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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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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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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2 by 2 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) = 5.379 | 5.379 | 5.379 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 0.0054997327
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9000 0.93104065 0.071628784 1.0026694 0.011330629
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10000 0.75494389 0.15204106 0.90698496 0.021702127
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11000 0.72349155 0.11102332 0.83451487 0.019264192
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12000 0.56216536 0.11705898 0.67922434 -0.028296196
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13000 0.63793556 0.11701866 0.75495421 0.029469295
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14000 0.62999448 0.020866813 0.65086129 0.008609569
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15000 0.6404504 0.0090011224 0.64945152 0.01706906
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16000 0.70195749 0.044735201 0.74669269 0.0179597
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17000 0.69097976 0.03894214 0.72992191 0.015704476
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18000 0.75303457 0.0019263825 0.75496095 0.021536711
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19000 0.6459718 0.10419136 0.75016317 0.033861092
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20000 0.73026363 0.13023974 0.86050337 0.022207497
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21000 0.77107035 0.30464112 1.0757115 0.013967631
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22000 0.44134768 0.22883887 0.67018655 0.014202518
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23000 0.53410601 0.16702381 0.70112983 0.009305779
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24000 0.5144312 0.19041122 0.70484242 -0.0059836303
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25000 0.60922681 0.15475207 0.76397888 0.016370526
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26000 0.70922367 0.25374443 0.9629681 0.027301754
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27000 0.67289133 0.39287626 1.0657676 0.025562031
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28000 0.62112601 0.017177715 0.63830372 0.018556767
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29000 0.56492546 0.087573524 0.65249898 0.025132036
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30000 0.62612507 -0.01835118 0.60777389 0.050139664
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31000 0.69157641 0.064849873 0.75642628 0.033954585
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32000 0.72648211 0.08597545 0.81245756 0.038082388
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33000 0.58608821 0.13013111 0.71621932 0.054766043
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34000 0.49330983 0.080490598 0.57380043 0.034154681
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35000 0.54570666 0.075020466 0.62072713 0.03879264
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36000 0.60305736 0.10717781 0.71023516 0.030701059
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37000 0.52801767 0.12516316 0.65318083 0.007411688
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38000 0.5838277 0.12569072 0.70951842 0.03272916
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39000 0.53999819 0.043261294 0.58325949 0.084115917
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40000 0.64957099 0.040023268 0.68959426 0.027021958
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41000 0.59235949 0.10449793 0.69685742 0.045773377
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42000 0.71752786 0.043289363 0.76081722 0.040926021
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43000 0.78581005 0.024363927 0.81017398 0.034694164
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44000 0.6396541 0.06004252 0.69969662 0.037227348
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45000 0.35753293 0.11456039 0.47209332 0.033569048
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46000 0.11031158 0.11831834 0.22862991 0.076545681
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47000 0.11720754 0.035471414 0.15267896 0.022093929
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48000 0.13370328 0.031802339 0.16550562 0.053298269
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49000 0.2700883 0.15584422 0.42593252 0.057108168
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50000 0.53837779 0.13398219 0.67235998 0.047704986
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51000 0.38133073 0.011372933 0.39270366 0.04696367
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52000 0.32448241 0.009137008 0.33361942 0.033573259
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53000 0.25798301 -0.016530605 0.2414524 0.04623663
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54000 0.2842707 0.054504088 0.33877479 0.03751156
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55000 0.28895106 0.025307766 0.31425882 0.03935955
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56000 0.19130753 0.099678989 0.29098652 0.051888728
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57000 0.12237303 0.057536458 0.17990949 0.09984021
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58000 0.17962003 0.012450682 0.19207072 0.028644351
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59000 0.21667262 -0.013693164 0.20297945 0.048086277
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60000 0.4298123 -0.012970819 0.41684148 0.019347498
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61000 0.69591654 -0.027048452 0.66886809 0.069793861
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62000 1.0040382 -0.044228622 0.95980957 0.056563167
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63000 0.78189663 -0.053045577 0.72885106 0.059491526
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64000 0.57051419 -0.050757181 0.51975701 0.061863162
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65000 0.62584243 -0.050616328 0.5752261 0.068924362
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66000 0.85558894 -0.051396155 0.80419278 0.059309337
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67000 0.86314978 -0.052635701 0.81051408 0.071855924
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68000 0.65427495 -0.05147951 0.60279544 0.064001735
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69000 0.60658011 -0.050623824 0.55595629 0.0715805
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70000 0.76353932 -0.050863795 0.71267553 0.06771349
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71000 0.87559332 -0.051720153 0.82387317 0.071884106
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72000 0.71924774 -0.051167456 0.66808029 0.071010747
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73000 0.6100998 -0.050025233 0.56007457 0.073319802
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74000 0.71838075 -0.049907287 0.66847346 0.07314982
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75000 0.91863251 -0.051069435 0.86756308 0.07493433
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76000 0.78459189 -0.050803207 0.73378868 0.075397431
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77000 0.70827012 -0.049701237 0.65856888 0.076901086
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78000 0.72333497 -0.04940986 0.67392511 0.077456938
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79000 0.76543474 -0.049588137 0.7158466 0.078792278
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80000 0.77759003 -0.049596899 0.72799313 0.079470668
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81000 0.67474562 -0.048929658 0.62581596 0.080740407
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82000 0.60162355 -0.047698966 0.55392459 0.081758686
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83000 0.7602675 -0.047827179 0.71244032 0.082547083
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84000 0.9061851 -0.049481366 0.85670374 0.083443845
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85000 0.74071256 -0.048645397 0.69206717 0.084605474
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86000 0.67634638 -0.046894309 0.62945207 0.085608904
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87000 0.71669859 -0.046524067 0.67017453 0.086561551
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88000 0.77025498 -0.047090994 0.72316398 0.087515495
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89000 0.76590655 -0.047083362 0.71882319 0.088522842
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90000 0.61372503 -0.045529779 0.56819526 0.08963777
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91000 0.58583927 -0.043777544 0.54206173 0.093090208
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92000 0.80507421 -0.04423346 0.76084075 0.093861418
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93000 0.84631942 -0.046878171 0.79944125 0.093279847
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94000 0.70915593 -0.04570489 0.66345104 0.092425564
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95000 0.66813988 -0.043460537 0.62467934 0.093467021
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96000 0.71739316 -0.042402374 0.67499079 0.095183179
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97000 0.74132854 -0.042457291 0.69887124 0.096665917
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98000 0.74033914 -0.042269007 0.69807013 0.097869908
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99000 0.72447372 -0.041519159 0.68295457 0.098825459
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100000 0.6968193 -0.040321034 0.65649827 0.099797629
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Loop time of 2.55809 on 4 procs for 100000 steps with 32 atoms
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Performance: 3377521.712 tau/day, 39091.686 timesteps/s, 1.251 Matom-step/s
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91.9% 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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Pair | 0.53547 | 0.78258 | 1.0169 | 21.0 | 30.59
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Neigh | 0.0010868 | 0.0011973 | 0.0013608 | 0.3 | 0.05
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Comm | 0.57019 | 0.78963 | 1.0091 | 19.2 | 30.87
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Output | 0.00075581 | 0.0030547 | 0.0098741 | 7.1 | 0.12
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Modify | 0.80723 | 0.81855 | 0.83849 | 1.3 | 32.00
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Other | | 0.1631 | | | 6.37
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Nlocal: 8 ave 12 max 2 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 15.25 ave 19 max 13 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Neighs: 12 ave 18 max 1 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 48
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Ave neighs/atom = 1.5
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Neighbor list builds = 1420
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Dangerous builds = 0
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Total wall time: 0:00:02
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