256 lines
11 KiB
Groff
256 lines
11 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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1 by 1 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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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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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair soft, 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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 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 0.167265 on 1 procs for 1000 steps with 1200 atoms
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Performance: 2582728.958 tau/day, 5978.539 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 | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
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Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
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Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
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Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
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Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
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Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
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Other | | 0.006227 | | | 3.72
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Nlocal: 1200 ave 1200 max 1200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 195 ave 195 max 195 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3136 ave 3136 max 3136 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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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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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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 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 -1.9727655 0.058608715 -1.4645318 1.9982298
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2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
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3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
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4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
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5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
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6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
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7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
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8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
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9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
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10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
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11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
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12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
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13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
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14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
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15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
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16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
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17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
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18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
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19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
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20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
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21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
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22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
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23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
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24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
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25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
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26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
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27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
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28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
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29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
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30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
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31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
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32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
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33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
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34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
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35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
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36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
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37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
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38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
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39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
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40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
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41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
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42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
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43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
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44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
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45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
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46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
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47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
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48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
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49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
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50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
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51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
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52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
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53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
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54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
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55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
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56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
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57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
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58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
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59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
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60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
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Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
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Performance: 1859917.639 tau/day, 4305.365 timesteps/s
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99.8% 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 | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
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Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
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Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
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Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
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Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
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Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
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Other | | 0.3493 | | | 2.51
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Nlocal: 1200 ave 1200 max 1200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 405 ave 405 max 405 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9565 ave 9565 max 9565 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9565
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Ave neighs/atom = 7.97083
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Ave special neighs/atom = 0.5
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Neighbor list builds = 4876
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Dangerous builds = 0
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Total wall time: 0:00:14
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