224 lines
10 KiB
Groff
224 lines
10 KiB
Groff
LAMMPS (29 Jun 2018)
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# 2d rounded polygon bodies
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variable r index 4
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variable steps index 100000
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variable T index 0.5
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variable P index 0.1
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variable seed index 980411
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units lj
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dimension 2
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atom_style body rounded/polygon 1 6
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atom_modify map array
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read_data data.squares
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orthogonal box = (0 0 -0.5) to (12 12 0.5)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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2 atoms
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2 bodies
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replicate $r $r 1
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replicate 4 $r 1
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replicate 4 4 1
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orthogonal box = (0 0 -0.5) to (48 48 0.5)
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2 by 2 by 1 MPI processor grid
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32 atoms
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Time spent = 0.000386 secs
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velocity all create $T ${seed} dist gaussian mom yes rot yes
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velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
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velocity all create 0.5 980411 dist gaussian mom yes rot yes
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change_box all boundary p f p
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variable cut_inner equal 0.5
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variable k_n equal 100
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variable k_na equal 2
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variable c_n equal 0.1
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variable c_t equal 0.1
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variable mu equal 0.1
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variable delta_ua equal 0.5
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pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
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pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
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pair_coeff * * ${k_n} ${k_na}
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pair_coeff * * 100 ${k_na}
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pair_coeff * * 100 2
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comm_modify vel yes
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neighbor 0.5 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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#fix 1 all nve/body
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#fix 1 all nvt/body temp $T $T 1.0
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fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
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fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
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fix 2 all enforce2d
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fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
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#compute 1 all body/local id 1 2 3
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#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
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thermo_style custom step ke pe etotal press
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thermo 1000
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#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
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#dump_modify 2 pad 6
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run ${steps}
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run 100000
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Neighbor list info ...
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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 = 6.15685
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ghost atom cutoff = 6.15685
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binsize = 3.07843, bins = 16 16 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair body/rounded/polygon, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/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) = 4.773 | 4.773 | 4.773 Mbytes
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Step KinEng PotEng TotEng Press
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0 0.484375 0.25 0.734375 0.0067274306
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1000 0.49241101 0.0031318767 0.49554289 0.017768281
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2000 0.56118632 0.0026068888 0.56379321 0.003410416
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3000 0.75565115 0.025578366 0.78122951 0.0071862988
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4000 0.72298647 0.093150646 0.81613712 0.003190158
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5000 0.51684166 0.049164868 0.56600653 0.0096960168
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6000 0.56627905 0.048132853 0.6144119 0.020733586
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7000 0.58122129 0.018223718 0.59944501 0.0038160759
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8000 0.64297977 0.025934821 0.66891459 0.0041091784
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9000 0.41748404 0.0077890042 0.42527305 0.0039270065
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10000 0.35738377 0.078487805 0.43587158 3.9079865e-05
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11000 0.41529307 0.13619284 0.55148591 -0.0067482285
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12000 0.43274718 0.071315527 0.50406271 0.007006369
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13000 0.4748324 0.069905666 0.54473807 0.0010385254
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14000 0.62603727 0.098905625 0.7249429 0.0048876764
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15000 0.44512086 0.10415235 0.54927321 0.01902062
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16000 0.47460177 0.18053316 0.65513493 0.045013976
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17000 0.52742676 0.10110706 0.62853382 0.013615471
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18000 0.46111734 0.096118795 0.55723613 0.0073676834
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19000 0.59668439 0.13652292 0.73320731 0.029403553
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20000 0.46840192 0.11611719 0.58451911 -0.00034412499
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21000 0.53550533 0.096457461 0.6319628 0.0019785732
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22000 0.46599715 0.13206373 0.59806087 0.031970672
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23000 0.49280776 0.20404726 0.69685501 0.03657433
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24000 0.60901688 0.18255214 0.79156902 0.044955017
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25000 0.47345185 0.13671357 0.61016542 0.020313539
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26000 0.47653832 0.12448225 0.60102057 0.01878099
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27000 0.50008212 0.24740634 0.74748845 0.021862639
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28000 0.41627204 0.2519463 0.66821834 0.054683701
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29000 0.55608273 0.23100212 0.78708485 -0.0043318497
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30000 0.53884537 0.3001584 0.83900377 -0.012838186
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31000 0.53036238 0.2300328 0.76039518 -0.0061688449
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32000 0.42666792 0.20536256 0.63203048 0.045305282
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33000 0.62908185 0.1652033 0.79428515 0.0072777588
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34000 0.47028154 0.388736 0.85901754 0.04332288
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35000 0.54602322 0.2775624 0.82358562 0.02898206
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36000 0.59860544 0.21824655 0.81685199 0.0025936194
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37000 0.62467827 0.11983499 0.74451326 0.050052743
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38000 0.72594229 0.36584781 1.0917901 0.04280621
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39000 0.51129656 0.23859043 0.74988699 0.050817447
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40000 0.53263836 0.24212889 0.77476725 0.036245922
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41000 0.50288088 0.36668283 0.86956371 0.018381415
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42000 0.46653688 0.21974887 0.68628574 0.012661062
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43000 0.61738785 0.32131037 0.93869821 0.012709433
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44000 0.56603903 0.26515554 0.83119457 0.03315102
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45000 0.56231638 0.32111693 0.88343331 0.06079756
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46000 0.7096208 0.2570131 0.96663391 0.048770468
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47000 0.588755 0.1880748 0.7768298 0.035962604
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48000 0.56296339 0.25783519 0.82079858 0.053019928
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49000 0.419885 0.42328618 0.84317118 0.038105269
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50000 0.63073351 0.41426285 1.0449964 0.0015271048
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51000 0.59357935 0.184222 0.77780136 0.015996218
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52000 0.60608471 0.36247533 0.96856003 0.10984665
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53000 0.5227842 0.27686739 0.79965159 0.02761699
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54000 0.39435923 0.34197355 0.73633278 0.061183263
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55000 0.46748455 0.34230903 0.80979358 0.077441382
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56000 0.59819827 0.29212061 0.89031889 0.043772353
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57000 0.61682559 0.32788566 0.94471124 0.03992069
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58000 0.52702478 0.24891506 0.77593984 0.058480883
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59000 0.66925719 0.4109031 1.0801603 0.072434423
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60000 0.66807714 0.39233068 1.0604078 0.082370324
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61000 0.5724275 0.43308567 1.0055132 0.0072945426
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62000 0.49433556 0.38453743 0.87887299 0.0036097443
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63000 0.57575143 0.54067119 1.1164226 0.073339638
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64000 0.68045383 0.38246533 1.0629192 0.025314593
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65000 0.59843527 0.42928622 1.0277215 -0.030096445
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66000 0.60274797 0.50186417 1.1046121 0.069797184
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67000 0.47450407 0.52689807 1.0014021 0.008758012
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68000 0.5514135 0.64113187 1.1925454 0.093863314
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69000 0.52008074 0.45749565 0.97757639 -0.066061381
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70000 0.69042662 0.50416006 1.1945867 0.014128617
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71000 0.63925854 0.35153425 0.9907928 -0.01134957
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72000 0.52088835 0.47626986 0.99715821 0.10198133
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73000 0.46333852 0.5515537 1.0148922 0.00060582772
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74000 0.53481418 0.50409531 1.0389095 0.00919451
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75000 0.67182749 0.50380162 1.1756291 0.043301985
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76000 0.70492289 0.4112122 1.1161351 0.14880484
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77000 0.59781817 0.50197661 1.0997948 -0.057111711
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78000 0.51677429 0.4348232 0.95159749 -0.0074619446
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79000 0.50663297 0.55000424 1.0566372 0.0052071216
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80000 0.59392006 0.48394003 1.0778601 -0.018990234
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81000 0.66323593 0.40358336 1.0668193 -0.02961345
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82000 0.61596979 0.49177944 1.1077492 0.1314853
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83000 0.63917554 0.61656584 1.2557414 0.11908351
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84000 0.49305291 0.46161646 0.95466937 0.033558488
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85000 0.52552044 0.54250555 1.068026 0.13015174
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86000 0.55140914 0.38924725 0.94065638 0.047412499
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87000 0.60952504 0.52603688 1.1355619 0.039230066
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88000 0.50119735 0.547539 1.0487364 0.019659933
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89000 0.40331401 0.50331134 0.90662535 -0.056906034
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90000 0.47067839 0.51306911 0.9837475 0.11918166
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91000 0.45564995 0.38693455 0.8425845 0.12040045
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92000 0.64163032 0.34232532 0.98395564 0.0057051641
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93000 0.70375593 0.53646186 1.2402178 0.16044241
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94000 0.53378112 0.51971406 1.0534952 0.11389004
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95000 0.47055342 0.50396004 0.97451346 0.079424215
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96000 0.59543473 0.40204536 0.99748009 0.096813093
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97000 0.64821917 0.50051728 1.1487365 0.054071312
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98000 0.55723937 0.4945909 1.0518303 0.047316424
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99000 0.56044424 0.50773312 1.0681774 0.0149959
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100000 0.68254229 0.32704484 1.0095871 0.0069212661
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Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms
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Performance: 3926501.701 tau/day, 45445.622 timesteps/s
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100.0% 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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---------------------------------------------------------------
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Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80
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Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14
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Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88
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Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05
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Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78
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Other | | 0.1618 | | | 7.36
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Nlocal: 8 ave 9 max 7 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 12.75 ave 14 max 12 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 11 ave 19 max 5 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 44
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Ave neighs/atom = 1.375
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Neighbor list builds = 2663
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Dangerous builds = 0
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Total wall time: 0:00:02
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