forked from lijiext/lammps
245 lines
10 KiB
Groff
245 lines
10 KiB
Groff
LAMMPS (5 Oct 2016)
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# 2d micelle simulation
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dimension 2
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_style bond
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# Soft potential push-off
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read_data data.micelle
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orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1200 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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300 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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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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pair_style soft 1.12246
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pair_coeff * * 0.0 1.12246
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bond_style harmonic
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bond_coeff 1 50.0 0.75
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velocity all create 0.45 2349852
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variable prefactor equal ramp(1.0,20.0)
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fix 1 all nve
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fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
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fix 3 all adapt 1 pair soft a * * v_prefactor
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fix 4 all enforce2d
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thermo 50
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run 1000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.42246
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ghost atom cutoff = 1.42246
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binsize = 0.71123 -> bins = 51 51 1
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Memory usage per processor = 3.55365 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
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50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
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100 0.45 0.73046745 0.054836584 1.234929 2.3196516
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150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
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200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
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250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
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300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
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350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
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400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
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450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
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500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
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550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
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600 0.45 0.58193041 0.088386617 1.119942 5.131481
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650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
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700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
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750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
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800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
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850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
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900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
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950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
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1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
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Loop time of 0.0670803 on 4 procs for 1000 steps with 1200 atoms
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Performance: 6440046.660 tau/day, 14907.515 timesteps/s
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98.4% CPU use with 4 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 | 0.033971 | 0.034628 | 0.036162 | 0.5 | 51.62
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Bond | 0.001687 | 0.0017596 | 0.0018852 | 0.2 | 2.62
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Neigh | 0.0068789 | 0.0069902 | 0.0070932 | 0.1 | 10.42
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Comm | 0.011152 | 0.012883 | 0.013872 | 0.9 | 19.20
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Output | 0.00035501 | 0.00038034 | 0.00044274 | 0.2 | 0.57
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Modify | 0.0065997 | 0.0067009 | 0.0068605 | 0.1 | 9.99
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Other | | 0.003738 | | | 5.57
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Nlocal: 300 ave 305 max 292 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 100.25 ave 108 max 93 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 784 ave 815 max 739 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 3136
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Ave neighs/atom = 2.61333
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Ave special neighs/atom = 0.5
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Neighbor list builds = 92
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Dangerous builds = 0
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unfix 3
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# Main run
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pair_style lj/cut 2.5
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# solvent/head - full-size and long-range
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 2 2 1.0 1.0 2.5
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pair_coeff 1 2 1.0 1.0 2.5
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# tail/tail - size-averaged and long-range
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pair_coeff 3 3 1.0 0.75 2.5
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pair_coeff 4 4 1.0 0.50 2.5
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pair_coeff 3 4 1.0 0.67 2.5
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# solvent/tail - full-size and repulsive
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pair_coeff 1 3 1.0 1.0 1.12246
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pair_coeff 1 4 1.0 1.0 1.12246
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# head/tail - size-averaged and repulsive
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pair_coeff 2 3 1.0 0.88 1.12246
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pair_coeff 2 4 1.0 0.75 1.12246
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thermo 1000
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#dump 1 all atom 2000 dump.micelle
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#dump 2 all image 2000 image.*.jpg type type zoom 1.6
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#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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#dump 3 all movie 2000 movie.mpg type type zoom 1.6
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#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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reset_timestep 0
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run 60000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 5 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 = 26 26 1
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Memory usage per processor = 3.55365 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
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1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389
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2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222
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3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627
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4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681
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5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201
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6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697
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7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258
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8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483
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9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073
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10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504
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11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919
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12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597
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13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604
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14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118
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15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383
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16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698
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17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709
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18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376
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19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446
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20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174
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21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426
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22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367
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23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975
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24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971
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25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418
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26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166
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27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525
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28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874
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29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766
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30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889
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31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188
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32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981
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33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562
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34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582
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35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438
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36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389
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37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583
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38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974
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39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261
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40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332
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41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574
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42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091
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43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812
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44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595
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45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258
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46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898
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47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032
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48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819
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49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508
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50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822
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51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123
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52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016
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53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287
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54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909
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55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805
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56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345
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57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346
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58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
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59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
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60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
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Loop time of 4.56204 on 4 procs for 60000 steps with 1200 atoms
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Performance: 5681665.051 tau/day, 13152.002 timesteps/s
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99.5% CPU use with 4 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 | 2.3705 | 2.4423 | 2.4948 | 2.9 | 53.54
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Bond | 0.084795 | 0.10292 | 0.11359 | 3.4 | 2.26
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Neigh | 0.63938 | 0.64418 | 0.64857 | 0.4 | 14.12
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Comm | 0.81947 | 0.8785 | 0.9618 | 5.7 | 19.26
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Output | 0.0012863 | 0.0013551 | 0.0015438 | 0.3 | 0.03
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Modify | 0.26717 | 0.27596 | 0.28816 | 1.5 | 6.05
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Other | | 0.2168 | | | 4.75
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Nlocal: 300 ave 305 max 293 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Nghost: 211 ave 215 max 205 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Neighs: 2448.75 ave 2531 max 2414 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Total # of neighbors = 9795
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Ave neighs/atom = 8.1625
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Ave special neighs/atom = 0.5
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Neighbor list builds = 4880
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Dangerous builds = 0
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Total wall time: 0:00:04
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