forked from lijiext/lammps
453 lines
28 KiB
Groff
453 lines
28 KiB
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
|