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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1 by 1 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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1 by 1 by 1 MPI processor grid
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32 atoms
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Time spent = 0.00029707 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) = 4.771 | 4.771 | 4.771 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 3.9079782e-05
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11000 0.41529308 0.13619284 0.55148592 -0.0067482285
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12000 0.43274718 0.071315497 0.50406268 0.007006378
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13000 0.4748331 0.069904647 0.54473775 0.0010384372
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14000 0.6287791 0.12721033 0.75598943 0.0047792448
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15000 0.4692413 0.12344005 0.59268136 0.018033616
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16000 0.43157074 0.14306789 0.57463862 0.042356676
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17000 0.53085999 0.22126296 0.75212294 0.027509646
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18000 0.52688968 0.13225282 0.6591425 0.0021558013
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19000 0.55032328 0.12513047 0.67545375 0.025036251
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20000 0.48465097 0.1431055 0.62775647 0.017193781
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21000 0.53166734 0.21928574 0.75095307 0.011564317
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22000 0.62177353 0.09296159 0.71473512 0.017660922
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23000 0.6972939 0.12434123 0.82163514 0.024432327
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24000 0.42767372 0.22152311 0.64919684 -0.013712449
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25000 0.4816037 0.19272865 0.67433236 0.052386055
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26000 0.72642579 0.19697046 0.92339625 0.020407694
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27000 0.39649144 0.15058326 0.5470747 0.023705766
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28000 0.44896324 0.18500106 0.6339643 -0.0089410286
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29000 0.5565759 0.11085772 0.66743362 0.048437166
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30000 0.58173584 0.21773281 0.79946865 0.0057357773
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31000 0.49199415 0.23601982 0.72801397 0.046744152
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32000 0.55665496 0.20542161 0.76207658 -0.0038756805
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33000 0.62730739 0.24460524 0.87191263 0.045330682
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34000 0.58107044 0.16395278 0.74502322 -0.0049496051
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35000 0.56838849 0.21842922 0.78681771 0.0062086036
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36000 0.45910273 0.28464172 0.74374445 -0.011700747
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37000 0.37092037 0.27646862 0.647389 0.022305679
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38000 0.7278047 0.30674438 1.0345491 0.07698342
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39000 0.5132923 0.27395066 0.78724295 0.026898634
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40000 0.62348649 0.24424644 0.86773293 0.039403899
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41000 0.3658401 0.15512326 0.52096337 0.022559003
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42000 0.4912253 0.35712978 0.84835508 -0.010336341
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43000 0.70225957 0.36314638 1.0654059 0.004148866
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44000 0.56958157 0.25488927 0.82447084 0.067537066
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45000 0.45854352 0.30149439 0.76003791 -0.017002401
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46000 0.62787247 0.34567995 0.97355242 0.11894801
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47000 0.61348914 0.29378625 0.90727539 0.067873976
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48000 0.71301829 0.34135284 1.0543711 0.021077736
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49000 0.53520804 0.30593196 0.84113999 0.0059257647
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50000 0.44966403 0.35370793 0.80337195 0.0020395669
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51000 0.5236113 0.32296924 0.84658054 -0.051011506
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52000 0.53905573 0.351771 0.89082672 0.013720106
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53000 0.55978158 0.41293947 0.97272106 0.068558589
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54000 0.52170459 0.2718066 0.7935112 0.0093138985
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55000 0.61078876 0.43353897 1.0443277 0.045377392
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56000 0.51300655 0.33182278 0.84482933 -0.018418487
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57000 0.54882822 0.38380093 0.93262915 0.10249946
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58000 0.72106212 0.45361279 1.1746749 0.030313481
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59000 0.55871447 0.63823029 1.1969448 0.019079703
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60000 0.49395192 0.58283102 1.0767829 0.0179349
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61000 0.45991079 0.62540573 1.0853165 0.074398804
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62000 0.4655788 0.60862262 1.0742014 0.11472976
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63000 0.55634524 0.63069255 1.1870378 -0.0025676135
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64000 0.57688903 0.45435264 1.0312417 0.0083813852
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65000 0.57168922 0.42217005 0.99385927 0.044931269
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66000 0.6206044 0.46727538 1.0878798 0.019686229
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67000 0.61037155 0.41840109 1.0287726 0.0195109
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68000 0.63848598 0.41305347 1.0515395 0.072940144
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69000 0.49244916 0.3834095 0.87585866 0.07963677
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70000 0.41847062 0.51907975 0.93755037 0.18447904
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71000 0.45198986 0.52973709 0.98172695 0.078419371
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72000 0.47064262 0.37808165 0.84872427 -0.00046308054
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73000 0.6690143 0.37549359 1.0445079 0.061208432
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74000 0.60444955 0.33779636 0.94224592 -0.068840321
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75000 0.61762382 0.3916421 1.0092659 0.16253292
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76000 0.63657961 0.50277989 1.1393595 0.013857508
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77000 0.52524028 0.43597896 0.96121924 -0.03296482
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78000 0.43803533 0.33172284 0.76975817 0.078763029
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79000 0.67156089 0.55272177 1.2242827 0.080822223
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80000 0.68678238 0.46061627 1.1473987 0.0027036992
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81000 0.64956678 0.44959229 1.0991591 0.11201483
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82000 0.51060477 0.43508342 0.9456882 0.028000608
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83000 0.59550548 0.69026083 1.2857663 -0.0015809004
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84000 0.64222145 0.38768816 1.0299096 0.014153173
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85000 0.7661229 0.43445261 1.2005755 0.048034534
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86000 0.60025257 0.53027929 1.1305319 0.0056865157
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87000 0.46220939 0.47470035 0.93690974 0.075311946
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88000 0.54123847 0.62899839 1.1702369 0.13260162
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89000 0.61212272 0.6114241 1.2235468 0.033284822
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90000 0.63924773 0.6916249 1.3308726 0.045088296
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91000 0.49316865 0.51037033 1.003539 0.023203598
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92000 0.57572123 0.43496319 1.0106844 0.297092
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93000 0.65187559 0.56815972 1.2200353 0.1538215
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94000 0.64107331 0.58948521 1.2305585 0.031117778
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95000 0.64584158 0.6364688 1.2823104 0.096154676
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96000 0.60509093 0.601487 1.2065779 0.03457172
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97000 0.68837218 0.77974186 1.468114 0.17801164
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98000 0.62725266 0.64137144 1.2686241 0.17449001
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99000 0.46861221 0.67000291 1.1386151 0.2429588
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100000 0.5879119 0.7140612 1.3019731 0.064634257
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Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms
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Performance: 3447804.126 tau/day, 39905.140 timesteps/s
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100.0% CPU use with 1 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 | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41
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Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35
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Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35
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Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05
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Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34
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Other | | 0.03781 | | | 1.51
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Nlocal: 32 ave 32 max 32 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 20 ave 20 max 20 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 57 ave 57 max 57 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 57
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Ave neighs/atom = 1.78125
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Neighbor list builds = 2705
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Dangerous builds = 0
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Total wall time: 0:00:02
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