222 lines
10 KiB
Groff
222 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 = 0.00020504 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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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 1
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variable c_t equal 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 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
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pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
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pair_style body/rounded/polygon 1 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 $P 1.0 couple xy 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 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
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fix 2 all enforce2d
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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) = 4.781 | 4.781 | 4.781 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 0.39423376 0.0017918048 0.39602557 0.0021941612
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2000 0.42284177 0.01346585 0.43630762 0.0029377883
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3000 0.58154405 0.011321689 0.59286574 0.003667871
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4000 0.73518304 0.034603175 0.76978621 0.0018689207
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5000 0.84367476 0.025292163 0.86896692 0.0089161373
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6000 0.70803236 0.0085631016 0.71659546 0.0045552895
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7000 0.56206452 0.10453031 0.66659483 0.010255161
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8000 0.64538994 0.088817673 0.73420761 0.0037633655
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9000 0.90540819 0.063696004 0.96910419 0.0077673359
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10000 0.68632042 0.093265016 0.77958544 0.0057864838
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11000 0.59118074 0.025654748 0.61683549 0.012518759
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12000 0.67522767 0.038176401 0.71340407 0.01741153
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13000 0.7644843 0.10429844 0.86878274 0.013161339
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14000 0.56152694 0.067836655 0.62936359 0.016852121
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15000 0.41895506 0.019513348 0.43846841 0.015225695
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16000 0.55799421 0.1564559 0.71445011 0.011703561
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17000 0.59391964 0.034450221 0.62836986 0.026215002
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18000 0.75911858 0.030885726 0.7900043 0.018396366
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19000 0.64417995 0.12110912 0.76528907 0.010247952
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20000 0.57751435 0.16965651 0.74717086 0.023392323
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21000 0.7613368 0.13405354 0.89539034 0.021498982
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22000 0.57676692 0.18011879 0.75688571 0.024469161
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23000 0.54043723 0.11842026 0.65885749 0.019799067
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24000 0.62276061 0.038967924 0.66172853 0.019080086
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25000 0.53157536 0.11651937 0.64809473 0.017019298
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26000 0.72213293 0.039012448 0.76114538 0.015434904
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27000 0.62157832 0.13697494 0.75855326 0.028711011
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28000 0.41323738 0.16301101 0.57624839 0.041792632
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29000 0.45774328 0.17569066 0.63343394 0.019975231
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30000 0.78901796 0.099791386 0.88880934 0.024116947
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31000 0.85205397 0.11977547 0.97182945 0.026667489
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32000 0.37137095 0.1232622 0.49463315 0.00087637364
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33000 0.26860871 0.26056381 0.52917252 0.036110517
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34000 0.3018636 0.21336905 0.51523265 0.040315549
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35000 0.39915129 0.28245957 0.68161085 0.034876856
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36000 0.25761236 0.2352705 0.49288286 0.022772767
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37000 0.1071233 0.31692858 0.42405188 0.017994666
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38000 0.083729577 0.28473145 0.36846103 -0.0045370431
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39000 0.070355565 0.26682083 0.33717639 0.017921556
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40000 0.075894079 0.20077896 0.27667304 0.014873186
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41000 0.05891028 0.15989064 0.21880092 0.025547873
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42000 0.1225107 0.16583605 0.28834675 0.038842785
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43000 0.17049189 0.14323991 0.3137318 0.029550161
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44000 0.26823939 0.15208257 0.42032196 0.028113612
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45000 0.10172203 0.1729706 0.27469264 -0.013769913
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46000 0.14841355 0.19085074 0.33926429 -0.00073741985
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47000 0.27654927 0.19097937 0.46752864 0.04021431
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48000 0.53432331 0.080769923 0.61509323 0.029932845
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49000 0.69111634 0.13064951 0.82176585 0.028985406
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50000 0.24520806 0.18317453 0.42838258 0.05179746
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51000 0.23541368 0.14281364 0.37822732 0.071884238
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52000 0.25464996 0.095730242 0.3503802 0.034488204
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53000 0.53677633 0.1058745 0.64265084 0.059932498
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54000 0.32970921 0.27979128 0.60950049 0.062869716
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55000 0.49094054 0.096735015 0.58767556 0.04728005
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56000 0.54398249 0.2216472 0.76562969 0.056712022
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57000 0.60869068 0.2338422 0.84253288 0.077143302
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58000 0.72175509 0.18687368 0.90862877 0.019357656
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59000 0.79442757 0.092502981 0.88693055 0.066882632
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60000 0.6810555 0.077699385 0.75875488 0.095975173
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61000 0.63178834 0.05071143 0.68249977 0.043586668
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62000 0.76589344 0.044615704 0.81050914 0.085718411
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63000 0.84815889 0.030527848 0.87868674 0.053072795
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64000 0.7309043 0.051938637 0.78284294 0.058887766
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65000 0.62498816 0.034474465 0.65946262 0.068446407
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66000 0.69817494 0.068546004 0.76672094 0.062634433
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67000 0.86444275 0.010184259 0.87462701 0.073635055
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68000 0.77820319 0.0079319524 0.78613515 0.090330925
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69000 0.56938919 0.0092629332 0.57865213 0.061838729
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70000 0.61870712 0.010047381 0.6287545 0.066501338
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71000 0.71651803 0.0088366199 0.72535465 0.079136316
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72000 0.76278925 0.008828151 0.77161741 0.063672771
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73000 0.75447428 0.0083985526 0.76287283 0.078256913
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74000 0.66185251 0.0091910052 0.67104351 0.069840511
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75000 0.58458829 0.0097671568 0.59435544 0.076123422
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76000 0.7487564 0.0100022 0.7587586 0.076171741
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77000 0.89505465 0.009250681 0.90430533 0.074921699
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78000 0.73738164 0.0092029279 0.74658457 0.078835344
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79000 0.65735281 0.010099528 0.66745233 0.077940627
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80000 0.70247542 0.010306464 0.71278189 0.079560093
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81000 0.74839505 0.010199092 0.75859415 0.080835104
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82000 0.75193767 0.010274058 0.76221173 0.081086684
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83000 0.71392598 0.010495573 0.72442156 0.082746145
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84000 0.58498928 0.011027388 0.59601667 0.08356465
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85000 0.59022869 0.011729474 0.60195817 0.084519397
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86000 0.81753578 0.011208964 0.82874475 0.085490261
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87000 0.83480682 0.010542579 0.8453494 0.086268527
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88000 0.67322538 0.011170734 0.68439611 0.08751623
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89000 0.62637389 0.012033316 0.6384072 0.088548094
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90000 0.92828557 0.011750388 0.94003596 0.089199823
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91000 0.96072564 0.010324509 0.97105015 0.090204803
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92000 0.72105071 0.011484152 0.73253486 0.09140819
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93000 0.65762527 0.012558219 0.67018349 0.092453474
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94000 0.73991591 0.01261909 0.752535 0.093373477
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95000 0.91791653 0.011980455 0.92989699 0.094182136
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96000 0.76562561 0.011807085 0.7774327 0.095323684
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97000 0.57292104 0.013610205 0.58653124 0.096505977
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98000 0.68141076 0.013863204 0.69527396 0.097380069
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99000 0.82390969 0.013002341 0.83691203 0.098235926
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100000 0.77639728 0.012989342 0.78938662 0.099274147
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Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms
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Performance: 2221655.884 tau/day, 25713.610 timesteps/s
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99.9% 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 | 3.056 | 3.056 | 3.056 | 0.0 | 78.58
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Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13
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Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35
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Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03
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Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98
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Other | | 0.03616 | | | 0.93
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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: 21 ave 21 max 21 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 = 1445
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Dangerous builds = 0
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Total wall time: 0:00:03
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