forked from lijiext/lammps
453 lines
28 KiB
Groff
453 lines
28 KiB
Groff
LAMMPS (5 Oct 2016)
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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 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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1 neighbor list requests
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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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Memory usage per processor = 7.32042 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 6.51777 on 1 procs for 5000 steps with 5600 atoms
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Performance: 331401.531 tau/day, 767.133 timesteps/s
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99.8% CPU use with 1 MPI tasks x no 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 | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
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Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
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Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
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Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
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Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
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Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
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Other | | 0.1774 | | | 2.72
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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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Memory usage per processor = 7.32042 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 1.37139 on 1 procs for 1000 steps with 5600 atoms
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Performance: 315008.398 tau/day, 729.186 timesteps/s
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100.0% CPU use with 1 MPI tasks x no 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 | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
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Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
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Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
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Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
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Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
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Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
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Other | | 0.03562 | | | 2.60
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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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Memory usage per processor = 7.32042 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 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
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6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
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6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
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6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
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6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
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6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
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6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
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6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
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6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
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7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
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Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
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Performance: 311550.061 tau/day, 721.181 timesteps/s
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99.9% CPU use with 1 MPI tasks x no 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 | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
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Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
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Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
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Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
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Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
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Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
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Other | | 0.03559 | | | 2.57
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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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Memory usage per processor = 7.32042 Mbytes
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Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
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7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
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7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
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7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
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7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
|
|
7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
|
|
7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
|
|
7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
|
|
7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
|
|
7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
|
|
7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
|
|
8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
|
|
Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 141281.224 tau/day, 327.040 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
|
|
Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
|
|
Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
|
|
Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
|
|
Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
|
|
Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
|
|
Other | | 0.04962 | | | 1.62
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2963 ave 2963 max 2963 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 25797 ave 25797 max 25797 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 25797
|
|
Ave neighs/atom = 4.60661
|
|
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
|
|
Memory usage per processor = 7.32428 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
|
|
8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
|
|
8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
|
|
8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
|
|
8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
|
|
8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
|
|
8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
|
|
8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
|
|
8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
|
|
8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
|
|
9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
|
|
Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 146727.069 tau/day, 339.646 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
|
|
Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
|
|
Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
|
|
Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
|
|
Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
|
|
Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
|
|
Other | | 0.03878 | | | 1.32
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3244 ave 3244 max 3244 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 30929 ave 30929 max 30929 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 30929
|
|
Ave neighs/atom = 5.52304
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 165
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nph iso"
|
|
rigid/nph iso
|
|
run 1000
|
|
Memory usage per processor = 7.32428 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
|
|
9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
|
|
9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
|
|
9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
|
|
9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
|
|
9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
|
|
9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
|
|
9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
|
|
9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
|
|
9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
|
|
10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
|
|
Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 137864.384 tau/day, 319.131 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
|
|
Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
|
|
Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
|
|
Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
|
|
Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
|
|
Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
|
|
Other | | 0.03924 | | | 1.25
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3635 ave 3635 max 3635 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 38235 ave 38235 max 38235 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 38235
|
|
Ave neighs/atom = 6.82768
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 165
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nph xy couple"
|
|
rigid/nph xy couple
|
|
run 1000
|
|
Memory usage per processor = 7.32811 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
|
|
10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
|
|
10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
|
|
10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
|
|
10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
|
|
10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
|
|
10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
|
|
10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
|
|
10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
|
|
10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
|
|
11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
|
|
Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Performance: 134004.591 tau/day, 310.196 timesteps/s
|
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
|
|
Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
|
|
Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
|
|
Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
|
|
Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
|
|
Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
|
|
Other | | 0.03903 | | | 1.21
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3799 ave 3799 max 3799 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 39646 ave 39646 max 39646 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 39646
|
|
Ave neighs/atom = 7.07964
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 158
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:21
|