forked from lijiext/lammps
225 lines
10 KiB
Groff
225 lines
10 KiB
Groff
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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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 = 0.000329733 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 0.51467204 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 0.57710119 0.069052154 0.64615335 0.00053937664
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6000 0.53848104 0.041891152 0.58037219 0.0018693259
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7000 0.61777485 0.033380825 0.65115568 0.0027584782
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8000 0.47427732 0.059553658 0.53383098 0.017087698
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9000 0.46820943 0.064379697 0.53258913 0.02325702
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10000 0.46605511 0.02332689 0.489382 0.013699209
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11000 0.57547516 0.090133398 0.66560855 0.0083913962
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12000 0.465348 0.084853345 0.55020135 0.006231552
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13000 0.55340889 0.07116165 0.62457054 0.030622563
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14000 0.58866362 0.052281859 0.64094548 0.0079106838
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15000 0.51757672 0.12255618 0.6401329 0.014005369
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16000 0.42696011 0.086987541 0.51394765 -0.0017128649
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17000 0.37612579 0.13054778 0.50667357 0.0046284992
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18000 0.47659682 0.14670523 0.62330205 0.02206928
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19000 0.47897909 0.15540332 0.63438241 0.02544138
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20000 0.59377323 0.15357757 0.7473508 0.030262926
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21000 0.52781204 0.22074491 0.74855695 -0.0022170167
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22000 0.44843285 0.12779345 0.5762263 0.0097268482
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23000 0.60400735 0.18098124 0.78498858 0.05778325
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24000 0.58254338 0.1570243 0.73956769 0.022530491
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25000 0.60524318 0.23660272 0.8418459 0.062530421
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26000 0.45892702 0.34294121 0.80186823 0.038657393
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27000 0.58418023 0.19551937 0.7796996 -0.0055396645
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28000 0.45655369 0.26718934 0.72374303 0.006593108
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29000 0.50277299 0.1747088 0.67748179 0.016059369
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30000 0.38640717 0.1631573 0.54956447 0.036055723
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31000 0.46944541 0.22076826 0.69021367 0.014334038
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32000 0.53862858 0.26867594 0.80730452 0.057406282
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33000 0.45666352 0.21796554 0.67462906 0.056555205
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34000 0.51644038 0.21866786 0.73510824 0.015713
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35000 0.50489584 0.1596236 0.66451945 0.040400644
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36000 0.41723489 0.16227853 0.57951342 0.02863261
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37000 0.481638 0.28830624 0.76994424 0.038381986
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38000 0.6036094 0.33479287 0.93840227 0.0032059452
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39000 0.47822122 0.18876355 0.66698476 0.029252649
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40000 0.54949607 0.35011086 0.89960693 0.093909148
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41000 0.54876522 0.27501735 0.82378257 -0.0084167014
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42000 0.67801592 0.18102522 0.85904114 -0.0058395209
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43000 0.54342066 0.34322081 0.88664146 0.12263806
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44000 0.46672513 0.29749157 0.76421671 0.051073701
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45000 0.4679867 0.25820875 0.72619545 0.069790993
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46000 0.59598501 0.22285276 0.81883777 0.050578807
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47000 0.48858341 0.29811577 0.78669917 0.080971431
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48000 0.41238073 0.29362937 0.7060101 0.031893588
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49000 0.61516435 0.33082609 0.94599044 -0.010710982
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50000 0.57576635 0.37137185 0.94713819 0.062160249
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51000 0.54614001 0.36960628 0.91574629 -0.0083424769
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52000 0.42232354 0.25214442 0.67446796 0.028666126
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53000 0.43025129 0.24479385 0.67504514 0.030342054
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54000 0.54614922 0.29602426 0.84217348 0.083070642
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55000 0.60719748 0.3577285 0.96492598 0.053799744
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56000 0.47073149 0.31070429 0.78143579 0.083895368
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57000 0.56861582 0.33249784 0.90111366 0.032324233
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58000 0.75061035 0.33313728 1.0837476 0.031039937
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59000 0.59473893 0.48870773 1.0834467 0.039503585
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60000 0.55252481 0.38350562 0.93603043 0.0027643882
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61000 0.45010855 0.43945065 0.8895592 0.028168222
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62000 0.63942467 0.53372899 1.1731537 0.13790959
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63000 0.69407873 0.37980402 1.0738828 0.035919608
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64000 0.54898275 0.39910419 0.94808693 0.0015016851
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65000 0.58229838 0.42300361 1.005302 0.089787193
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66000 0.53443537 0.5597136 1.094149 -0.015781756
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67000 0.59212426 0.56172146 1.1538457 0.030464683
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68000 0.68164926 0.48724393 1.1688932 0.071465948
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69000 0.59721737 0.49476309 1.0919805 0.07575647
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70000 0.52314551 0.31950477 0.84265028 0.11206672
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71000 0.53230509 0.53846575 1.0707708 0.0047204701
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72000 0.71341933 0.4924749 1.2058942 0.116568
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73000 0.70498496 0.54121008 1.246195 0.11210249
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74000 0.54188682 0.61729607 1.1591829 0.044083048
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75000 0.44073609 0.42072284 0.86145893 -0.041508511
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76000 0.51225567 0.36848317 0.88073884 -0.028636748
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77000 0.6517329 0.5503086 1.2020415 0.049605026
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78000 0.60053898 0.52760266 1.1281416 0.094361256
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79000 0.51560788 0.46563043 0.98123832 -0.03336136
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80000 0.53357884 0.60743981 1.1410186 0.027259883
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81000 0.6256228 0.40412923 1.029752 0.083274981
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82000 0.6903519 0.69599412 1.386346 0.168747
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83000 0.62621394 0.50082841 1.1270424 0.12294403
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84000 0.5682146 0.73827702 1.3064916 0.085884707
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85000 0.48179077 0.73669563 1.2184864 0.065002035
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86000 0.61101399 0.80673836 1.4177523 0.037555163
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87000 0.52278725 0.71608722 1.2388745 0.020943688
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88000 0.53318823 0.50916748 1.0423557 -0.01946691
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89000 0.56428713 0.56042234 1.1247095 0.040998134
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90000 0.58720508 0.66023073 1.2474358 0.040313529
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91000 0.61509407 0.86254343 1.4776375 0.15215034
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92000 0.5640475 0.57694543 1.1409929 0.10238679
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93000 0.60586378 0.67978456 1.2856483 -0.043948113
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94000 0.75406595 0.74795347 1.5020194 0.015341415
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95000 0.4974314 0.60192267 1.0993541 -0.018173218
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96000 0.50048302 0.82845218 1.3289352 0.045394283
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97000 0.65335222 0.6470855 1.3004377 0.011624967
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98000 0.65693072 0.45222133 1.109152 0.13763684
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99000 0.60573344 0.50284289 1.1085763 0.12853674
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100000 0.50677068 0.58143063 1.0882013 0.11351254
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Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms
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Performance: 2661396.711 tau/day, 30803.203 timesteps/s
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94.4% 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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---------------------------------------------------------------
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Pair | 0.64148 | 0.70244 | 0.76391 | 6.5 | 21.64
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Neigh | 0.0049012 | 0.0050417 | 0.0052478 | 0.2 | 0.16
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Comm | 0.79447 | 0.88412 | 0.97443 | 8.1 | 27.23
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Output | 0.001776 | 0.0031438 | 0.0072262 | 4.2 | 0.10
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Modify | 1.325 | 1.3684 | 1.4049 | 2.4 | 42.15
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Other | | 0.2833 | | | 8.73
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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: 14 ave 15 max 13 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 13.25 ave 16 max 11 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Total # of neighbors = 53
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Ave neighs/atom = 1.65625
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Neighbor list builds = 2654
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Dangerous builds = 0
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Total wall time: 0:00:03
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