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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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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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) = 3.758 | 3.85 | 4.126 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 0.0641922 on 4 procs for 1000 steps with 1200 atoms
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Performance: 6729792.131 tau/day, 15578.223 timesteps/s
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90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
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Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
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Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
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Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
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Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
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Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
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Other | | 0.003891 | | | 6.06
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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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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) = 4.001 | 4.032 | 4.124 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 -1.9727661 0.05860859 -1.4645325 1.9982402
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2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
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3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
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4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
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5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
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6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
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7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
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8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
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9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
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10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
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11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
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12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
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13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
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14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
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15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
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16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
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17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
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18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
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19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
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20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
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21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
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22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
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23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
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24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
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25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
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26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
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27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
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28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
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29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
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30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
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31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
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32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
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33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
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34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
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35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
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36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
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37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
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38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
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39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
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40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
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41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
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42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
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43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
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44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
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45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
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46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
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47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
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48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
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49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
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50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
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51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
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52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
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53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
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54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
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55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
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56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
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57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
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58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
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59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
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60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
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Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
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Performance: 5681397.232 tau/day, 13151.382 timesteps/s
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97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
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Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
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Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
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Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
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Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
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Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
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Other | | 0.2346 | | | 5.14
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Nlocal: 300 ave 306 max 289 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Nghost: 227.25 ave 250 max 216 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Neighs: 2373.25 ave 2489 max 2283 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Total # of neighbors = 9493
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Ave neighs/atom = 7.91083
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Ave special neighs/atom = 0.5
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Neighbor list builds = 4888
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Dangerous builds = 0
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Total wall time: 0:00:04
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