294 lines
13 KiB
Groff
294 lines
13 KiB
Groff
LAMMPS (8 Apr 2021)
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# Coarse-Grained SPC/E Water
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variable T equal 300.0
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variable rc equal 9.0
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variable rcD equal 10.0
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units real
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boundary p p p
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atom_style atomic
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dimension 3
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newton on
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comm_modify vel yes
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read_data cg_spce.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2180 atoms
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read_data CPU = 0.005 seconds
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pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
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pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
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pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
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pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
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pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
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pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
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WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
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Should only be flagged at inflection points (../pair_table.cpp:461)
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pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
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pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
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timestep 1.0
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run_style verlet
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velocity all create ${T} 68768932
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velocity all create 300 68768932
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thermo_style custom step time temp press
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thermo 10
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fix 1 all nve
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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 = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 7 7 7
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2 neighbor lists, perpetual/occasional/extra = 2 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/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair dpd/ext/tstat, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
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Step Time Temp Press
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0 0 300 5965.5396
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10 10 303.16391 8779.1574
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20 20 306.9014 8268.573
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30 30 305.84291 9976.0547
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40 40 301.20527 8832.3902
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50 50 305.72012 8041.0146
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60 60 305.1676 7118.8042
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70 70 305.01132 9423.9307
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80 80 308.10236 10781.423
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90 90 309.18703 3637.9961
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100 100 305.11814 7726.7672
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110 110 298.37346 8575.1602
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120 120 304.79786 8910.8048
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130 130 309.05401 6351.4839
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140 140 304.28367 4805.137
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150 150 300.28903 7412.6411
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160 160 299.39358 10183.593
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170 170 296.80729 5437.1054
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180 180 295.2755 8317.0414
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190 190 303.25949 8338.3453
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200 200 303.24607 9636.5224
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210 210 298.56684 10288.264
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220 220 293.42999 9001.0482
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230 230 293.12497 9083.5194
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240 240 291.92847 9659.3388
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250 250 299.2202 6328.759
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260 260 297.45209 10405.677
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270 270 292.12257 7273.9369
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280 280 289.81113 8957.8747
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290 290 299.06683 6695.3776
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300 300 300.75468 6298.5705
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310 310 296.26524 7432.4815
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320 320 294.21403 9941.7038
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330 330 293.01776 4750.2993
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340 340 295.22553 4968.3595
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350 350 293.95589 9224.5496
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360 360 297.94278 8792.0395
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370 370 298.99075 5453.7814
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380 380 302.1188 6229.2283
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390 390 298.48943 8517.5273
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400 400 295.3701 11328.394
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410 410 287.74238 4058.0382
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420 420 288.83732 5706.6773
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430 430 298.8242 6178.7142
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440 440 304.42682 10138.321
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450 450 300.28695 9731.3417
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460 460 300.34539 9249.4691
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470 470 303.32231 11638.718
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480 480 301.46777 4186.402
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490 490 292.56069 9184.8386
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500 500 297.26162 11766.733
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510 510 295.34018 6436.33
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520 520 300.16314 9325.3669
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530 530 305.00513 5947.6408
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540 540 300.88805 5222.7384
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550 550 301.56707 6669.1808
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560 560 304.89854 10730.053
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570 570 299.50424 7956.1042
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580 580 301.23382 10192.246
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590 590 298.81222 6017.2125
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600 600 300.57891 4575.433
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610 610 301.95936 6309.7515
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620 620 301.09393 5993.6489
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630 630 300.47565 4388.7137
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640 640 299.31886 9535.6093
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650 650 295.06025 7954.5811
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660 660 298.72666 8630.7466
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670 670 302.53833 5636.1305
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680 680 306.32833 12539.149
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690 690 296.1951 11345.293
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700 700 297.00325 6352.1448
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710 710 298.51181 6922.4379
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720 720 293.80125 4849.4922
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730 730 296.52677 11141.583
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740 740 294.15306 3527.8677
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750 750 294.74737 8454.0815
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760 760 292.53913 8187.9032
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770 770 294.37078 7487.5703
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780 780 297.50085 9198.7697
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790 790 298.37773 8969.0024
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800 800 293.29879 6506.6479
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810 810 296.58266 8805.7872
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820 820 290.85616 5248.8123
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830 830 292.29488 5123.8203
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840 840 292.77623 8263.5675
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850 850 297.88225 6777.7444
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860 860 300.01913 10439.087
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870 870 295.79578 7318.1322
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880 880 301.5994 8242.4774
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890 890 306.63208 8090.6106
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900 900 303.53759 6831.2666
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910 910 300.70481 3811.0498
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920 920 299.96274 8351.1573
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930 930 299.67435 7046.0534
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940 940 310.81742 6887.6925
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950 950 305.09984 4811.088
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960 960 301.33039 4184.851
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970 970 301.19205 6417.6542
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980 980 299.6491 7738.2233
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990 990 297.33655 9264.0874
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1000 1000 302.33418 7166.2751
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1010 1010 300.08402 9121.0882
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1020 1020 302.82225 6405.7109
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1030 1030 304.01683 6944.0839
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1040 1040 305.82618 6160.3838
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1050 1050 308.12518 4356.0931
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1060 1060 307.64811 6954.7245
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1070 1070 313.70509 5558.9804
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1080 1080 316.09239 7250.6147
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1090 1090 310.2845 5441.3722
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1100 1100 300.18899 4417.8774
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1110 1110 304.02471 5609.1668
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1120 1120 303.46016 10355.031
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1130 1130 305.68165 6400.913
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1140 1140 308.78348 7235.1894
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1150 1150 299.30025 9246.4856
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1160 1160 302.70799 9866.9536
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1170 1170 302.0977 8643.5532
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1180 1180 307.15407 8866.4664
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1190 1190 305.78146 7562.4911
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1200 1200 302.54605 7974.9973
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1210 1210 306.14264 9554.2381
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1220 1220 308.89843 6219.5361
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1230 1230 305.71844 7633.9105
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1240 1240 306.51911 7705.4795
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1250 1250 304.78473 8590.5595
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1260 1260 300.82969 9281.5964
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1270 1270 305.9271 4951.1323
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1280 1280 310.32728 9446.3989
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1290 1290 318.27879 9102.5544
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1300 1300 310.45777 5931.5457
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1310 1310 304.81268 1214.4291
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1320 1320 307.08811 10315.961
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1330 1330 306.86917 8584.9658
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1340 1340 307.26912 7254.864
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1350 1350 310.02754 8508.6256
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1360 1360 306.12763 4912.6641
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1370 1370 301.67924 6715.8196
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1380 1380 298.37239 6149.8821
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1390 1390 299.62894 8181.4761
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1400 1400 301.60395 6714.4244
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1410 1410 297.65752 7035.6575
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1420 1420 297.02817 7510.2637
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1430 1430 303.59177 10361.937
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1440 1440 300.10771 8473.2311
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1450 1450 291.21837 6097.9954
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1460 1460 291.58663 7729.0841
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1470 1470 292.52447 6555.8661
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1480 1480 294.48264 6960.0201
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1490 1490 298.34869 8044.2321
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1500 1500 296.8193 11731.289
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1510 1510 296.52073 5452.8935
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1520 1520 294.54819 9591.7969
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1530 1530 297.36394 5148.5383
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1540 1540 289.08137 6057.0981
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1550 1550 288.27007 8965.1965
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1560 1560 294.84398 8316.9487
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1570 1570 299.79573 8760.7322
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1580 1580 295.66745 5045.5322
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1590 1590 298.14356 7161.1834
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1600 1600 297.10402 6529.9938
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1610 1610 299.69137 7741.6027
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1620 1620 304.93043 11222.109
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1630 1630 302.01322 10893.107
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1640 1640 295.47422 8400.3124
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1650 1650 301.93122 7190.2609
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1660 1660 305.02639 6140.5552
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1670 1670 302.86047 8651.5366
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1680 1680 304.82151 9909.407
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1690 1690 300.48426 8428.8845
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1700 1700 293.06643 5333.8144
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1710 1710 295.43687 9103.4353
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1720 1720 298.77208 8162.1053
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1730 1730 300.08189 9603.4371
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1740 1740 303.16004 10693.291
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1750 1750 303.54199 9151.023
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1760 1760 300.99281 4641.2985
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1770 1770 297.36657 3888.5753
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1780 1780 298.32969 7286.2299
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1790 1790 297.34183 8975.8956
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1800 1800 295.83042 6366.7607
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1810 1810 295.92044 9308.4953
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1820 1820 298.10087 7117.2369
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1830 1830 296.13936 4849.3739
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1840 1840 296.5869 8321.4011
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1850 1850 296.74513 9530.6806
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1860 1860 298.57398 8788.0603
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1870 1870 299.12825 6015.4777
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1880 1880 301.91639 11706.441
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1890 1890 309.85968 10909.493
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1900 1900 302.64998 8779.8967
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1910 1910 301.62919 9176.3902
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1920 1920 300.66238 5369.8681
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1930 1930 297.64499 8185.09
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1940 1940 296.47852 10188.803
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1950 1950 297.802 6679.4466
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1960 1960 299.78754 7316.8198
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1970 1970 300.09083 6008.9414
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1980 1980 297.94119 5615.6403
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1990 1990 298.37687 9727.308
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2000 2000 296.08394 6400.2746
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Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms
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Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
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99.5% CPU use with 4 MPI tasks x no 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 | 38.667 | 38.954 | 39.453 | 4.8 | 93.83
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Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27
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Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70
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Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02
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Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06
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Other | | 0.05335 | | | 0.13
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Nlocal: 545.000 ave 559 max 531 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 3619.00 ave 3655 max 3594 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Neighs: 65415.5 ave 66835 max 64310 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 261662
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Ave neighs/atom = 120.02844
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Neighbor list builds = 26
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Dangerous builds = 0
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Total wall time: 0:00:41
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