260 lines
11 KiB
Groff
260 lines
11 KiB
Groff
LAMMPS (28 Feb 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
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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 CPU = 0.000130415 secs
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read_data CPU = 0.00132132 secs
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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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special bonds CPU = 4.76837e-05 secs
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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 0.0377742 on 4 procs for 1000 steps with 1200 atoms
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Performance: 11436375.633 tau/day, 26473.092 timesteps/s
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96.6% 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 | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80
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Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81
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Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86
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Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52
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Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75
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Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55
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Other | | 0.002912 | | | 7.71
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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 -1.9727652 0.058608073 -1.4645321 1.9982444
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2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263
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3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772
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4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276
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5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351
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6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586
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7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035
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8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914
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9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868
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10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581
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11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435
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12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059
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13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813
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14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778
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15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821
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16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235
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17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504
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18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232
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19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496
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20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973
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21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522
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22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529
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23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844
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24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138
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25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438
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26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386
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27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759
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28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249
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29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527
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30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894
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31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973
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32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153
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33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104
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34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425
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35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751
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36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487
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37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821
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38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923
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39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695
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40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322
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41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684
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42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362
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43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741
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44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946
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45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542
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46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494
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47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899
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48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556
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49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984
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50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037
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51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462
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52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227
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53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365
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54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429
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55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299
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56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556
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57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633
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58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658
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59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272
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60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511
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Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
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Performance: 9821248.084 tau/day, 22734.371 timesteps/s
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97.3% 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 | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43
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Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49
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Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78
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Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19
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Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07
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Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77
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Other | | 0.1131 | | | 4.28
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Nlocal: 300 ave 309 max 281 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Nghost: 232.75 ave 234 max 231 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 2450.25 ave 2576 max 2179 min
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Histogram: 1 0 0 0 0 0 0 0 1 2
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Total # of neighbors = 9801
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Ave neighs/atom = 8.1675
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Ave special neighs/atom = 0.5
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Neighbor list builds = 4887
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Dangerous builds = 0
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Total wall time: 0:00:02
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