forked from lijiext/lammps
459 lines
29 KiB
Groff
459 lines
29 KiB
Groff
LAMMPS (27 Nov 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 -0.00088278432
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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 0.00016862131 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 0.00098119436 -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 0.0062444034 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 -0.00063825026
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2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
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2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
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2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
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2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
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2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
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3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
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3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
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3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
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3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
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3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
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3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
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3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
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3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
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3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
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3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
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4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
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4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
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4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
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4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
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4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
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4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
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4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
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4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
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4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
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4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
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5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
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Loop time of 3.70354 on 4 procs for 5000 steps with 5600 atoms
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Performance: 583225.455 tau/day, 1350.059 timesteps/s
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92.9% 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 | 0.081073 | 0.13498 | 0.20108 | 14.4 | 3.64
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Bond | 0.032352 | 0.048566 | 0.066671 | 7.0 | 1.31
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Neigh | 0.71345 | 0.72477 | 0.73658 | 1.3 | 19.57
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Comm | 0.29998 | 0.37027 | 0.42722 | 8.9 | 10.00
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Output | 0.0026417 | 0.0048325 | 0.0085185 | 3.2 | 0.13
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Modify | 1.9807 | 2.1035 | 2.263 | 8.1 | 56.80
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Other | | 0.3166 | | | 8.55
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Nlocal: 1400 ave 1868 max 905 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 648.25 ave 688 max 598 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Neighs: 1202.5 ave 1821 max 698 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Total # of neighbors = 4810
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Ave neighs/atom = 0.858929
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 759
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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 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
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5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
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5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
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5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
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5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
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5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
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5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
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5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
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5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
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5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
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6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
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Loop time of 0.84847 on 4 procs for 1000 steps with 5600 atoms
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Performance: 509151.820 tau/day, 1178.592 timesteps/s
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94.3% 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 | 0.020741 | 0.03547 | 0.053064 | 7.5 | 4.18
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Bond | 0.0064373 | 0.0096895 | 0.013065 | 3.0 | 1.14
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Neigh | 0.14992 | 0.15174 | 0.15392 | 0.4 | 17.88
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Comm | 0.068751 | 0.081259 | 0.10084 | 4.2 | 9.58
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Output | 0.00054288 | 0.00096381 | 0.0017593 | 0.0 | 0.11
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Modify | 0.45914 | 0.48587 | 0.51316 | 2.8 | 57.26
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Other | | 0.08348 | | | 9.84
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Nlocal: 1400 ave 1868 max 935 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 633.75 ave 695 max 541 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Neighs: 1263 ave 1799 max 710 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 5052
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Ave neighs/atom = 0.902143
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 153
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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 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
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6100 1.3829575 5.9055308 6.9917699 0.0022904842 7.090405 62.244 62.244 62.244 -0.00045870123 0.0040556461 0.0032745076
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6200 1.3942692 5.90506 7.0001838 0.0046406766 7.2000253 62.244 62.244 62.244 0.0042263485 0.0051632793 0.0045324021
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6300 1.4009885 5.902399 7.0028005 0.0077682466 7.3373246 62.244 62.244 62.244 0.0071636876 0.0098268446 0.0063142075
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6400 1.3627532 5.9075588 6.9779284 0.0093180831 7.3791932 62.244 62.244 62.244 0.0062401458 0.01302262 0.0086914833
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6500 1.3341203 5.9012967 6.9491767 0.01010805 7.3844599 62.244 62.244 62.244 0.0031876185 0.011099561 0.01603697
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6600 1.3572847 5.8915298 6.9576042 -0.00034416901 6.9427833 62.244 62.244 62.244 0.0025579012 -0.0011308802 -0.0024595281
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6700 1.366374 5.8985277 6.9717413 0.0029472772 7.0986599 62.244 62.244 62.244 0.0022469424 -0.00042869772 0.0070235868
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6800 1.381673 5.8909304 6.9761606 -9.1063397e-05 6.9722391 62.244 62.244 62.244 -0.0048194377 -0.00080972169 0.0053559692
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6900 1.4011472 5.8881927 6.9887188 0.0010086058 7.0321524 62.244 62.244 62.244 0.0012132619 -0.0025916747 0.0044042301
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7000 1.3973658 5.8867938 6.9843498 0.0070015187 7.2858563 62.244 62.244 62.244 0.0058913402 0.0076802028 0.0074330131
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Loop time of 0.902266 on 4 procs for 1000 steps with 5600 atoms
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Performance: 478794.425 tau/day, 1108.320 timesteps/s
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92.5% 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 | 0.022644 | 0.037091 | 0.054025 | 7.4 | 4.11
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Bond | 0.0066526 | 0.0098482 | 0.012934 | 2.8 | 1.09
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Neigh | 0.15815 | 0.16028 | 0.16242 | 0.5 | 17.76
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Comm | 0.086046 | 0.10069 | 0.11568 | 3.7 | 11.16
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Output | 0.00047731 | 0.00090772 | 0.0016732 | 0.0 | 0.10
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Modify | 0.46692 | 0.49338 | 0.52973 | 3.5 | 54.68
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Other | | 0.1001 | | | 11.09
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Nlocal: 1400 ave 1832 max 970 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 652.5 ave 749 max 561 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 1407.5 ave 2071 max 748 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 5630
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Ave neighs/atom = 1.00536
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 149
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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 1.3973658 5.8867938 6.9843498 0.0026564535 7.0987447 62.244 62.244 62.244 0.033711862 -0.0068580786 -0.018884423
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7100 1.463906 5.861189 7.0110088 0.011521299 7.3924648 57.022165 57.022165 57.022165 0.010788399 0.0093706759 0.014404821
|
|
7200 1.4950346 5.817724 6.9919936 0.023104537 7.516484 50.28164 50.28164 50.28164 0.023252537 0.018108267 0.027952807
|
|
7300 1.5103539 5.7757334 6.9620355 0.02265972 7.3367664 45.242961 45.242961 45.242961 0.023588139 0.022279352 0.022111669
|
|
7400 1.5583184 5.7576833 6.9816589 0.028383162 7.3460731 41.582206 41.582206 41.582206 0.027312172 0.029876235 0.027961079
|
|
7500 1.5988886 5.6930714 6.9489127 0.046500933 7.4415595 39.00204 39.00204 39.00204 0.057497139 0.031007247 0.050998413
|
|
7600 1.5458926 5.6844397 6.8986555 0.034168406 7.2068206 36.96428 36.96428 36.96428 0.037874991 0.027247969 0.037382258
|
|
7700 1.5179913 5.6416448 6.8339457 0.070322183 7.3856048 35.284894 35.284894 35.284894 0.054248771 0.10402305 0.052694729
|
|
7800 1.4797888 5.6045532 6.7668481 0.07801402 7.3126319 33.963465 33.963465 33.963465 0.096058241 0.061172194 0.076811627
|
|
7900 1.4846305 5.54982 6.7159177 0.065303374 7.1325712 32.936376 32.936376 32.936376 0.089117046 0.06069295 0.046100127
|
|
8000 1.4352665 5.5157472 6.6430722 0.065962965 7.0326574 32.099391 32.099391 32.099391 0.032126133 0.070109418 0.095653344
|
|
Loop time of 1.72334 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 250675.661 tau/day, 580.268 timesteps/s
|
|
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.060282 | 0.099801 | 0.13824 | 10.8 | 5.79
|
|
Bond | 0.0095227 | 0.013491 | 0.017217 | 3.2 | 0.78
|
|
Neigh | 0.58793 | 0.59546 | 0.60654 | 1.0 | 34.55
|
|
Comm | 0.17903 | 0.21403 | 0.24615 | 6.5 | 12.42
|
|
Output | 0.00045562 | 0.00076783 | 0.0017018 | 0.0 | 0.04
|
|
Modify | 0.64959 | 0.68513 | 0.70671 | 2.8 | 39.76
|
|
Other | | 0.1147 | | | 6.65
|
|
|
|
Nlocal: 1400 ave 1768 max 981 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Nghost: 1574 ave 1663 max 1447 min
|
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
Neighs: 6338 ave 9521 max 3068 min
|
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
|
|
Total # of neighbors = 25352
|
|
Ave neighs/atom = 4.52714
|
|
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
|
|
Per MPI rank memory allocation (min/avg/max) = 7.226 | 7.412 | 7.597 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
8000 1.4352665 5.5157472 6.6430722 0.073641793 7.0780095 32.099391 32.099391 32.099391 0.13359913 0.13991003 -0.052583787
|
|
8100 1.4385682 5.5149882 6.6449064 0.092621097 7.1894426 31.952972 32.099391 32.099391 0.10729401 0.11619987 0.054369411
|
|
8200 1.42735 5.5149024 6.6360094 0.023903894 6.7756304 31.745099 32.099391 32.099391 0.051524189 0.013370811 0.006816681
|
|
8300 1.4335369 5.5031396 6.629106 0.024536474 6.7705237 31.324638 32.099391 32.099391 0.042356568 -0.0039258365 0.035178692
|
|
8400 1.4502714 5.4659017 6.6050122 0.06575457 6.9774701 30.785462 32.099391 32.099391 0.056998298 0.084852971 0.055412441
|
|
8500 1.4432366 5.4541505 6.5877355 0.03322226 6.7725932 30.241461 32.099391 32.099391 0.045871758 0.024443739 0.029351281
|
|
8600 1.436491 5.4272043 6.5554911 0.039811655 6.7732608 29.729098 32.099391 32.099391 0.037709456 0.060942551 0.020782958
|
|
8700 1.4099251 5.4106713 6.5180919 0.013490442 6.590596 29.209958 32.099391 32.099391 0.025833003 -0.0021161354 0.016754458
|
|
8800 1.3801478 5.3926425 6.4766747 0.028808964 6.6280205 28.552039 32.099391 32.099391 0.012603549 0.018713073 0.055110271
|
|
8900 1.4411695 5.3583474 6.4903088 0.053464468 6.7655624 27.980937 32.099391 32.099391 0.055084927 0.073292013 0.032016464
|
|
9000 1.4264395 5.3680298 6.4884216 0.066557314 6.8276318 27.69922 32.099391 32.099391 0.05380086 0.069450871 0.076420212
|
|
Loop time of 1.45936 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 296020.704 tau/day, 685.233 timesteps/s
|
|
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.097855 | 0.1563 | 0.20542 | 12.5 | 10.71
|
|
Bond | 0.010222 | 0.01371 | 0.016844 | 2.6 | 0.94
|
|
Neigh | 0.43646 | 0.44419 | 0.4668 | 2.0 | 30.44
|
|
Comm | 0.10136 | 0.14589 | 0.19563 | 11.6 | 10.00
|
|
Output | 0.00046229 | 0.00076181 | 0.0016556 | 0.0 | 0.05
|
|
Modify | 0.59971 | 0.62524 | 0.65776 | 2.9 | 42.84
|
|
Other | | 0.07327 | | | 5.02
|
|
|
|
Nlocal: 1400 ave 1680 max 1049 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Nghost: 1627.25 ave 1775 max 1488 min
|
|
Histogram: 1 1 0 0 0 0 0 1 0 1
|
|
Neighs: 7842 ave 10600 max 4326 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 31368
|
|
Ave neighs/atom = 5.60143
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 166
|
|
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) = 7.227 | 7.412 | 7.597 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
9000 1.4264395 5.3680298 6.4884216 0.0098629166 6.5386881 27.69922 32.099391 32.099391 -0.32352455 -0.020288613 0.37340191
|
|
9100 1.4501008 5.3468478 6.4858243 0.059250929 6.7846766 27.60347 31.988431 31.988431 0.076039445 0.051409059 0.050304282
|
|
9200 1.4635102 5.3406895 6.4901983 0.035210102 6.6656151 27.490192 31.857158 31.857158 0.0079484246 0.066653954 0.031027926
|
|
9300 1.4503713 5.3595734 6.4987624 0.020794 6.6013231 27.398334 31.750708 31.750708 0.053098983 0.0019379163 0.0073450997
|
|
9400 1.4701421 5.3186993 6.4734172 0.039118143 6.6618027 27.181055 31.498913 31.498913 0.076457868 -0.0028405762 0.043737137
|
|
9500 1.4495442 5.323167 6.4617063 0.073591495 6.8091096 27.000921 31.290164 31.290164 0.037777789 0.097624306 0.085372389
|
|
9600 1.4668438 5.3002222 6.4523494 0.06758294 6.7648428 26.814997 31.074705 31.074705 0.057941415 0.09775976 0.047047645
|
|
9700 1.4926839 5.2883964 6.4608196 0.059125916 6.7288224 26.637713 30.869258 30.869258 0.049817515 0.032285203 0.095275031
|
|
9800 1.4644558 5.2702597 6.4205112 0.0076221617 6.4543756 26.460515 30.663911 30.663911 -0.0060723629 0.010616271 0.018322577
|
|
9900 1.4669549 5.2511861 6.4034006 0.044167302 6.5961243 26.30195 30.480157 30.480157 0.026274163 0.013826125 0.092401618
|
|
10000 1.460983 5.2470476 6.3945715 0.10536479 6.8483021 26.186495 30.346361 30.346361 0.088951294 0.11273872 0.11440435
|
|
Loop time of 1.61361 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 267722.758 tau/day, 619.729 timesteps/s
|
|
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.13322 | 0.18643 | 0.259 | 12.5 | 11.55
|
|
Bond | 0.012367 | 0.014462 | 0.016771 | 1.6 | 0.90
|
|
Neigh | 0.46284 | 0.46471 | 0.46675 | 0.3 | 28.80
|
|
Comm | 0.10183 | 0.17241 | 0.22246 | 12.4 | 10.68
|
|
Output | 0.00044584 | 0.00074542 | 0.0016396 | 0.0 | 0.05
|
|
Modify | 0.691 | 0.7057 | 0.72761 | 1.8 | 43.73
|
|
Other | | 0.06915 | | | 4.29
|
|
|
|
Nlocal: 1400 ave 1633 max 1183 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 1747.75 ave 1847 max 1624 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Neighs: 9290.75 ave 12454 max 6621 min
|
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 37163
|
|
Ave neighs/atom = 6.63625
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 162
|
|
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 1.460983 5.2470476 6.3945715 0.18376191 7.1859023 26.186495 30.346361 30.346361 0.015959435 0.68341409 -0.14808778
|
|
10100 1.4487259 5.2485513 6.3864479 0.060157728 6.6465409 26.238844 30.407026 30.346361 0.10289596 0.022823411 0.05475381
|
|
10200 1.4335646 5.2420513 6.3680395 0.013676852 6.4271554 26.235255 30.402867 30.346361 -0.017328522 0.040786509 0.017572569
|
|
10300 1.4334952 5.2377534 6.3636871 0.030978458 6.4967192 26.150168 30.304264 30.346361 0.044154015 0.036133394 0.012647966
|
|
10400 1.4209473 5.2242736 6.3403516 -0.00094467594 6.3363148 26.085773 30.22964 30.346361 0.030664991 0.018005544 -0.051504563
|
|
10500 1.4262805 5.2044624 6.3247294 0.045042501 6.5149748 25.934148 30.053928 30.346361 0.031103656 0.045410964 0.058612885
|
|
10600 1.4516048 5.2017459 6.3419036 0.069565209 6.6313867 25.741959 29.831208 30.346361 0.021768778 0.11302833 0.073898515
|
|
10700 1.4841074 5.1911212 6.356808 0.046866825 6.5493087 25.574636 29.637306 30.346361 0.073969059 0.064901506 0.0017299084
|
|
10800 1.4646257 5.1958815 6.3462665 0.050747116 6.5534926 25.500146 29.550982 30.346361 0.076646556 0.070734108 0.004860682
|
|
10900 1.461356 5.1821605 6.3299773 0.069060447 6.610166 25.417723 29.455466 30.346361 0.051399011 0.065631311 0.090151019
|
|
11000 1.4395386 5.1786243 6.3093047 -0.0087983274 6.2737059 25.383039 29.415273 30.346361 -0.060891892 0.037235898 -0.0027389884
|
|
Loop time of 1.56065 on 4 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 276807.605 tau/day, 640.758 timesteps/s
|
|
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.15892 | 0.20364 | 0.2564 | 9.2 | 13.05
|
|
Bond | 0.011486 | 0.014652 | 0.01918 | 2.6 | 0.94
|
|
Neigh | 0.43915 | 0.43981 | 0.44125 | 0.1 | 28.18
|
|
Comm | 0.093711 | 0.14431 | 0.18183 | 9.9 | 9.25
|
|
Output | 0.00044441 | 0.00073904 | 0.0016198 | 0.0 | 0.05
|
|
Modify | 0.66889 | 0.68497 | 0.70418 | 1.5 | 43.89
|
|
Other | | 0.07254 | | | 4.65
|
|
|
|
Nlocal: 1400 ave 1610 max 1237 min
|
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
Nghost: 1832 ave 1919 max 1765 min
|
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
|
Neighs: 10008.2 ave 12428 max 7982 min
|
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 40033
|
|
Ave neighs/atom = 7.14875
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 157
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:11
|