lammps/examples/rigid/log.15Feb16.rigid.tnr.g++.4

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Groff

LAMMPS (15 Feb 2016)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 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 = 45 45 45
Memory usage per processor = 6.96454 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
Loop time of 3.13958 on 4 procs for 5000 steps with 5600 atoms
Performance: 687990.006 tau/day, 1592.569 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.079872 | 0.12791 | 0.18245 | 13.2 | 4.07
Bond | 0.038984 | 0.058535 | 0.077727 | 7.4 | 1.86
Neigh | 0.63649 | 0.63904 | 0.64148 | 0.2 | 20.35
Comm | 0.15118 | 0.22089 | 0.28197 | 13.0 | 7.04
Output | 0.0019264 | 0.0028899 | 0.0034878 | 1.1 | 0.09
Modify | 1.8465 | 1.9323 | 2.0081 | 5.4 | 61.55
Other | | 0.158 | | | 5.03
Nlocal: 1400 ave 1868 max 905 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 648.25 ave 688 max 598 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1202.5 ave 1821 max 698 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 4810
Ave neighs/atom = 0.858929
Ave special neighs/atom = 0.571429
Neighbor list builds = 759
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
Loop time of 0.745001 on 4 procs for 1000 steps with 5600 atoms
Performance: 579865.026 tau/day, 1342.280 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020505 | 0.033631 | 0.048735 | 7.0 | 4.51
Bond | 0.0078509 | 0.011774 | 0.015532 | 3.2 | 1.58
Neigh | 0.13791 | 0.13834 | 0.13874 | 0.1 | 18.57
Comm | 0.029133 | 0.04799 | 0.064085 | 7.4 | 6.44
Output | 0.0004046 | 0.00066173 | 0.00084162 | 0.6 | 0.09
Modify | 0.46937 | 0.48315 | 0.4976 | 1.9 | 64.85
Other | | 0.02945 | | | 3.95
Nlocal: 1400 ave 1868 max 935 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 633.75 ave 695 max 541 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1263 ave 1799 max 710 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5052
Ave neighs/atom = 0.902143
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
Loop time of 0.760565 on 4 procs for 1000 steps with 5600 atoms
Performance: 567998.937 tau/day, 1314.812 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.021564 | 0.034813 | 0.049583 | 6.9 | 4.58
Bond | 0.0080154 | 0.011744 | 0.015375 | 3.2 | 1.54
Neigh | 0.13546 | 0.13583 | 0.13616 | 0.1 | 17.86
Comm | 0.029489 | 0.047668 | 0.06437 | 7.4 | 6.27
Output | 0.00040579 | 0.00063974 | 0.00079918 | 0.6 | 0.08
Modify | 0.48726 | 0.50088 | 0.51473 | 1.7 | 65.86
Other | | 0.02899 | | | 3.81
Nlocal: 1400 ave 1832 max 970 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 652.5 ave 749 max 561 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1407.5 ave 2071 max 748 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 5630
Ave neighs/atom = 1.00536
Ave special neighs/atom = 0.571429
Neighbor list builds = 149
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
Memory usage per processor = 6.98553 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
Loop time of 1.41333 on 4 procs for 1000 steps with 5600 atoms
Performance: 305661.545 tau/day, 707.550 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.057705 | 0.096282 | 0.13813 | 11.4 | 6.81
Bond | 0.012531 | 0.01785 | 0.023392 | 3.7 | 1.26
Neigh | 0.50189 | 0.5024 | 0.50294 | 0.1 | 35.55
Comm | 0.058384 | 0.10518 | 0.14841 | 12.2 | 7.44
Output | 0.00038195 | 0.00049835 | 0.0007689 | 0.7 | 0.04
Modify | 0.62292 | 0.64876 | 0.67248 | 2.8 | 45.90
Other | | 0.04236 | | | 3.00
Nlocal: 1400 ave 1820 max 1010 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 1576 ave 1694 max 1470 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 6543 ave 9989 max 3497 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 26172
Ave neighs/atom = 4.67357
Ave special neighs/atom = 0.571429
Neighbor list builds = 337
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
Loop time of 1.40527 on 4 procs for 1000 steps with 5600 atoms
Performance: 307413.312 tau/day, 711.605 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.09198 | 0.15293 | 0.22726 | 14.1 | 10.88
Bond | 0.01415 | 0.01816 | 0.022801 | 2.8 | 1.29
Neigh | 0.40174 | 0.40202 | 0.40228 | 0.0 | 28.61
Comm | 0.053445 | 0.13222 | 0.19624 | 16.1 | 9.41
Output | 0.00037909 | 0.00046462 | 0.00065279 | 0.5 | 0.03
Modify | 0.6409 | 0.65867 | 0.6806 | 2.2 | 46.87
Other | | 0.04081 | | | 2.90
Nlocal: 1400 ave 1770 max 1095 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1578.5 ave 1693 max 1493 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 7868 ave 12041 max 4579 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 31472
Ave neighs/atom = 5.62
Ave special neighs/atom = 0.571429
Neighbor list builds = 167
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
Loop time of 1.41589 on 4 procs for 1000 steps with 5600 atoms
Performance: 305107.630 tau/day, 706.268 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11437 | 0.17662 | 0.24699 | 12.6 | 12.47
Bond | 0.014617 | 0.018159 | 0.022451 | 2.4 | 1.28
Neigh | 0.40766 | 0.40784 | 0.40799 | 0.0 | 28.80
Comm | 0.054544 | 0.12898 | 0.19363 | 15.6 | 9.11
Output | 0.00037289 | 0.00046611 | 0.00066733 | 0.6 | 0.03
Modify | 0.62801 | 0.64468 | 0.6664 | 2.1 | 45.53
Other | | 0.03915 | | | 2.76
Nlocal: 1400 ave 1669 max 1139 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1761.5 ave 1898 max 1632 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 9311.75 ave 12525 max 5959 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 37247
Ave neighs/atom = 6.65125
Ave special neighs/atom = 0.571429
Neighbor list builds = 165
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
Memory usage per processor = 7.00192 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
Loop time of 1.39005 on 4 procs for 1000 steps with 5600 atoms
Performance: 310781.162 tau/day, 719.401 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14204 | 0.19795 | 0.25554 | 10.2 | 14.24
Bond | 0.015064 | 0.018318 | 0.021846 | 2.0 | 1.32
Neigh | 0.37625 | 0.37681 | 0.37726 | 0.1 | 27.11
Comm | 0.058424 | 0.11817 | 0.17563 | 13.6 | 8.50
Output | 0.00036097 | 0.00047255 | 0.00073051 | 0.7 | 0.03
Modify | 0.63824 | 0.64799 | 0.66001 | 1.1 | 46.62
Other | | 0.03034 | | | 2.18
Nlocal: 1400 ave 1607 max 1199 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1819.25 ave 1940 max 1712 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 9882 ave 12628 max 7201 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 39528
Ave neighs/atom = 7.05857
Ave special neighs/atom = 0.571429
Neighbor list builds = 156
Dangerous builds = 0
Total wall time: 0:00:10