 0.094144249 -1.5869197 2.3617147 14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645
15000 0.44020572 -1.7540214 0.094144249 -1.5771552 6.6780537 15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206
16000 0.40238891 -1.795345 0.094144249 -1.6255852 3.9488478 16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281
17000 0.45191638 -1.7874875 0.094144249 -1.6084206 -4.6290962 17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975
18000 0.49064485 -1.7647644 0.094144249 -1.5784198 1.7453052 18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943
19000 0.46160705 -1.7769365 0.094144249 -1.5960486 -1.1662864 19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417
20000 0.47959574 -1.7800673 0.094144249 -1.595799 -0.98697816 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952
Loop time of 1.7116 on 4 procs for 20000 steps with 1200 atoms Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
Performance: 5047917.690 tau/day, 11684.995 timesteps/s Performance: 5025468.853 tau/day, 11633.030 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads 98.2% 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 | 0.37681 | 0.38516 | 0.39458 | 1.0 | 22.50 Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77
Bond | 0.020415 | 0.021627 | 0.022797 | 0.7 | 1.26 Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27
Neigh | 0.10577 | 0.10609 | 0.10629 | 0.1 | 6.20 Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16
Comm | 0.13426 | 0.14677 | 0.15824 | 2.6 | 8.58 Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92
Output | 0.0002625 | 0.00055283 | 0.0014203 | 0.0 | 0.03 Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03
Modify | 0.98032 | 0.99445 | 1.0072 | 1.0 | 58.10 Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76
Other | | 0.05693 | | | 3.33 Other | | 0.05327 | | | 3.10
Nlocal: 300 ave 303 max 297 min Nlocal: 300 ave 303 max 298 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 218.25 ave 220 max 216 min Nghost: 218.5 ave 226 max 215 min
Histogram: 1 0 0 0 0 1 0 1 0 1 Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 2200 ave 2256 max 2100 min Neighs: 2258.75 ave 2283 max 2216 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 8800 Total # of neighbors = 9035
Ave neighs/atom = 7.33333 Ave neighs/atom = 7.52917
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 1151 Neighbor list builds = 1580
Dangerous builds = 0 Dangerous builds = 0
unfix 5 unfix 5
unfix 4 unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
151 rigid bodies with 1200 atoms create bodies CPU = 5.43594e-05 secs
25.2208 = max distance from body owner to body atom 150 rigid bodies with 450 atoms
0.916597 = max distance from body owner to body atom
fix 4 all enforce2d fix 4 all enforce2d
run 20000 run 20000
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.566 | 8.567 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
20000 0.47959574 -1.7800673 0.094144249 -1.595799 2.1834568 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643
21000 0.45192649 -1.7677564 0.094144249 -1.5886876 5.0300353 21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285
22000 0.48175977 -1.7671661 0.094144249 -1.5824911 2.3411062 22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965
23000 0.46753063 -1.7602689 0.094144249 -1.5782678 5.8757813 23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871
24000 0.45718166 -1.7635844 0.094144249 -1.5835281 -1.1327974 24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675
25000 0.45674572 -1.7712591 0.094144249 -1.5912847 -6.0018365 25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122
26000 0.44622761 -1.7601243 0.094144249 -1.5821264 5.1254356 26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501
27000 0.41586479 -1.7807035 0.094144249 -1.6084114 -5.3810671 27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661
28000 0.41308577 -1.7679534 0.094144249 -1.5961835 0.71052669 28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448
29000 0.43702439 -1.7690454 0.094144249 -1.592777 1.9213508 29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989
30000 0.43066072 -1.7724511 0.094144249 -1.5973785 2.4355851 30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951
31000 0.48969168 -1.7625278 0.094144249 -1.5763624 5.7700505 31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891
32000 0.39884729 -1.7714506 0.094144249 -1.6023563 11.053577 32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966
33000 0.4347186 -1.7737143 0.094144249 -1.5978792 -2.6480619 33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641
34000 0.44709286 -1.7661896 0.094144249 -1.5880292 6.5468593 34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091
35000 0.45546222 -1.7718546 0.094144249 -1.5921214 0.52103696 35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508
36000 0.48138774 -1.770575 0.094144249 -1.58597 1.1512536 36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696
37000 0.42613993 -1.7639698 0.094144249 -1.5897468 1.9532262 37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854
38000 0.45269407 -1.7624131 0.094144249 -1.5832001 4.9018622 38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763
39000 0.47640838 -1.7756583 0.094144249 -1.591989 0.3741248 39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345
40000 0.50397124 -1.7866289 0.094144249 -1.59778 1.704803 40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727
Loop time of 1.21517 on 4 procs for 20000 steps with 1200 atoms Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
Performance: 7110090.321 tau/day, 16458.542 timesteps/s Performance: 6885775.862 tau/day, 15939.296 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads 98.1% 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 | 0.38099 | 0.38923 | 0.40336 | 1.4 | 32.03 Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30
Bond | 0.020087 | 0.021536 | 0.022812 | 0.7 | 1.77 Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72
Neigh | 0.10813 | 0.10901 | 0.10931 | 0.2 | 8.97 Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51
Comm | 0.12643 | 0.14414 | 0.15438 | 3.0 | 11.86 Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27
Output | 0.00025606 | 0.00054097 | 0.0013928 | 0.0 | 0.04 Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04
Modify | 0.50525 | 0.50958 | 0.52151 | 1.0 | 41.93 Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52
Other | | 0.04114 | | | 3.39 Other | | 0.03321 | | | 2.65
Nlocal: 300 ave 303 max 296 min Nlocal: 300 ave 304 max 293 min
Histogram: 1 0 0 0 1 0 0 0 1 1 Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 216 ave 221 max 212 min Nghost: 215.25 ave 217 max 213 min
Histogram: 1 0 0 1 1 0 0 0 0 1 Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 2205 ave 2277 max 2105 min Neighs: 2340 ave 2378 max 2290 min
Histogram: 1 0 0 0 0 0 2 0 0 1 Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8820 Total # of neighbors = 9360
Ave neighs/atom = 7.35 Ave neighs/atom = 7.8
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 1150 Neighbor list builds = 1579
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:02 Total wall time: 0:00:03

233
examples/micelle/log.28Feb2019.micelle.g++.1
View File

@ -1,5 +1,5 @@
LAMMPS (28 Feb 2019) LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation # 2d micelle simulation
@ -13,7 +13,7 @@ atom_style bond
# Soft potential push-off # Soft potential push-off
read_data data.micelle read_data data.micelle
orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1) orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
1200 atoms 1200 atoms
@ -25,9 +25,12 @@ read_data data.micelle
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000394821 secs
read_data CPU = 0.00212336 secs
special_bonds fene special_bonds fene
2 = max # of 1-2 neighbors 2 = max # of 1-2 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.00018549 secs
pair_style soft 1.12246 pair_style soft 1.12246
pair_coeff * * 0.0 1.12246 pair_coeff * * 0.0 1.12246
@ -60,54 +63,54 @@ Neighbor list info ...
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 0.40179153 0.017198847 0.86861538 0.75625658 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73189198 0.056737309 1.2382543 2.321972 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78767975 0.079977445 1.3172822 3.0463605 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76847924 0.069944127 1.2880484 3.7420091 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.69469019 0.094115526 1.2384307 4.4786122 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64066675 0.080351857 1.1706436 4.7965076 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58371075 0.088545932 1.1218817 5.0963739 600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.5394553 0.10365542 1.0927357 5.3370157 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.51563293 0.1030928 1.0683507 5.5156219 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.4758065 0.098479812 1.0239113 5.6783722 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.10837 on 1 procs for 1000 steps with 1200 atoms Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms
Performance: 3986358.208 tau/day, 9227.681 timesteps/s Performance: 3792167.464 tau/day, 8778.165 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% 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 | 0.071949 | 0.071949 | 0.071949 | 0.0 | 66.39 Pair | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44
Bond | 0.0039806 | 0.0039806 | 0.0039806 | 0.0 | 3.67 Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67
Neigh | 0.01737 | 0.01737 | 0.01737 | 0.0 | 16.03 Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98
Comm | 0.0019217 | 0.0019217 | 0.0019217 | 0.0 | 1.77 Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67
Output | 0.00016022 | 0.00016022 | 0.00016022 | 0.0 | 0.15 Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15
Modify | 0.010607 | 0.010607 | 0.010607 | 0.0 | 9.79 Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85
Other | | 0.002382 | | | 2.20 Other | | 0.002551 | | | 2.24
Nlocal: 1200 ave 1200 max 1200 min Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 206 ave 206 max 206 min Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3191 ave 3191 max 3191 min Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3191 Total # of neighbors = 3136
Ave neighs/atom = 2.65917 Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 99 Neighbor list builds = 92
Dangerous builds = 0 Dangerous builds = 0
unfix 3 unfix 3
@ -164,93 +167,93 @@ Neighbor list info ...
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7061976 0.094144249 -1.1624283 3.8015113 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9656133 0.065736052 -1.4502522 1.8870315 1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326
2000 0.45917162 -1.9677772 0.06512989 -1.4438584 1.6197525 2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269
3000 0.45029543 -1.9993287 0.060436068 -1.4889724 1.6749521 3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618
4000 0.44658614 -2.0150793 0.070735372 -1.49813 1.4982834 4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016
5000 0.45 -2.0317981 0.06873808 -1.513435 1.375846 5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164
6000 0.46323984 -2.0135007 0.067698691 -1.4829482 1.3342928 6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891
7000 0.46154055 -2.0268144 0.064313941 -1.5013445 1.2936811 7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333
8000 0.45911863 -2.032873 0.058832094 -1.5153049 1.1717652 8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396
9000 0.46126695 -2.0435575 0.060645049 -1.5220299 1.1810833 9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554
10000 0.44212317 -2.0552317 0.066386857 -1.5470901 1.1217265 10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213
11000 0.46455191 -2.0852383 0.064035544 -1.557038 1.0722284 11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469
12000 0.45647983 -2.0711846 0.058592351 -1.5564929 1.1487056 12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225
13000 0.44296686 -2.0532457 0.059554979 -1.551093 1.1665292 13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283
14000 0.44154216 -2.045874 0.059814984 -1.5448848 1.1231544 14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427
15000 0.43921469 -2.0642415 0.057245543 -1.5681472 1.1342333 15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836
16000 0.44278133 -2.0696899 0.053114875 -1.5741627 1.0881442 16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323
17000 0.45 -2.0847259 0.060756733 -1.5743441 0.94801701 17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919
18000 0.45115973 -2.0899292 0.061273297 -1.5778721 0.86251832 18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638
19000 0.45210059 -2.0822877 0.061618471 -1.5689454 0.80428644 19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341
20000 0.44516679 -2.0789966 0.060221274 -1.5739795 0.98113308 20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768
21000 0.44850103 -2.0920747 0.060514536 -1.5834329 0.92324 21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935
22000 0.44679652 -2.0669569 0.067895097 -1.5526376 1.106608 22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734
23000 0.45651863 -2.0904722 0.06387795 -1.5704561 0.850672 23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013
24000 0.4584402 -2.0845866 0.062994228 -1.5635342 0.78607061 24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789
25000 0.45668297 -2.0867185 0.057694285 -1.5727218 0.85872516 25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875
26000 0.45509931 -2.0887933 0.057944017 -1.5761293 0.97591479 26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118
27000 0.44666043 -2.1050106 0.056793397 -1.601929 0.86053641 27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415
28000 0.44305811 -2.0986076 0.06061175 -1.595307 0.8337899 28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526
29000 0.43309506 -2.0797769 0.057836836 -1.5892059 0.781554 29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376
30000 0.45295672 -2.1062574 0.059985016 -1.5936931 0.82009912 30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113
31000 0.44732019 -2.097185 0.050654563 -1.599583 0.85301217 31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708
32000 0.44266582 -2.0953191 0.054789729 -1.5982324 0.71512496 32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106
33000 0.4453828 -2.0994714 0.060417004 -1.5940427 0.72747171 33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458
34000 0.46294819 -2.1152896 0.057702794 -1.5950244 0.76689535 34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584
35000 0.45151588 -2.1057688 0.067282487 -1.5873467 0.58239461 35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396
36000 0.43762794 -2.110522 0.064864579 -1.6083942 0.67640246 36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939
37000 0.45 -2.1238558 0.055080557 -1.6191502 0.66264135 37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603
38000 0.45242633 -2.090514 0.052892245 -1.5855725 0.82462117 38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359
39000 0.46220707 -2.1171223 0.066563814 -1.5887366 0.61579423 39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385
40000 0.46129497 -2.1127774 0.052158545 -1.5997083 0.7450628 40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955
41000 0.44910025 -2.1105051 0.055407892 -1.6063712 0.63060789 41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756
42000 0.43949477 -2.1111359 0.053274048 -1.6187333 0.7589387 42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561
43000 0.44780419 -2.1131157 0.064089346 -1.6015953 0.66207693 43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063
44000 0.45601736 -2.103811 0.05661822 -1.5915554 0.82031717 44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473
45000 0.4444893 -2.1288758 0.064280408 -1.6204765 0.63115787 45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054
46000 0.4412452 -2.126527 0.069196255 -1.6164532 0.5245319 46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974
47000 0.46558295 -2.1302034 0.061017021 -1.6039914 0.47795265 47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182
48000 0.4447318 -2.10327 0.051780625 -1.6071281 0.56768661 48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142
49000 0.45152907 -2.1159427 0.052803985 -1.6119859 0.79924946 49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467
50000 0.43009519 -2.1080874 0.067204222 -1.6111465 0.85332392 50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865
51000 0.46317379 -2.1123268 0.058408991 -1.59113 0.72230777 51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859
52000 0.45417978 -2.1200771 0.065575223 -1.6007006 0.7742118 52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593
53000 0.43662759 -2.0916043 0.061621629 -1.593719 0.80656554 53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158
54000 0.44985568 -2.1167148 0.063414372 -1.6038197 0.63989449 54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814
55000 0.44499083 -2.1104573 0.056857917 -1.6089794 0.73153307 55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307
56000 0.44760788 -2.1162558 0.061556514 -1.6074644 0.62340704 56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892
57000 0.43753788 -2.1127115 0.05633761 -1.6192006 0.7012971 57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988
58000 0.46476788 -2.121983 0.057525001 -1.6000774 0.64993478 58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146
59000 0.45 -2.1329625 0.069789212 -1.6135483 0.63819024 59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911
60000 0.44526017 -2.1213789 0.071976974 -1.6045128 0.71055045 60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471
Loop time of 7.83001 on 1 procs for 60000 steps with 1200 atoms Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
Performance: 3310339.921 tau/day, 7662.824 timesteps/s Performance: 3233199.903 tau/day, 7484.259 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% 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 | 5.2292 | 5.2292 | 5.2292 | 0.0 | 66.78 Pair | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39
Bond | 0.23627 | 0.23627 | 0.23627 | 0.0 | 3.02 Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94
Neigh | 1.5068 | 1.5068 | 1.5068 | 0.0 | 19.24 Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95
Comm | 0.14386 | 0.14386 | 0.14386 | 0.0 | 1.84 Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80
Output | 0.00068521 | 0.00068521 | 0.00068521 | 0.0 | 0.01 Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01
Modify | 0.56151 | 0.56151 | 0.56151 | 0.0 | 7.17 Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03
Other | | 0.1516 | | | 1.94 Other | | 0.1508 | | | 1.88
Nlocal: 1200 ave 1200 max 1200 min Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 374 ave 374 max 374 min Nghost: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9604 ave 9604 max 9604 min Neighs: 9652 ave 9652 max 9652 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9604 Total # of neighbors = 9652
Ave neighs/atom = 8.00333 Ave neighs/atom = 8.04333
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 4881 Neighbor list builds = 4886
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:07 Total wall time: 0:00:08

251
examples/micelle/log.28Feb2019.micelle.g++.4
View File

@ -1,5 +1,5 @@
LAMMPS (28 Feb 2019) LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation # 2d micelle simulation
@ -13,7 +13,7 @@ atom_style bond
# Soft potential push-off # Soft potential push-off
read_data data.micelle read_data data.micelle
orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1) orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid 2 by 2 by 1 MPI processor grid
reading atoms ... reading atoms ...
1200 atoms 1200 atoms
@ -25,9 +25,12 @@ read_data data.micelle
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000130415 secs
read_data CPU = 0.00132132 secs
special_bonds fene special_bonds fene
2 = max # of 1-2 neighbors 2 = max # of 1-2 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 4.76837e-05 secs
pair_style soft 1.12246 pair_style soft 1.12246
pair_coeff * * 0.0 1.12246 pair_coeff * * 0.0 1.12246
@ -58,56 +61,56 @@ Neighbor list info ...
pair build: half/bin/newton pair build: half/bin/newton
stencil: half/bin/2d/newton stencil: half/bin/2d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.758 | 3.758 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 0.40179153 0.017198847 0.86861538 0.75625658 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73189198 0.056737309 1.2382543 2.321972 100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78767975 0.079977445 1.3172822 3.0463605 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76847924 0.069944127 1.2880484 3.7420091 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.69469019 0.094115526 1.2384307 4.4786122 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64066675 0.080351857 1.1706436 4.7965076 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58371075 0.088545932 1.1218817 5.0963739 600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.5394553 0.10365542 1.0927357 5.3370157 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.51563293 0.1030928 1.0683507 5.5156219 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.4758065 0.098479812 1.0239113 5.6783722 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.038061 on 4 procs for 1000 steps with 1200 atoms Loop time of 0.0377742 on 4 procs for 1000 steps with 1200 atoms
Performance: 11350211.981 tau/day, 26273.639 timesteps/s Performance: 11436375.633 tau/day, 26473.092 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads 96.6% 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 | 0.016952 | 0.017563 | 0.018236 | 0.3 | 46.14 Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80
Bond | 0.00098968 | 0.0010636 | 0.0011351 | 0.2 | 2.79 Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81
Neigh | 0.0048919 | 0.0049396 | 0.0049865 | 0.1 | 12.98 Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86
Comm | 0.0075874 | 0.0083745 | 0.0094497 | 0.7 | 22.00 Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52
Output | 0.00021791 | 0.00024784 | 0.00033474 | 0.0 | 0.65 Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75
Modify | 0.0035474 | 0.0036926 | 0.0038188 | 0.2 | 9.70 Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55
Other | | 0.00218 | | | 5.73 Other | | 0.002912 | | | 7.71
Nlocal: 300 ave 305 max 295 min Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 105.5 ave 109 max 102 min Nghost: 100.25 ave 108 max 93 min
Histogram: 1 1 0 0 0 0 0 0 1 1 Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 797.75 ave 810 max 792 min Neighs: 784 ave 815 max 739 min
Histogram: 2 0 1 0 0 0 0 0 0 1 Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3191 Total # of neighbors = 3136
Ave neighs/atom = 2.65917 Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 99 Neighbor list builds = 92
Dangerous builds = 0 Dangerous builds = 0
unfix 3 unfix 3
@ -162,95 +165,95 @@ Neighbor list info ...
pair build: half/bin/newton pair build: half/bin/newton
stencil: half/bin/2d/newton stencil: half/bin/2d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.001 | 4.001 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7061976 0.094144249 -1.1624283 3.8015113 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9656272 0.065737702 -1.4502645 1.8869504 1000 0.45 -1.9727652 0.058608073 -1.4645321 1.9982444
2000 0.45643021 -1.9804979 0.06069692 -1.4637511 1.7840488 2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263
3000 0.45 -2.0069774 0.063273903 -1.4940785 1.5344808 3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772
4000 0.46877185 -2.0118089 0.063511162 -1.4799165 1.5112039 4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276
5000 0.45037477 -2.0202928 0.064675812 -1.5056176 1.5614253 5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351
6000 0.46516417 -2.041891 0.0633751 -1.5137393 1.302917 6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586
7000 0.43402321 -2.0309525 0.080389027 -1.5169019 1.2526669 7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035
8000 0.44698877 -2.0438825 0.056384491 -1.5408818 1.2320847 8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914
9000 0.46716896 -2.0490995 0.055185945 -1.5271339 1.1323067 9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868
10000 0.45585592 -2.0534599 0.059172717 -1.5388112 1.2103699 10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581
11000 0.44678446 -2.0702287 0.064814108 -1.5590025 0.93753889 11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435
12000 0.46238947 -2.0533635 0.061899722 -1.5294596 1.039375 12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059
13000 0.44497125 -2.0582622 0.055753243 -1.5579085 1.105247 13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813
14000 0.46197842 -2.0700459 0.061177996 -1.5472745 1.0365751 14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778
15000 0.45391975 -2.0698433 0.071128012 -1.5451738 0.94060338 15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821
16000 0.44617128 -2.0921643 0.064669811 -1.5816951 0.96199988 16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235
17000 0.45205591 -2.0892946 0.073532323 -1.5640831 0.72042835 17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504
18000 0.44742647 -2.0667234 0.066469731 -1.5532 1.0881956 18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232
19000 0.45154441 -2.0603669 0.0589846 -1.5502142 1.1682254 19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496
20000 0.44930673 -2.0699762 0.060197 -1.5608469 0.93709988 20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973
21000 0.44952144 -2.0787365 0.054909176 -1.5746805 0.91906714 21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522
22000 0.45094085 -2.1027668 0.05970659 -1.5924952 0.76875966 22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529
23000 0.45653288 -2.0752194 0.057879405 -1.5611875 0.90288603 23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844
24000 0.45659718 -2.1051589 0.061071012 -1.5878712 0.67941553 24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138
25000 0.44943892 -2.0785434 0.063137757 -1.5663412 0.91848225 25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438
26000 0.46662896 -2.0912992 0.060997699 -1.5640614 0.84321344 26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386
27000 0.45990587 -2.0872861 0.062249833 -1.5655136 0.7970408 27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759
28000 0.44904041 -2.0887241 0.067592763 -1.5724651 0.83063368 28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249
29000 0.44840621 -2.082931 0.063504343 -1.5713941 0.85259731 29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527
30000 0.45 -2.1005553 0.061020694 -1.5899096 0.85076517 30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894
31000 0.43293607 -2.0834216 0.062211326 -1.588635 0.87798767 31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973
32000 0.45 -2.1041864 0.056583773 -1.5979776 0.74721991 32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153
33000 0.45483731 -2.0843819 0.064702707 -1.5652209 0.72878185 33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104
34000 0.45 -2.0946388 0.056465271 -1.5885485 0.81958535 34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425
35000 0.45561477 -2.0962413 0.058642378 -1.5823639 0.86190757 35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751
36000 0.46372156 -2.0819766 0.061679429 -1.556962 0.92734228 36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487
37000 0.46602014 -2.0978422 0.05861007 -1.5736003 0.87514767 37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821
38000 0.45496066 -2.0993783 0.054914099 -1.5898827 0.7885952 38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923
39000 0.45215206 -2.0997742 0.061140603 -1.5868584 0.83434324 39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695
40000 0.43961538 -2.095479 0.061779306 -1.5944507 0.79151814 40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322
41000 0.45065436 -2.0992641 0.058334617 -1.5906507 0.84329542 41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684
42000 0.44063989 -2.0911919 0.058682846 -1.5922364 0.83653642 42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362
43000 0.45090762 -2.1109187 0.056792395 -1.6035945 0.66699616 43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741
44000 0.43620597 -2.1163977 0.068503171 -1.6120521 0.72985642 44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946
45000 0.4536995 -2.1169236 0.06222035 -1.6013818 0.6724514 45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542
46000 0.44961963 -2.0949168 0.056381135 -1.5892907 0.85934269 46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494
47000 0.45429621 -2.0982372 0.05977093 -1.5845486 0.78798948 47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899
48000 0.45889422 -2.1042317 0.062692038 -1.5830278 0.80652424 48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556
49000 0.44973607 -2.1107622 0.05251269 -1.6088882 0.80305097 49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984
50000 0.45422606 -2.1083846 0.05061301 -1.603924 0.81750837 50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037
51000 0.45545299 -2.1154627 0.053581638 -1.6068076 0.77970255 51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462
52000 0.46382715 -2.1001689 0.053408569 -1.5833197 0.77034515 52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227
53000 0.44707619 -2.1134818 0.055878089 -1.6109001 0.63749083 53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365
54000 0.45951971 -2.1155704 0.05958078 -1.5968529 0.81426779 54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429
55000 0.45588645 -2.1128869 0.060361673 -1.5970187 0.70242718 55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299
56000 0.44752186 -2.0917439 0.058352116 -1.5862429 0.89773952 56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556
57000 0.44921415 -2.115356 0.05318821 -1.613328 0.81456406 57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633
58000 0.44046295 -2.1119294 0.063384551 -1.6084489 0.59683679 58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658
59000 0.4349702 -2.0981796 0.059156694 -1.6044152 0.71438644 59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272
60000 0.4568814 -2.1060323 0.06038074 -1.5891509 0.70442841 60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511
Loop time of 2.49332 on 4 procs for 60000 steps with 1200 atoms Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
Performance: 10395764.892 tau/day, 24064.271 timesteps/s Performance: 9821248.084 tau/day, 22734.371 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 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 | 1.1638 | 1.2432 | 1.3093 | 4.7 | 49.86 Pair | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43
Bond | 0.055561 | 0.063918 | 0.072427 | 2.4 | 2.56 Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49
Neigh | 0.45107 | 0.45366 | 0.45616 | 0.3 | 18.20 Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78
Comm | 0.40982 | 0.48044 | 0.56933 | 8.4 | 19.27 Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19
Output | 0.00072122 | 0.0013784 | 0.0033441 | 3.1 | 0.06 Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07
Modify | 0.14899 | 0.15204 | 0.15837 | 1.0 | 6.10 Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77
Other | | 0.09871 | | | 3.96 Other | | 0.1131 | | | 4.28
Nlocal: 300 ave 307 max 288 min Nlocal: 300 ave 309 max 281 min
Histogram: 1 0 0 0 0 0 0 2 0 1 Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 216 ave 222 max 212 min Nghost: 232.75 ave 234 max 231 min
Histogram: 1 1 0 0 0 1 0 0 0 1 Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 2391.75 ave 2543 max 2194 min Neighs: 2450.25 ave 2576 max 2179 min
Histogram: 1 0 0 0 0 0 2 0 0 1 Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 9567 Total # of neighbors = 9801
Ave neighs/atom = 7.9725 Ave neighs/atom = 8.1675
Ave special neighs/atom = 0.5 Ave special neighs/atom = 0.5
Neighbor list builds = 4889 Neighbor list builds = 4887
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:02 Total wall time: 0:00:02