mirror of https://github.com/lammps/lammps.git
225 lines
10 KiB
Groff
225 lines
10 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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 = 0.000318766 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 0.51467204 0.00099202506 0.51566407 0.013452386
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2000 0.55674899 0.0040762275 0.56082522 0.0034529066
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3000 0.7546177 0.02259362 0.77721132 0.003650781
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4000 0.72710218 0.10284108 0.82994326 0.0059629371
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5000 0.5771012 0.069052145 0.64615335 0.00053937622
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6000 0.53848154 0.041891239 0.58037277 0.0018693312
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7000 0.61777556 0.033379829 0.65115538 0.0027584418
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8000 0.47427227 0.059558934 0.5338312 0.017087187
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9000 0.46822364 0.064382578 0.53260622 0.023258465
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10000 0.46511051 0.027799371 0.49290988 0.015319493
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11000 0.58686703 0.088016891 0.67488392 0.0088428936
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12000 0.49962603 0.09879099 0.59841702 0.00074311497
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13000 0.53160049 0.069625775 0.60122626 0.017019775
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14000 0.49574902 0.041214164 0.53696318 0.0060355978
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15000 0.56620415 0.13621516 0.70241931 0.045583297
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16000 0.40942564 0.11469877 0.52412441 0.029905784
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17000 0.608066 0.096938921 0.70500493 0.018509814
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18000 0.45622168 0.057018077 0.51323975 0.0034035281
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19000 0.48763322 0.057832224 0.54546545 0.0022972169
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20000 0.41577025 0.14480819 0.56057844 0.023882542
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21000 0.58565738 0.1601676 0.74582498 0.01702799
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22000 0.60430354 0.16740706 0.7717106 -0.0047632836
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23000 0.45659601 0.13740896 0.59400497 0.0191143
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24000 0.42741367 0.25490516 0.68231884 0.051459175
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25000 0.40851048 0.077823072 0.48633355 0.024392284
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26000 0.53392894 0.14504323 0.67897217 0.028964572
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27000 0.39775205 0.13101153 0.52876358 0.0080564916
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28000 0.63138106 0.17706612 0.80844718 0.017594524
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29000 0.57897788 0.26855503 0.84753292 0.019310624
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30000 0.37401002 0.2274666 0.60147663 0.0044804008
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31000 0.60924323 0.23142663 0.84066986 0.088271242
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32000 0.60310397 0.35719837 0.96030234 0.0096762289
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33000 0.47468105 0.17727177 0.65195282 0.0078486602
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34000 0.42270829 0.20131235 0.62402064 0.090216203
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35000 0.49578606 0.1697981 0.66558416 0.079099134
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36000 0.50744538 0.29600416 0.80344954 0.018819487
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37000 0.66728184 0.28166655 0.94894838 -0.01679437
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38000 0.38972905 0.25798163 0.64771068 0.040442456
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39000 0.38292839 0.21774389 0.60067228 0.016754932
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40000 0.61770336 0.34202184 0.9597252 0.10986262
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41000 0.42252651 0.13424708 0.5567736 0.040987711
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42000 0.67513868 0.29515562 0.9702943 0.0013757417
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43000 0.36768915 0.20349753 0.57118668 0.031443504
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44000 0.49371025 0.095615653 0.5893259 0.032289477
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45000 0.42144079 0.28894639 0.71038718 0.040302569
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46000 0.36360136 0.33117431 0.69477567 0.010881881
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47000 0.4206309 0.19557595 0.61620685 0.051137535
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48000 0.4131465 0.37027912 0.78342561 0.11903042
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49000 0.544703 0.38013565 0.92483865 0.054939742
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50000 0.47394272 0.32384493 0.79778764 0.088363602
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51000 0.55377533 0.38103395 0.93480927 0.097981664
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52000 0.60648433 0.30877364 0.91525797 0.088877781
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53000 0.62933509 0.33187159 0.96120668 0.10275954
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54000 0.55077522 0.39050008 0.94127529 0.066721412
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55000 0.41646397 0.34545572 0.76191969 0.011056796
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56000 0.44244954 0.39274744 0.83519698 0.039963853
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57000 0.41963092 0.33483982 0.75447073 0.032555938
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58000 0.37941475 0.36905323 0.74846798 0.043952263
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59000 0.53008564 0.32843795 0.85852359 0.080787301
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60000 0.43408908 0.19840268 0.63249176 0.06421165
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61000 0.56287814 0.31500577 0.87788391 0.12031895
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62000 0.5185192 0.18275672 0.70127592 -0.0086212356
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63000 0.57275413 0.45147395 1.0242281 0.054617465
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64000 0.28322907 0.33687722 0.62010629 0.07268947
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65000 0.40230876 0.37989067 0.78219943 -0.029604066
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66000 0.58601209 0.52721274 1.1132248 -0.00037054404
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67000 0.52669356 0.44276199 0.96945554 0.18969356
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68000 0.41566831 0.47320489 0.8888732 0.040635264
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69000 0.52140574 0.4261935 0.94759923 0.016566201
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70000 0.42034133 0.55867009 0.97901142 0.047465899
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71000 0.48720036 0.43749264 0.924693 0.15984789
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72000 0.5244238 0.55854139 1.0829652 0.10155994
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73000 0.69990219 0.57313852 1.2730407 0.11108648
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74000 0.38274347 0.23359664 0.61634011 0.027968087
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75000 0.47493369 0.49472607 0.96965976 0.10961568
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76000 0.57064727 0.37996383 0.9506111 0.034746271
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77000 0.50401727 0.34437588 0.84839315 0.015116686
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78000 0.59504118 0.44154772 1.0365889 0.059341875
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79000 0.4920801 0.58935767 1.0814378 0.12139906
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80000 0.56992818 0.38916606 0.95909424 0.073618074
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81000 0.38446945 0.77314417 1.1576136 0.12173381
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82000 0.48734531 0.56198203 1.0493273 0.1080115
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83000 0.5516933 0.56743096 1.1191243 0.13936805
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84000 0.53336893 0.62914863 1.1625176 0.0084970895
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85000 0.46456977 0.77446084 1.2390306 0.18024688
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86000 0.58067599 0.53109608 1.1117721 0.012492021
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87000 0.55096446 0.61715622 1.1681207 0.13264723
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88000 0.56548774 0.74463701 1.3101247 0.14491188
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89000 0.52492634 0.58482194 1.1097483 0.21155245
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90000 0.64973565 0.85514474 1.5048804 0.036911953
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91000 0.55367722 0.74046971 1.2941469 0.23918851
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92000 0.44863249 0.56773761 1.0163701 0.00042860088
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93000 0.64728356 0.66594086 1.3132244 0.0022850006
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94000 0.65255497 0.82136644 1.4739214 0.10037643
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95000 0.62266654 0.82642147 1.449088 0.11964602
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96000 0.50656004 0.83312844 1.3396885 0.078491084
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97000 0.47126712 0.70469684 1.175964 0.12956056
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98000 0.48661103 1.0121726 1.4987837 0.043537851
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99000 0.48379797 0.9520931 1.4358911 0.082047522
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100000 0.54266361 1.0959698 1.6386334 -0.13092175
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Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms
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Performance: 2242290.202 tau/day, 25952.433 timesteps/s
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98.8% CPU use with 1 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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---------------------------------------------------------------
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Pair | 2.3917 | 2.3917 | 2.3917 | 0.0 | 62.07
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Neigh | 0.012386 | 0.012386 | 0.012386 | 0.0 | 0.32
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Comm | 0.11307 | 0.11307 | 0.11307 | 0.0 | 2.93
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Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 0.03
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Modify | 1.246 | 1.246 | 1.246 | 0.0 | 32.34
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Other | | 0.08895 | | | 2.31
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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: 55 ave 55 max 55 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 55
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Ave neighs/atom = 1.71875
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Neighbor list builds = 2886
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Dangerous builds = 0
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Total wall time: 0:00:03
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