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 1 by 1 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) = 7.769 | 7.769 | 7.769 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 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
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200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
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300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
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400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
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500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
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600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
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700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
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800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
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900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
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1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
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1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
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1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
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1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
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1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
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1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
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1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
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1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
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1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
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1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
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2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
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2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
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2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
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2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
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2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
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2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
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2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
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2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
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2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
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2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
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3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
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3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
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3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
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3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
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3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
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3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
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3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
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3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
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3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
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3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
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4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
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4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
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4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
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4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
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4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
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4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
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4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
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4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
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4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
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4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
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5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
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Loop time of 6.84203 on 1 procs for 5000 steps with 5600 atoms
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Performance: 315695.745 tau/day, 730.777 timesteps/s
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99.5% CPU use with 1 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 | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77
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Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66
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Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34
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Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70
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Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06
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Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72
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Other | | 0.1873 | | | 2.74
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Nlocal: 5600 ave 5600 max 5600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1351 ave 1351 max 1351 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5254 ave 5254 max 5254 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5254
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Ave neighs/atom = 0.938214
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 766
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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) = 7.77 | 7.77 | 7.77 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
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5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
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5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
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5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
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5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
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5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
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5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
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5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
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5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
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5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
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6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
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Loop time of 1.40593 on 1 procs for 1000 steps with 5600 atoms
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Performance: 307270.224 tau/day, 711.274 timesteps/s
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99.1% CPU use with 1 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 | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56
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Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62
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Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83
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Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60
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Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06
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Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67
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Other | | 0.03729 | | | 2.65
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Nlocal: 5600 ave 5600 max 5600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1347 ave 1347 max 1347 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5399 ave 5399 max 5399 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5399
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Ave neighs/atom = 0.964107
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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) = 7.77 | 7.77 | 7.77 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
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6100 1.4199699 5.8764035 6.9917138 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432
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6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918
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6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093
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6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027
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6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009
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6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745
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6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716
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6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459
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6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962
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7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474
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Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms
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Performance: 306284.404 tau/day, 708.992 timesteps/s
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99.6% CPU use with 1 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 | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61
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Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60
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Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55
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Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57
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Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06
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Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96
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Other | | 0.03715 | | | 2.63
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Nlocal: 5600 ave 5600 max 5600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1284 ave 1284 max 1284 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5677 ave 5677 max 5677 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5677
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Ave neighs/atom = 1.01375
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Ave special neighs/atom = 0.571429
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Neighbor list builds = 151
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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) = 7.77 | 7.77 | 7.77 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194
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7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387
|
|
7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218
|
|
7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034
|
|
7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241
|
|
7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916
|
|
7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883
|
|
7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381
|
|
7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741
|
|
7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317
|
|
8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723
|
|
Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 137012.841 tau/day, 317.159 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76
|
|
Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60
|
|
Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08
|
|
Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57
|
|
Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03
|
|
Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41
|
|
Other | | 0.0491 | | | 1.56
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2954 ave 2954 max 2954 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 25585 ave 25585 max 25585 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 25585
|
|
Ave neighs/atom = 4.56875
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 334
|
|
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) = 7.785 | 7.785 | 7.785 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916
|
|
8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384
|
|
8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089
|
|
8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686
|
|
8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456
|
|
8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733
|
|
8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024
|
|
8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995
|
|
8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323
|
|
8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942
|
|
9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421
|
|
Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 139611.779 tau/day, 323.175 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65
|
|
Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67
|
|
Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52
|
|
Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14
|
|
Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03
|
|
Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70
|
|
Other | | 0.03994 | | | 1.29
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3381 ave 3381 max 3381 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 31737 ave 31737 max 31737 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 31737
|
|
Ave neighs/atom = 5.66732
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 169
|
|
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) = 7.788 | 7.788 | 7.788 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342
|
|
9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166
|
|
9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737
|
|
9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425
|
|
9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923
|
|
9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484
|
|
9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208
|
|
9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559
|
|
9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778
|
|
9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363
|
|
10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921
|
|
Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 132904.162 tau/day, 307.649 timesteps/s
|
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99
|
|
Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60
|
|
Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82
|
|
Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14
|
|
Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03
|
|
Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19
|
|
Other | | 0.04037 | | | 1.24
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3756 ave 3756 max 3756 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 37360 ave 37360 max 37360 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 37360
|
|
Ave neighs/atom = 6.67143
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 158
|
|
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) = 7.795 | 7.795 | 7.795 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643
|
|
10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646
|
|
10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971
|
|
10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087
|
|
10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349
|
|
10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949
|
|
10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845
|
|
10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824
|
|
10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645
|
|
10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245
|
|
11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542
|
|
Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 125663.855 tau/day, 290.889 timesteps/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84
|
|
Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55
|
|
Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49
|
|
Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12
|
|
Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03
|
|
Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78
|
|
Other | | 0.0412 | | | 1.20
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3904 ave 3904 max 3904 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 39666 ave 39666 max 39666 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 39666
|
|
Ave neighs/atom = 7.08321
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 159
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:22
|