forked from lijiext/lammps
227 lines
12 KiB
Groff
227 lines
12 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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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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Reading data file ...
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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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read_data CPU = 0.001 seconds
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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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Replication is creating a 4x4x1 = 16 times larger system...
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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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replicate CPU = 0.001 seconds
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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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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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 = 6.1568542
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ghost atom cutoff = 6.1568542
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binsize = 3.0784271, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.386 | 5.386 | 5.386 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 0.39720235 0.0015845731 0.39878692 0.00223489
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2000 0.42893425 0.011718891 0.44065314 0.0027413224
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3000 0.57823511 0.012407489 0.5906426 0.0025306081
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4000 0.71610647 0.028149437 0.74425591 0.0016504948
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5000 0.84027279 0.018917017 0.8591898 0.0037451875
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6000 0.72410001 0.073495378 0.79759539 0.00018672875
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7000 0.53886484 0.077723366 0.61658821 0.004729216
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8000 0.66196054 0.05502242 0.71698296 0.0054997323
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9000 0.93104065 0.071628784 1.0026694 0.011330629
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10000 0.75494389 0.15204106 0.90698495 0.021702117
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11000 0.72349154 0.11102332 0.83451486 0.019264158
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12000 0.56216531 0.117059 0.67922431 -0.028295891
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13000 0.63793498 0.11701868 0.75495366 0.029470631
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14000 0.62996509 0.020871971 0.65083706 0.0086224023
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15000 0.6403927 0.0091092209 0.64950192 0.016897685
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16000 0.70288045 0.046856749 0.7497372 0.02312871
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17000 0.6820593 0.038994474 0.72105377 0.0068705173
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18000 0.75623543 0.0069908315 0.76322626 0.025170959
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19000 0.85962145 0.059005169 0.91862661 0.012725758
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20000 0.73334823 0.033043489 0.76639172 0.023661433
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21000 0.60850654 0.081277767 0.68978431 0.021031136
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22000 0.38251144 0.27624263 0.65875407 0.047336318
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23000 0.4288127 0.30632792 0.73514062 0.034108416
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24000 0.4452138 0.13179024 0.57700404 0.010303821
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25000 0.48091107 0.1816109 0.66252197 0.021201342
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26000 0.67970784 0.088616708 0.76832455 0.034997245
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27000 0.8223642 0.08699442 0.90935862 0.023508839
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28000 0.60062179 0.1119578 0.71257959 -0.0010008016
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29000 0.54629437 0.1202995 0.66659387 0.040613547
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30000 0.28102412 0.38657163 0.66759575 -0.0086538064
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31000 0.12433474 0.18824131 0.31257605 0.049899211
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32000 0.089510322 0.20890679 0.29841711 0.045555094
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33000 0.12657665 0.17720119 0.30377784 0.028306214
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34000 0.18400652 0.17677189 0.36077841 0.034628531
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35000 0.24048631 0.11010844 0.35059475 0.029848365
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36000 0.33435006 0.077341882 0.41169194 0.055963098
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37000 0.46088842 0.1210638 0.58195222 0.072006022
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38000 0.76551752 0.07037755 0.83589507 0.018204686
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39000 0.89388464 0.080990198 0.97487484 0.038361105
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40000 0.65618718 0.078644754 0.73483193 0.040567246
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41000 0.47284043 0.16391389 0.63675432 0.027523843
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42000 0.52454668 0.057988616 0.58253529 0.03122996
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43000 0.78769394 0.08405077 0.87174471 0.044743697
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44000 0.92932837 0.093922981 1.0232514 0.042510479
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45000 0.5722596 0.17607834 0.74833794 0.034646914
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46000 0.54352389 0.085652886 0.62917677 0.033203865
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47000 0.45608912 0.25183842 0.70792754 0.08370224
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48000 0.47530886 0.10106466 0.57637352 0.046113986
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49000 0.67945305 0.0065249477 0.68597799 0.054743491
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50000 0.49661922 0.097381596 0.59400082 0.006998965
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51000 0.60992235 0.059017331 0.66893968 0.09445106
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52000 0.69563455 0.18702969 0.88266424 0.034154598
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53000 0.87598532 0.18260917 1.0585945 0.065734536
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54000 0.58822846 0.27562038 0.86384884 0.0764045
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55000 0.43454899 0.17174441 0.6062934 0.026434052
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56000 0.4004495 0.12778644 0.52823594 0.065986005
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57000 0.36272102 0.09849578 0.4612168 0.064217596
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58000 0.40987214 0.21777618 0.62764832 0.058625636
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59000 0.64813089 0.1479689 0.79609979 0.033378701
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60000 0.90328265 0.11049926 1.0137819 0.055828397
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61000 0.82921839 0.074638688 0.90385707 0.062488824
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62000 0.63223087 0.094386302 0.72661718 0.054784559
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63000 0.62946839 0.087807829 0.71727622 0.058398323
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64000 0.79784108 0.094756776 0.89259786 0.065765914
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65000 0.87500942 0.13514078 1.0101502 0.068123475
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66000 0.66961949 0.19942965 0.86904914 0.065587832
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67000 0.61612396 0.11436282 0.73048678 0.061233427
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68000 0.74149449 0.03129016 0.77278465 0.072517897
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69000 0.84060202 0.027261803 0.86786382 0.063374451
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70000 0.78182528 0.023528774 0.80535405 0.07431822
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71000 0.71611101 0.023512727 0.73962374 0.069575276
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72000 0.68437263 0.023941199 0.70831382 0.069821154
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73000 0.75652323 0.023580324 0.78010355 0.075046425
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74000 0.92077658 0.023272419 0.944049 0.070992373
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75000 0.75277766 0.023186631 0.77596429 0.074859227
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76000 0.59333539 0.024276648 0.61761204 0.076132037
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77000 0.68243436 0.024600726 0.70703508 0.075525977
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78000 0.79699751 0.024238959 0.82123647 0.078255526
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79000 0.77318109 0.024249895 0.79743099 0.078223339
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80000 0.72004911 0.024522473 0.74457159 0.079009398
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81000 0.71732947 0.024702988 0.74203245 0.080902007
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82000 0.73395391 0.024817681 0.75877159 0.081203115
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83000 0.74389794 0.02487774 0.76877568 0.082273058
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84000 0.73219737 0.024967311 0.75716468 0.08359401
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85000 0.66523255 0.025299293 0.69053184 0.084260931
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86000 0.67031201 0.02564609 0.6959581 0.085495986
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87000 0.81345283 0.025297963 0.8387508 0.086292085
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88000 0.85008513 0.024879647 0.87496478 0.087116741
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89000 0.62893149 0.025674927 0.65460642 0.088514693
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90000 0.58336052 0.026632218 0.60999274 0.089459637
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91000 0.72615388 0.026181899 0.75233578 0.090289473
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92000 0.76593408 0.025893082 0.79182717 0.091294308
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93000 0.73475998 0.026113022 0.76087301 0.092256366
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94000 0.68995562 0.026409704 0.71636532 0.093332419
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95000 0.69491284 0.026726159 0.721639 0.094314615
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96000 0.83274635 0.026420125 0.85916648 0.09513317
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97000 0.85486073 0.025941089 0.88080181 0.096122793
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98000 0.63095894 0.027021709 0.65798064 0.097348373
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99000 0.60847495 0.027908563 0.63638351 0.098362493
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100000 0.75867487 0.027331375 0.78600625 0.099184572
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Loop time of 3.87848 on 1 procs for 100000 steps with 32 atoms
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Performance: 2227674.150 tau/day, 25783.266 timesteps/s, 825.065 katom-step/s
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97.7% 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 | 2.9048 | 2.9048 | 2.9048 | 0.0 | 74.90
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Neigh | 0.0027304 | 0.0027304 | 0.0027304 | 0.0 | 0.07
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Comm | 0.071653 | 0.071653 | 0.071653 | 0.0 | 1.85
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Output | 0.00069287 | 0.00069287 | 0.00069287 | 0.0 | 0.02
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Modify | 0.85771 | 0.85771 | 0.85771 | 0.0 | 22.11
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Other | | 0.04088 | | | 1.05
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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: 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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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 = 1379
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Dangerous builds = 0
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Total wall time: 0:00:03
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