forked from lijiext/lammps
459 lines
29 KiB
Groff
459 lines
29 KiB
Groff
LAMMPS (20 Apr 2018)
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using 1 OpenMP thread(s) per MPI task
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# Tethered nanorods
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atom_style molecular
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read_data data.rigid.tnr
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orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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5600 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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1600 bonds
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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# Specify bond parameters
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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special_bonds fene
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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# Specify initial velocities
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velocity all create 1.4 109345
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# Specify rigid components
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group rods type 2
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4000 atoms in group rods
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group tethers subtract all rods
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1600 atoms in group tethers
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neigh_modify exclude molecule/intra rods delay 0 every 1
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# Specify the pair potentials
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pair_style lj/cut 2.5
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pair_modify shift yes
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pair_coeff * * 1.0 1.0 1.122
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pair_coeff 2 2 1.0 1.0 2.5
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# Specify output
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thermo 100
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thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
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thermo_modify flush yes lost warn
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timestep 0.005
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fix 1 rods rigid molecule
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800 rigid bodies with 4000 atoms
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fix 2 tethers nve
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fix 3 all langevin 1.4 1.4 1.0 437624
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 45 45 45
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
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100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
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200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
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300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
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400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
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500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
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600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
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700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
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800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
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900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
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1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
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1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
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1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
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1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
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1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
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1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431
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1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
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1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
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1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
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1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
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2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901
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2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
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2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
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2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
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2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028
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2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539
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2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112
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2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357
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2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412
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2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892
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3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658
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3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485
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3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783
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3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048
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3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724
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3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433
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3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225
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3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455
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3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624
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3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689
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4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626
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4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172
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4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746
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4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924
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4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638
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4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334
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4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263
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4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225
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4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449
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4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056
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5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771
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Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms
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Performance: 624133.913 tau/day, 1444.754 timesteps/s
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98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85
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Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91
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Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76
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Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58
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Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10
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Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02
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Other | | 0.2 | | | 5.78
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Nlocal: 1400 ave 1844 max 907 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 642 ave 714 max 581 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 1307.25 ave 1883 max 682 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 5229
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Ave neighs/atom = 0.93375
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 762
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Dangerous builds = 0
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# Replace fix rigid and fix langevin with new ones
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unfix 1
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unfix 3
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fix 3 tethers langevin 1.4 1.4 1.0 198450
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# Test different integrators for rods
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fix 1 rods rigid/nve molecule
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800 rigid bodies with 4000 atoms
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print "rigid/nve"
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rigid/nve
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215
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5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298
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5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911
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5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068
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5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373
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5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707
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5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387
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5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341
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5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223
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5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198
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6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689
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Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms
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Performance: 544612.641 tau/day, 1260.677 timesteps/s
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98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55
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Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66
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Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30
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Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11
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Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09
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Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66
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Other | | 0.04459 | | | 5.62
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Nlocal: 1400 ave 1844 max 884 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 713.5 ave 818 max 656 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Neighs: 1315 ave 1956 max 573 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Total # of neighbors = 5260
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Ave neighs/atom = 0.939286
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 156
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Dangerous builds = 0
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unfix 1
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fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
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800 rigid bodies with 4000 atoms
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print "rigid/nvt"
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rigid/nvt
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779
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6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027
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6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881
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6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499
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6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801
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6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659
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6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155
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6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075
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6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066
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6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381
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7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375
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Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms
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Performance: 531376.713 tau/day, 1230.039 timesteps/s
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98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74
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Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62
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Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33
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Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10
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Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09
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Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04
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Other | | 0.04134 | | | 5.09
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Nlocal: 1400 ave 1861 max 953 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 732.5 ave 799 max 634 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 1478.5 ave 2087 max 852 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 5914
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Ave neighs/atom = 1.05607
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 154
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Dangerous builds = 0
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unfix 1
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compute myTemp all temp
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fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
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800 rigid bodies with 4000 atoms
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print "rigid/npt iso"
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rigid/npt iso
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fix_modify 1 temp myTemp
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619
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7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475
|
|
7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823
|
|
7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808
|
|
7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154
|
|
7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934
|
|
7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266
|
|
7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104
|
|
7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242
|
|
7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921
|
|
8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435
|
|
Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 292430.022 tau/day, 676.921 timesteps/s
|
|
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82
|
|
Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35
|
|
Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30
|
|
Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68
|
|
Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03
|
|
Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73
|
|
Other | | 0.04563 | | | 3.09
|
|
|
|
Nlocal: 1400 ave 1711 max 1074 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 1617 ave 1748 max 1514 min
|
|
Histogram: 1 0 0 2 0 0 0 0 0 1
|
|
Neighs: 6221.75 ave 8875 max 3829 min
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
|
|
Total # of neighbors = 24887
|
|
Ave neighs/atom = 4.44411
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 340
|
|
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
|
|
Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531
|
|
8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895
|
|
8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249
|
|
8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714
|
|
8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747
|
|
8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867
|
|
8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873
|
|
8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702
|
|
8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987
|
|
8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801
|
|
9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686
|
|
Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 304989.819 tau/day, 705.995 timesteps/s
|
|
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25
|
|
Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42
|
|
Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36
|
|
Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21
|
|
Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04
|
|
Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92
|
|
Other | | 0.03963 | | | 2.80
|
|
|
|
Nlocal: 1400 ave 1641 max 1120 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Nghost: 1593.5 ave 1674 max 1480 min
|
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
Neighs: 7766.25 ave 10004 max 5618 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 31065
|
|
Ave neighs/atom = 5.54732
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 168
|
|
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
|
|
Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595
|
|
9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716
|
|
9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967
|
|
9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325
|
|
9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319
|
|
9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422
|
|
9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125
|
|
9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226
|
|
9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283
|
|
9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026
|
|
10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892
|
|
Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 293069.938 tau/day, 678.403 timesteps/s
|
|
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07
|
|
Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37
|
|
Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66
|
|
Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03
|
|
Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04
|
|
Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18
|
|
Other | | 0.0391 | | | 2.65
|
|
|
|
Nlocal: 1400 ave 1629 max 1159 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
Nghost: 1760.25 ave 1871 max 1635 min
|
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
Neighs: 9467.75 ave 11967 max 6712 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 37871
|
|
Ave neighs/atom = 6.76268
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 163
|
|
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
|
|
Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506
|
|
10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812
|
|
10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461
|
|
10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255
|
|
10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884
|
|
10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428
|
|
10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401
|
|
10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703
|
|
10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507
|
|
10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896
|
|
11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759
|
|
Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 287222.965 tau/day, 664.868 timesteps/s
|
|
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15
|
|
Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36
|
|
Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36
|
|
Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19
|
|
Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03
|
|
Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41
|
|
Other | | 0.0375 | | | 2.49
|
|
|
|
Nlocal: 1400 ave 1605 max 1229 min
|
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
|
Nghost: 1859 ave 1964 max 1718 min
|
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
|
Neighs: 10208.2 ave 13091 max 7670 min
|
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
|
|
|
Total # of neighbors = 40833
|
|
Ave neighs/atom = 7.29161
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 160
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:10
|