190 lines
12 KiB
Plaintext
190 lines
12 KiB
Plaintext
LAMMPS (18 Sep 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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# ***
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# Example input for including electronic stopping effects using fix elec/drag
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# Perfect Si lattice with one primary knock-on atom (PKA) - single species simulation
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# ***
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units metal
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boundary p p p
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lattice diamond 5.431
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Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
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region box block -15 15 -15 15 -15 15
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create_box 1 box
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Created orthogonal box = (-81.465000 -81.465000 -81.465000) to (81.465000 81.465000 81.465000)
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2 by 2 by 4 MPI processor grid
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create_atoms 1 box
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Created 216000 atoms
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create_atoms CPU = 0.004 seconds
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pair_style tersoff/zbl
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pair_coeff * * Si.tersoff.zbl Si
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mass 1 28.0855
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velocity all create 300 42534 mom yes rot yes
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group pka id 1
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1 atoms in group pka
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velocity pka set 1120 1620 400
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fix 1 all nve
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fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
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fix 3 all elec/drag 4.63 3.3e-3 4.0e-8
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thermo 20
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thermo_style custom step dt time temp pe ke f_3
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thermo_modify lost warn flush yes
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dump 0 all custom 200 dump.pka_* id type x y z vx vy vz fx fy fz
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dump_modify 0 first yes
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run 2000
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5
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ghost atom cutoff = 5
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binsize = 2.5, bins = 66 66 66
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/zbl, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.68 | 10.68 | 10.68 Mbytes
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Step Dt Time Temp PotEng KinEng f_3
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0 2.4879625e-05 0 6509.9241 -999992.11 181757.49 0
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20 5.8535376e-06 0.00018285984 6504.2109 -999911.08 181597.97 78.573248
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40 7.3437077e-06 0.00032558782 6501.6468 -999900.7 181526.38 139.85652
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60 5.7782387e-06 0.00048338337 6499.9817 -999922.1 181479.89 207.59157
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80 1.7803041e-05 0.00062201376 6498.3851 -999937.11 181435.31 267.07596
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100 5.7695724e-06 0.0008764226 6491.6929 -999859.81 181248.47 376.21265
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120 1.4719757e-06 0.00092268759 6488.491 -999790.21 181159.07 396.03972
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140 2.040106e-06 0.0009541283 6488.9044 -999815.23 181170.61 409.51037
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160 1.1709752e-05 0.0011249721 6489.6218 -999908.14 181190.64 482.73616
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180 1.4052166e-06 0.0012237574 6482.8292 -999761.21 181000.99 525.05834
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200 7.0645649e-07 0.0012432698 6478.465 -999647.7 180879.15 533.40945
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220 5.3086492e-07 0.0012554161 6475.6927 -999575.49 180801.74 538.60481
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240 4.7640655e-07 0.0012653882 6474.3494 -999542.24 180764.24 542.86876
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260 4.8787977e-07 0.0012749228 6474.3825 -999547.24 180765.16 546.9453
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280 5.7550217e-07 0.0012853466 6475.7725 -999590.51 180803.97 551.40265
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300 8.4917452e-07 0.0012989169 6478.5144 -999672.88 180880.52 557.20767
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320 3.2530619e-06 0.0013265212 6482.5081 -999796.2 180992.03 569.02383
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340 9.1659616e-06 0.0014955314 6481.8343 -999849.09 180973.22 641.40448
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360 1.3432453e-05 0.0017808405 6476.4943 -999822.19 180824.12 763.54528
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380 8.0104844e-06 0.0020958913 6469.4698 -999760.52 180628 898.31998
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400 3.3669621e-06 0.0022009729 6464.0253 -999653.36 180475.99 943.23198
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420 1.4887493e-05 0.0024115306 6462.9467 -999712.65 180445.87 1033.2068
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440 7.6182614e-06 0.0025715115 6457.6166 -999632.22 180297.06 1101.5392
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460 2.4972112e-05 0.0029551455 6450.3406 -999593.38 180093.91 1265.318
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480 2.3561752e-05 0.0032880532 6442.0409 -999503.89 179862.18 1407.3073
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500 1.4420455e-05 0.0035074129 6433.361 -999354.82 179619.84 1500.7814
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520 1.1816914e-05 0.0038239154 6427.2604 -999318.69 179449.51 1635.5741
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540 1.3748768e-05 0.0042004194 6417.4523 -999205.3 179175.67 1795.789
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560 7.52018e-06 0.0043887882 6409.6827 -999068.82 178958.74 1875.8751
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580 1.257523e-05 0.004616805 6405.6624 -999053.63 178846.49 1972.7564
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600 1.9968416e-06 0.00472482 6398.5405 -998900.91 178647.65 2018.6254
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620 1.5482324e-06 0.0047571463 6396.6815 -998862.7 178595.74 2032.3426
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640 1.011291e-05 0.0048098552 6397.7948 -998915.97 178626.83 2054.7096
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660 9.8205405e-06 0.0051044128 6390.8702 -998847.14 178433.49 2179.7236
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680 7.6429983e-06 0.0053365884 6383.8042 -998748.69 178236.21 2278.1889
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700 6.3388347e-06 0.0054927256 6378.4359 -998665.06 178086.33 2344.3656
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720 2.3522106e-06 0.0056227115 6372.253 -998548.02 177913.7 2399.4307
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740 6.4757544e-07 0.0056460538 6365.5083 -998369.63 177725.39 2409.3096
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760 3.8324351e-07 0.005656035 6359.7035 -998211.79 177563.32 2413.5291
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780 2.7394838e-07 0.005662533 6354.5359 -998070.25 177419.04 2416.2735
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800 2.1564956e-07 0.0056674054 6349.9385 -997943.95 177290.68 2418.3296
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820 1.8023193e-07 0.0056713554 6345.8823 -997832.36 177177.43 2419.9952
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840 1.5702192e-07 0.0056747244 6342.3522 -997735.22 177078.87 2421.4148
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860 1.4112901e-07 0.0056777042 6339.3392 -997652.35 176994.74 2422.6698
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880 1.3002216e-07 0.0056804148 6336.838 -997583.66 176924.91 2423.8107
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900 1.2228805e-07 0.0056829369 6334.8452 -997529.08 176869.27 2424.872
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920 1.1709975e-07 0.0056853297 6333.3582 -997488.57 176827.75 2425.8784
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940 1.1397036e-07 0.0056876388 6332.3755 -997462.1 176800.32 2426.8495
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960 1.1263139e-07 0.0056899026 6331.8956 -997449.65 176786.92 2427.8014
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980 1.1297372e-07 0.0056921557 6331.9175 -997451.21 176787.53 2428.7487
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1000 1.1502522e-07 0.0056944318 6332.44 -997466.76 176802.12 2429.7058
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1020 1.1895651e-07 0.0056967663 6333.4621 -997496.27 176830.65 2430.6875
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1040 1.2511681e-07 0.0056991998 6334.9825 -997539.75 176873.11 2431.711
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1060 1.3411487e-07 0.0057017822 6337.0003 -997597.17 176929.44 2432.7975
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1080 1.4698231e-07 0.0057045791 6339.514 -997668.53 176999.62 2433.9747
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1100 1.6551147e-07 0.0057076833 6342.5222 -997753.83 177083.61 2435.2818
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1120 1.9300845e-07 0.0057112358 6346.0234 -997853.08 177181.37 2436.7785
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1140 2.3618478e-07 0.0057154712 6350.015 -997966.31 177292.81 2438.564
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1160 3.108468e-07 0.0057208289 6354.4922 -998093.58 177417.82 2440.8243
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1180 4.6429306e-07 0.0057282929 6359.4421 -998234.93 177556.02 2443.9758
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1200 9.2816707e-07 0.0057409335 6364.8148 -998390.27 177706.03 2449.3178
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1220 2.0979021e-05 0.0058204095 6369.2961 -998548.29 177831.14 2482.9438
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1240 3.2882081e-06 0.0060039745 6361.0026 -998394.02 177599.59 2560.609
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1260 3.6924049e-06 0.0060569852 6359.1486 -998364.67 177547.82 2583.0193
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1280 9.1658886e-06 0.0063262182 6353.595 -998323.02 177392.77 2696.8502
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1300 6.8768211e-06 0.0064666219 6347.4618 -998210.93 177221.53 2756.1664
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1320 6.9121863e-06 0.0066088699 6342.5533 -998134.15 177084.48 2816.2408
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1340 7.0074085e-06 0.0067699237 6337.3331 -998056.53 176938.73 2884.2214
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1360 1.6151257e-06 0.0068943644 6330.8472 -997929.72 176757.65 2936.7264
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1380 5.1421721e-07 0.0069122062 6323.1882 -997723.46 176543.81 2944.2462
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1400 2.9444595e-07 0.0069200351 6315.8333 -997521.42 176338.46 2947.5417
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1420 2.0082068e-07 0.0069249277 6308.579 -997320.95 176135.92 2949.5985
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1440 1.4987791e-07 0.0069284157 6301.3823 -997121.48 175934.99 2951.0631
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1460 1.1822986e-07 0.0069310902 6294.2263 -996922.81 175735.19 2952.1847
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1480 9.683654e-08 0.0069332389 6287.1024 -996724.81 175536.29 2953.0847
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1500 8.1500357e-08 0.0069350221 6280.0061 -996527.43 175338.16 2953.8306
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1520 7.0019944e-08 0.0069365379 6272.9345 -996330.63 175140.72 2954.464
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1540 6.1135299e-08 0.0069378503 6265.8856 -996134.37 174943.92 2955.0117
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1560 5.4075905e-08 0.0069390034 6258.8583 -995938.65 174747.71 2955.4923
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1580 4.8345462e-08 0.0069400286 6251.8517 -995743.45 174552.09 2955.9191
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1600 4.3610621e-08 0.0069409491 6244.8652 -995548.77 174357.03 2956.3019
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1620 3.9639615e-08 0.0069417824 6237.8984 -995354.6 174162.51 2956.648
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1640 3.6266563e-08 0.0069425423 6230.951 -995160.95 173968.54 2956.9632
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1660 3.3369776e-08 0.0069432394 6224.0227 -994967.8 173775.1 2957.2521
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1680 3.0858062e-08 0.0069438824 6217.1135 -994775.16 173582.2 2957.5182
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1700 2.8661809e-08 0.0069444782 6210.2233 -994583.03 173389.82 2957.7644
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1720 2.6727002e-08 0.0069450326 6203.3521 -994391.41 173197.98 2957.9934
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1740 2.5011123e-08 0.0069455505 6196.4998 -994200.31 173006.66 2958.2069
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1760 2.3480268e-08 0.0069460359 6189.6665 -994009.73 172815.87 2958.4068
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1780 2.2107089e-08 0.0069464923 6182.8523 -993819.66 172625.62 2958.5946
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1800 2.0869294e-08 0.0069469224 6176.0571 -993630.11 172435.9 2958.7713
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1820 1.9748543e-08 0.006947329 6169.2811 -993441.1 172246.71 2958.9382
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1840 1.8729611e-08 0.0069477141 6162.5244 -993252.61 172058.06 2959.0961
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1860 1.7799764e-08 0.0069480797 6155.787 -993064.65 171869.96 2959.2458
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1880 1.6948273e-08 0.0069484275 6149.0691 -992877.23 171682.39 2959.388
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1900 1.6166034e-08 0.006948759 6142.3708 -992690.34 171495.37 2959.5234
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1920 1.5445281e-08 0.0069490753 6135.6922 -992504.01 171308.91 2959.6525
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1940 1.4779344e-08 0.0069493778 6129.0335 -992318.22 171123 2959.7757
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1960 1.4162469e-08 0.0069496675 6122.3947 -992132.98 170937.64 2959.8936
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1980 1.3589666e-08 0.0069499452 6115.776 -991948.3 170752.85 2960.0066
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2000 1.3056587e-08 0.0069502119 6109.1776 -991764.18 170568.62 2960.1149
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Loop time of 102.285 on 16 procs for 2000 steps with 216000 atoms
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Performance: 0.000 ns/day, 1088049.652 hours/ns, 19.553 timesteps/s
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99.5% CPU use with 16 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 | 86.624 | 87.611 | 88.388 | 6.4 | 85.65
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Neigh | 0.88619 | 0.90996 | 0.92467 | 1.3 | 0.89
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Comm | 7.3456 | 8.144 | 9.1588 | 21.2 | 7.96
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Output | 2.2851 | 2.2855 | 2.2903 | 0.1 | 2.23
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Modify | 3.0244 | 3.0283 | 3.0332 | 0.1 | 2.96
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Other | | 0.3064 | | | 0.30
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Nlocal: 13500.0 ave 13528 max 13447 min
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Histogram: 1 0 0 2 1 2 2 2 3 3
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Nghost: 7282.56 ave 7336 max 7254 min
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Histogram: 3 3 2 2 2 1 2 0 0 1
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 16 0 0 0 0 0 0 0 0 0
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FullNghs: 378000.0 ave 378780 max 376516 min
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Histogram: 1 0 0 2 1 2 2 2 3 3
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Total # of neighbors = 6048000
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Ave neighs/atom = 28.000000
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Neighbor list builds = 56
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Dangerous builds = 24
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Total wall time: 0:01:42
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