198 lines
15 KiB
Groff
198 lines
15 KiB
Groff
LAMMPS (8 Feb 2023)
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Processor partition = 4
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 32 pad
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variable out_freq string 100
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variable job_name string H2
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units real
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atom_style full
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pair_style table linear 10000
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neighbor 2.0 bin
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neigh_modify every 1 delay 0 check no
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read_data H2.data
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Reading data file ...
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orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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180 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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pair_coeff 1 * pair.table PAIR_H2
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WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
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WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
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timestep 0.001
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velocity all create 1.0 1985 rot yes dist gaussian
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fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
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thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
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thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
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thermo ${out_freq}
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thermo 100
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#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
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#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
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run 10000
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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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 = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11.55117
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ghost atom cutoff = 11.55117
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binsize = 5.775585, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
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Step Temp PotEng TotEng Pzz espring T_ring virial
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0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14
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100 0.99799183 -50.292972 -49.760479 16.17637 1.1826193e-13 15.879159 -0.0025913805
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200 0.99208279 -50.292959 -49.763618 16.157337 7.489305e-12 15.785139 -0.0051808234
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300 0.98260503 -50.292946 -49.768662 16.126285 8.3895453e-11 15.634338 -0.0077662384
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400 0.97006821 -50.292933 -49.775339 16.085117 4.6129385e-10 15.434863 -0.010346287
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500 0.955104 -50.292921 -49.783311 16.036242 1.7157587e-09 15.196766 -0.012920943
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600 0.93840577 -50.292907 -49.792206 15.982224 4.9828406e-09 14.931079 -0.015491155
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700 0.92067358 -50.292891 -49.801652 15.925608 1.2201305e-08 14.64894 -0.018055916
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800 0.90257157 -50.292875 -49.811294 15.868782 2.6375763e-08 14.360917 -0.020616424
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900 0.88470061 -50.292856 -49.820811 15.813794 5.1849593e-08 14.07657 -0.02317448
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1000 0.86758559 -50.292836 -49.829923 15.762447 9.4579685e-08 13.804251 -0.025732882
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1100 0.85167475 -50.292814 -49.83839 15.716171 1.6240678e-07 13.551092 -0.028294045
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1200 0.83734745 -50.29279 -49.846011 15.676049 2.6532099e-07 13.323128 -0.030863385
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1300 0.82492738 -50.292764 -49.852612 15.643102 4.1573034e-07 13.125511 -0.033446749
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1400 0.81469842 -50.292737 -49.858042 15.618114 6.287493e-07 12.962757 -0.036050518
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1500 0.80692176 -50.292706 -49.862161 15.601972 9.2253166e-07 12.839022 -0.038681006
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1600 0.80185333 -50.292674 -49.864833 15.595319 1.3186783e-06 12.758377 -0.041346087
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1700 0.79976154 -50.292639 -49.865914 15.598922 1.8427553e-06 12.725095 -0.044055451
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1800 0.80094538 -50.2926 -49.865244 15.613674 2.524964e-06 12.743931 -0.046819731
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1900 0.80575381 -50.292559 -49.862637 15.640669 3.4010112e-06 12.820438 -0.049651934
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2000 0.81460709 -50.292514 -49.857868 15.681364 4.5132409e-06 12.961304 -0.052564979
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2100 0.82802133 -50.292465 -49.850661 15.73743 5.9121027e-06 13.174739 -0.055577058
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2200 0.84663739 -50.29241 -49.840674 15.810925 7.658054e-06 13.470942 -0.058707326
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2300 0.87125574 -50.292349 -49.827477 15.904535 9.82402e-06 13.862647 -0.061977077
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2400 0.90287875 -50.29228 -49.810536 16.021749 1.2498571e-05 14.365804 -0.065412927
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2500 0.94276188 -50.292203 -49.789178 16.16688 1.5790021e-05 15.000389 -0.069043572
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2600 0.99247524 -50.292117 -49.762567 16.345151 1.9831692e-05 15.791384 -0.072902664
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2700 1.0539756 -50.292019 -49.729655 16.56334 2.4788664e-05 16.769923 -0.077026939
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2800 1.1296879 -50.291903 -49.689141 16.830177 3.0866362e-05 17.97459 -0.081462018
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2900 1.222591 -50.29177 -49.639438 17.155398 3.8321389e-05 19.45278 -0.086262136
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3000 1.3362974 -50.291614 -49.578613 17.551553 4.7474995e-05 21.261976 -0.091484095
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3100 1.4751088 -50.291433 -49.504367 18.033555 5.872952e-05 23.47062 -0.097184337
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3200 1.6440134 -50.291218 -49.41403 18.618802 7.2587889e-05 26.158079 -0.10344427
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3300 1.8485776 -50.290963 -49.304627 19.3265 8.9675809e-05 29.412924 -0.11033444
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3400 2.0946648 -50.290659 -49.17302 20.177003 0.00011076549 33.328444 -0.11794183
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3500 2.3878978 -50.290296 -49.016197 21.189599 0.00013679846 37.994106 -0.12634541
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3600 2.7327842 -50.289862 -48.831744 22.380493 0.0001689033 43.481633 -0.13563052
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3700 3.1314527 -50.289342 -48.618508 23.757417 0.00020840179 49.824892 -0.1458703
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3800 3.5820304 -50.288721 -48.377475 25.31432 0.00025679499 56.994084 -0.15714078
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3900 4.0768367 -50.287983 -48.112726 27.026228 0.0003157187 64.867001 -0.1694959
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4000 4.6007641 -50.287108 -47.832302 28.841926 0.0003868587 73.203268 -0.18296156
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4100 5.1304148 -50.286087 -47.548677 30.682328 0.00047181946 81.6306 -0.19756083
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4200 5.6346511 -50.284903 -47.278451 32.442736 0.00057194846 89.653559 -0.21328268
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4300 6.0770778 -50.283545 -47.041029 33.999964 0.00068813116 96.69306 -0.23008376
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4400 6.4205225 -50.282013 -46.856246 35.229403 0.00082058594 102.15765 -0.24791296
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4500 6.6328762 -50.280301 -46.74123 36.023883 0.0009687004 105.53643 -0.26668503
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4600 6.6929711 -50.278423 -46.707288 36.312847 0.0011309529 106.49261 -0.28630381
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4700 6.5948589 -50.27639 -46.757604 36.078132 0.0013049526 104.93153 -0.3066628
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4800 6.3491697 -50.274211 -46.886517 35.357678 0.0014876083 101.02235 -0.32764627
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4900 5.9811042 -50.271915 -47.080607 34.23668 0.0016754063 95.166014 -0.34912704
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5000 5.5256699 -50.269516 -47.321212 32.833829 0.001864752 87.919547 -0.37098454
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5100 5.0215364 -50.267032 -47.587716 31.279327 0.002052314 79.898224 -0.39310129
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5200 4.5051023 -50.264473 -47.860708 29.694368 0.0022353117 71.681183 -0.41536062
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5300 4.0060486 -50.261854 -48.124367 28.177158 0.0024117009 63.740684 -0.43765657
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5400 3.5450378 -50.259179 -48.367671 26.795368 0.0025802379 56.405491 -0.45989585
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5500 3.1335423 -50.256452 -48.584504 25.585853 0.0027404289 49.858139 -0.48198401
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5600 2.7752685 -50.253675 -48.772889 24.559285 0.0028923937 44.157606 -0.50383681
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5700 2.4683952 -50.250848 -48.933799 23.707506 0.0030366865 39.27491 -0.52540813
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5800 2.2078802 -50.247975 -49.069927 23.012724 0.0031741148 35.129826 -0.54664422
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5900 1.987342 -50.245052 -49.184676 22.453088 0.0033055867 31.62082 -0.56749825
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6000 1.8003231 -50.242086 -49.281496 22.005599 0.0034320005 28.645141 -0.5879444
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6100 1.6409782 -50.239078 -49.363509 21.650929 0.0035541789 26.109787 -0.6079799
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6200 1.5043457 -50.236031 -49.433365 21.372354 0.0036728367 23.935811 -0.62757526
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6300 1.3863692 -50.23295 -49.493232 21.15608 0.0037885737 22.058674 -0.64672985
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6400 1.2838 -50.229836 -49.544845 20.99171 0.0039018814 20.426685 -0.66545129
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6500 1.1940599 -50.2267 -49.589591 20.870492 0.0040131566 18.998819 -0.68374953
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6600 1.115105 -50.223537 -49.628556 20.785791 0.0041227168 17.742559 -0.70162987
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6700 1.0453095 -50.220351 -49.66261 20.732525 0.0042308155 16.632035 -0.7190951
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6800 0.98337083 -50.217149 -49.692456 20.706334 0.0043376557 15.646523 -0.73616716
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6900 0.92823665 -50.213933 -49.718658 20.703509 0.0044434008 14.769276 -0.75286641
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7000 0.87904844 -50.210704 -49.741675 20.721268 0.0045481845 13.986637 -0.7692006
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7100 0.83509929 -50.207463 -49.761883 20.757758 0.0046521178 13.287358 -0.78517926
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7200 0.79580187 -50.204208 -49.779596 20.810709 0.0047552948 12.662092 -0.80082697
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7300 0.76066442 -50.200945 -49.795082 20.878241 0.0048577976 12.103016 -0.8161606
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7400 0.72927251 -50.197671 -49.808557 20.959362 0.0049596993 11.603536 -0.83120088
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7500 0.70127548 -50.194387 -49.820211 21.052437 0.0050610673 11.158072 -0.84595004
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7600 0.67637608 -50.191091 -49.830201 21.156826 0.005161965 10.761895 -0.86043159
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7700 0.65432278 -50.187783 -49.838659 21.271416 0.0052624536 10.411002 -0.87466503
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7800 0.63490405 -50.184459 -49.845696 21.395737 0.0053625933 10.102029 -0.88866261
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7900 0.61794415 -50.181125 -49.851412 21.52846 0.0054624448 9.8321781 -0.90243744
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8000 0.60330004 -50.177777 -49.855877 21.669443 0.0055620701 9.599174 -0.91600112
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8100 0.59085898 -50.174411 -49.859149 21.81797 0.0056615336 9.4012229 -0.92936588
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8200 0.58053641 -50.171025 -49.861271 21.974141 0.0057609033 9.2369793 -0.94255403
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8300 0.57227364 -50.16762 -49.862274 22.13688 0.0058602524 9.1055094 -0.95557385
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8400 0.5660345 -50.164193 -49.862177 22.306138 0.0059596607 9.0062378 -0.9684373
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8500 0.56180048 -50.160744 -49.860987 22.48185 0.0060592167 8.9388698 -0.98115048
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8600 0.55956345 -50.15727 -49.858706 22.663291 0.0061590199 8.9032763 -0.9937296
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8700 0.55931575 -50.15377 -49.855339 22.850832 0.0062591826 8.899335 -1.0061868
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8800 0.56103758 -50.150241 -49.850891 23.043918 0.006359832 8.9267313 -1.0185265
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8900 0.564683 -50.146681 -49.845386 23.242887 0.0064611118 8.984734 -1.0307694
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9000 0.57016633 -50.143095 -49.838874 23.44706 0.0065631821 9.0719798 -1.0429186
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9100 0.57735215 -50.139473 -49.831418 23.657034 0.0066662188 9.1863142 -1.0549883
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9200 0.58605231 -50.13582 -49.823123 23.872662 0.0067704103 9.3247434 -1.0669874
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9300 0.59603298 -50.132131 -49.814109 24.094175 0.0068759533 9.483547 -1.078929
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9400 0.60703315 -50.128412 -49.80452 24.321354 0.0069830466 9.6585719 -1.0908215
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9500 0.61879332 -50.124656 -49.79449 24.554693 0.0070918841 9.8456893 -1.1026826
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9600 0.63108995 -50.120866 -49.784139 24.794372 0.0072026473 10.041342 -1.1145246
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9700 0.64376884 -50.117043 -49.773551 25.040354 0.0073154993 10.243078 -1.1263585
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9800 0.6567696 -50.113185 -49.762755 25.293643 0.00743058 10.449934 -1.1381891
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9900 0.67013503 -50.109296 -49.751736 25.553866 0.0075480045 10.662593 -1.150037
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10000 0.68400233 -50.105373 -49.740413 25.821695 0.007667864 10.883237 -1.1619081
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Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
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Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
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96.6% 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 | 2.9541 | 2.9541 | 2.9541 | 0.0 | 20.11
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Bond | 0.00096595 | 0.00096595 | 0.00096595 | 0.0 | 0.01
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Neigh | 6.6965 | 6.6965 | 6.6965 | 0.0 | 45.58
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Comm | 0.55386 | 0.55386 | 0.55386 | 0.0 | 3.77
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Output | 0.0030352 | 0.0030352 | 0.0030352 | 0.0 | 0.02
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Modify | 4.4131 | 4.4131 | 4.4131 | 0.0 | 30.04
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Other | | 0.06945 | | | 0.47
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Nlocal: 180 ave 180 max 180 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1510 ave 1510 max 1510 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 13680 ave 13680 max 13680 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 13680
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Ave neighs/atom = 76
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Ave special neighs/atom = 0
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Neighbor list builds = 10000
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Dangerous builds not checked
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Total wall time: 0:00:14
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