forked from lijiext/lammps
247 lines
24 KiB
Groff
247 lines
24 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style lj/cut/coul/long 12.0 12.0
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kspace_style pppm 1.0e-3
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comm_modify vel yes
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read_data data.swm4-ndp
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orthogonal box = (-12 -12 -12) to (12 12 12)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2500 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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2000 bonds
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reading angles ...
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500 angles
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4 = max # of 1-2 neighbors
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3 = max # of 1-3 neighbors
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3 = max # of 1-4 neighbors
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4 = max # of special neighbors
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pair_coeff 1 1 0.210939 3.183950 # ODw ODw
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pair_coeff * 2* 0.000000 0.0
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group ATOMS type 1:3
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2000 atoms in group ATOMS
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group CORES type 1
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500 atoms in group CORES
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group DRUDES type 4
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500 atoms in group DRUDES
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variable TK equal 300.0
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variable TDK equal 1.0
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variable PBAR equal 1.0
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neighbor 2.0 bin
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timestep 1.0
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fix DRUDE all drude C N N D
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velocity ATOMS create ${TK} 12345
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velocity ATOMS create 300 12345
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velocity DRUDES create ${TDK} 12345
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velocity DRUDES create 1 12345
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delete_bonds ATOMS multi
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.217457
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grid = 10 10 10
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stencil order = 5
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estimated absolute RMS force accuracy = 0.197288
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estimated relative force accuracy = 0.000594128
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using double precision FFTs
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3d grid and FFT values/proc = 1500 300
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Rebuild special list taking Drude particles into account
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Old max number of 1-2 to 1-4 neighbors: 4
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New max number of 1-2 to 1-4 neighbors: 4 (+0)
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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, 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/newton
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bin: standard
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2000 total bonds, 500 turned on, 1500 turned off
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500 total angles, 0 turned on, 500 turned off
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0 total dihedrals, 0 turned on, 0 turned off
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0 total impropers, 0 turned on, 0 turned off
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fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
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fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
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fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
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fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
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fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
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fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
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500 rigid bodies with 2000 atoms
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0.832099 = max distance from body owner to body atom
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fix NVE DRUDES nve
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compute TEMP all temp/drude
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thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
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thermo 20
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.217457
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grid = 10 10 10
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stencil order = 5
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estimated absolute RMS force accuracy = 0.197288
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estimated relative force accuracy = 0.000594128
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using double precision FFTs
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3d grid and FFT values/proc = 1500 300
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Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes
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Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
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0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
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20 0.3966074 2915.1579 4579.5774 -1664.4194 561.91893 0 600.76451 155095.13 -157922.23 27379.771 14058.574 1024.9188 1455.9194 160.86778
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40 0.81358027 1320.1722 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914
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60 1.2173033 284.06793 2671.4324 -2387.3645 575.54155 0 387.8792 154580.74 -157931.53 12104.74 15031.425 597.87206 886.98502 18.450412
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80 1.6120358 -462.53073 2214.284 -2676.8148 560.36346 0 254.65244 154447.22 -157939.05 6285.2446 15651.216 495.56131 739.13811 7.4024414
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100 1.9901412 -965.1962 1839.8309 -2805.0271 544.5953 0 115.80813 154469.59 -157935.02 2361.9408 16295.72 411.75794 615.12768 4.1969771
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120 2.4076366 -1316.6354 1649.5851 -2966.2205 554.66642 0 50.928948 154365.49 -157937.3 -493.85718 16925.293 369.18054 552.03453 2.7331858
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140 2.7559175 -1590.9197 1440.667 -3031.5867 526.07695 0 -24.440541 154404.35 -157937.57 -2586.3198 17517.285 322.42423 482.1612 2.2975751
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160 3.1113834 -1742.3406 1326.8813 -3069.2219 539.49038 0 -43.846686 154369.1 -157933.96 -3549.2199 18059.707 296.95875 444.11027 2.0644718
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180 3.4379854 -1895.133 1224.1815 -3119.3145 555.27915 0 -18.261199 154275.94 -157932.27 -3762.2323 18545.519 273.97433 409.78407 1.8069068
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200 3.772357 -2004.4681 1176.8827 -3181.3508 565.04401 0 0.21397152 154190.38 -157936.99 -4346.6082 18973.343 263.38877 393.94854 1.740057
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220 4.0741081 -2094.1886 1098.386 -3192.5745 592.45711 0 36.50232 154113.36 -157934.89 -4135.0776 19341.735 245.82103 367.67719 1.6170754
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240 4.3758588 -2178.9977 1086.8337 -3265.8313 617.63759 0 96.837785 153957.25 -157937.56 -4121.8002 19651.8 243.23561 363.77451 1.6722528
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260 4.6875975 -2264.8204 1078.4367 -3343.2571 663.36053 0 167.77029 153763.13 -157937.51 -3799.2337 19907.053 241.35634 360.97449 1.6377088
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280 4.9870708 -2325.8017 1097.4329 -3423.2346 717.74153 0 235.01385 153562.93 -157938.92 -3696.4866 20111.415 245.60773 367.30986 1.7042226
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300 5.2866828 -2390.4714 1068.102 -3458.5734 751.64774 0 295.31519 153435.36 -157940.9 -3511.7651 20268.755 239.04342 357.49315 1.6658672
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320 5.587172 -2455.1882 1041.7365 -3496.9247 765.89806 0 331.14936 153345 -157938.97 -3020.2521 20383.476 233.14276 348.62201 1.7179837
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340 5.8844874 -2536.9586 1050.7417 -3587.7004 793.64691 0 352.69902 153205.76 -157939.81 -3447.4347 20457.614 235.15816 351.64191 1.7214644
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360 6.1785333 -2603.5522 966.91828 -3570.4705 819.14562 0 391.00832 153158.88 -157939.51 -3164.7275 20490.766 216.3983 323.52165 1.7255664
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380 6.475884 -2594.7716 1024.7965 -3619.5682 836.45788 0 434.31956 153047.12 -157937.46 -2902.8144 20485.924 229.35156 342.91613 1.7641391
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400 6.7656763 -2647.3629 982.4772 -3629.8401 864.60508 0 479.09794 152963.5 -157937.04 -2535.5559 20447.667 219.88041 328.70004 1.8030439
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420 7.0558476 -2687.5292 1023.0073 -3710.5365 928.03183 0 538.52272 152760.85 -157937.94 -2383.1875 20380.424 228.95113 342.29995 1.8044464
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440 7.3502834 -2765.1784 999.349 -3764.5274 966.2891 0 577.16135 152631.19 -157939.17 -2390.6308 20286.677 223.65636 334.36519 1.794568
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460 7.6480289 -2806.7277 1004.2012 -3810.9289 996.86402 0 599.42684 152532.82 -157940.04 -2476.2951 20168.787 224.74229 335.9677 1.8474231
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480 7.9473393 -2830.1149 1013.7084 -3843.8233 1009.5457 0 624.67244 152464.69 -157942.73 -2208.5836 20027.763 226.87003 339.15378 1.8588625
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500 8.2545588 -2849.2101 1033.8059 -3883.016 1018.8936 0 665.65423 152373.57 -157941.13 -1864.5049 19866.3 231.36788 345.90443 1.8323172
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520 8.591975 -2883.363 982.80834 -3866.1713 1046.7496 0 716.08257 152311.55 -157940.55 -1180.4653 19690.017 219.95452 328.79387 1.8393955
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540 8.9018662 -2922.4604 979.55307 -3902.0135 1068.293 0 739.88796 152230.57 -157940.76 -1048.6961 19504.92 219.22599 327.7909 1.6577051
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560 9.2518864 -2966.9519 973.53114 -3940.4831 1078.4149 0 742.20771 152177.5 -157938.6 -840.75895 19313.099 217.87827 325.70841 1.7798986
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580 9.5821679 -3053.0997 924.19412 -3977.2939 1102.7966 0 751.05657 152109.51 -157940.66 -919.12753 19115.431 206.83654 309.16882 1.7634757
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600 9.9095862 -3062.7056 960.18758 -4022.8932 1105.4131 0 725.33328 152088.02 -157941.66 -1565.9872 18911.303 214.89195 321.19255 1.860965
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620 10.237109 -3087.2168 1011.0151 -4098.2319 1138.4545 0 715.92859 151990.05 -157942.66 -1858.9668 18697.232 226.26725 338.29838 1.752463
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640 10.571446 -3104.3903 1013.9671 -4118.3574 1151.4213 0 771.17657 151902.66 -157943.62 -1042.667 18472.317 226.92791 339.23913 1.8477429
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660 10.904144 -3140.5527 1003.0482 -4143.6009 1209.2262 0 856.88154 151734.42 -157944.13 -209.63558 18243.884 224.48425 335.54573 1.90792
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680 11.269296 -3178.318 984.55406 -4162.872 1244.5687 0 912.27932 151624.96 -157944.68 342.27035 18019.714 220.34522 329.38006 1.8427138
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700 11.61204 -3220.4931 991.39835 -4211.8914 1287.1899 0 958.87881 151484.75 -157942.71 561.06968 17805.512 221.87699 331.61354 1.9544592
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720 11.956387 -3270.5677 968.72596 -4239.2937 1318.9328 0 1005.2488 151379.5 -157942.98 980.32825 17604.484 216.80286 324.06313 1.8724276
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740 12.307601 -3290.3786 992.65117 -4283.0298 1300.6067 0 994.6404 151364.88 -157943.15 981.03868 17418.67 222.15737 332.13302 1.7636245
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760 12.709807 -3328.535 955.47413 -4284.0092 1326.3889 0 996.60158 151337.63 -157944.63 1057.2942 17247.311 213.83707 319.58671 1.9099364
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780 13.073534 -3357.4814 992.18506 -4349.6664 1339.5541 0 988.34064 151267.55 -157945.11 569.82212 17090.619 222.05305 331.88822 1.9447924
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800 13.464632 -3375.243 920.44154 -4295.6846 1344.9357 0 1033.5805 151270.88 -157945.08 1522.7002 16947.373 205.99671 307.8875 1.8152213
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820 13.825511 -3384.8564 957.24296 -4342.0994 1353.9907 0 1040.4762 151209.02 -157945.59 1664.2884 16820.422 214.23294 320.13875 1.9919112
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840 14.161551 -3422.503 978.5056 -4401.0087 1362.0589 0 1015.2074 151166.38 -157944.65 799.30788 16709.133 218.99156 327.32752 1.887971
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860 14.533048 -3467.9469 967.207 -4435.1539 1359.5363 0 1012.6359 151135.59 -157942.92 781.21407 16610.402 216.46291 323.49791 1.9571626
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880 14.90632 -3453.3858 998.28194 -4451.6677 1357.904 0 965.66218 151167.88 -157943.11 327.66041 16521.416 223.41755 333.88219 2.0414314
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900 15.304111 -3462.8392 980.22919 -4443.0684 1356.3167 0 986.69144 151157.82 -157943.9 1027.2464 16438.193 219.37731 327.82432 2.0328217
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920 15.679265 -3447.1555 973.44396 -4420.5994 1360.7957 0 1016.6188 151146.99 -157945 1288.3873 16362.953 217.85876 325.51992 2.1081109
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940 16.057773 -3481.2586 989.56656 -4470.8252 1370.2709 0 978.71463 151124.98 -157944.79 462.51008 16297.794 221.46703 330.96437 2.0294765
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960 16.417333 -3513.0231 967.65653 -4480.6797 1332.0395 0 924.14851 151207.66 -157944.53 130.65949 16238.731 216.56352 323.68471 1.8694768
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980 16.809043 -3552.9742 930.52856 -4483.5028 1369.5671 0 943.1948 151148.51 -157944.78 162.05947 16182.544 208.2542 311.18346 1.9699974
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1000 17.204374 -3547.8316 928.6749 -4476.5065 1345.2729 0 939.82999 151183.66 -157945.27 165.47858 16127.801 207.83935 310.6291 1.8515304
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1020 17.596776 -3544.884 939.68436 -4484.5683 1339.8295 0 954.31534 151165.65 -157944.37 520.88879 16074.311 210.30329 314.30017 1.8816955
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1040 17.979123 -3574.7347 918.01852 -4492.7532 1348.2798 0 985.63357 151118.04 -157944.71 667.98123 16024.2 205.45443 307.00947 1.9378696
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1060 18.387169 -3558.0092 961.56557 -4519.5748 1357.9517 0 960.15956 151105.93 -157943.62 125.05193 15979.251 215.20035 321.61047 1.9569155
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1080 18.773684 -3578.9948 924.98329 -4503.9781 1328.198 0 963.29308 151149.83 -157945.3 446.98896 15936.835 207.01316 309.36635 1.8873208
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1100 19.16304 -3608.0441 897.53939 -4505.5835 1374.0861 0 1014.8258 151052.01 -157946.5 903.7649 15898.367 200.87116 300.13546 1.9333063
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1120 19.575293 -3614.8945 952.97919 -4567.8736 1384.5634 0 1021.0735 150973.5 -157947.01 900.30601 15866.787 213.2787 318.78179 1.850125
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1140 19.971095 -3618.8945 941.15802 -4560.0526 1413.1629 0 1052.0922 150920.8 -157946.1 946.48705 15842.856 210.6331 314.72329 2.0381081
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1160 20.367334 -3593.6555 965.54035 -4559.1959 1410.1926 0 1056.4577 150917.31 -157943.16 1255.7185 15827.388 216.08991 322.92339 1.9871263
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1180 20.80204 -3616.5746 928.17105 -4544.7457 1396.8419 0 1016.2295 150986.13 -157943.95 787.12503 15820.166 207.72659 310.40871 1.9519704
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1200 21.354242 -3640.0065 913.1866 -4553.1931 1389.564 0 1003.0365 150999.43 -157945.23 124.9066 15819.562 204.37304 305.34426 2.0128932
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1220 21.797356 -3633.6726 951.90864 -4585.5813 1378.6589 0 960.35277 151020.87 -157945.46 18.165228 15822.414 213.03911 318.39602 1.9062762
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1240 22.183053 -3647.5993 945.94087 -4593.5401 1389.2708 0 951.90886 151011.29 -157946.01 -36.466949 15826.558 211.70351 316.39869 1.8959
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1260 22.604321 -3652.8431 945.01497 -4597.8581 1429.1559 0 1004.3575 150913.05 -157944.42 362.05633 15830.563 211.49629 316.0745 1.946701
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1280 22.99465 -3653.7982 950.39456 -4604.1928 1435.3114 0 1049.5949 150856.36 -157945.46 625.62312 15836.724 212.70025 317.85889 1.9726129
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1300 23.381442 -3629.7936 957.73231 -4587.5259 1443.1612 0 1053.2561 150860.98 -157944.93 702.06174 15846.916 214.34246 320.25498 2.0929604
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1320 23.76752 -3646.7132 952.84473 -4599.5579 1452.1034 0 1053.24 150842.08 -157946.98 574.37181 15862.45 213.24861 318.70565 1.9106871
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1340 24.144538 -3671.1813 963.35534 -4634.5366 1444.4873 0 998.25657 150869.14 -157946.42 -322.65814 15883.001 215.6009 322.16079 2.04787
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1360 24.525885 -3706.8433 911.96869 -4618.812 1408.7597 0 994.56958 150923.67 -157945.81 -57.178556 15902.95 204.10046 304.98731 1.9206183
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1380 24.900833 -3729.8666 893.54172 -4623.4083 1421.5285 0 989.13168 150911.03 -157945.1 -299.2294 15921.536 199.97647 298.78606 1.9572022
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1400 25.273009 -3793.6665 896.59455 -4690.261 1407.5033 0 927.03218 150922.27 -157947.07 -1625.2355 15935.372 200.6597 299.82059 1.9326242
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1420 25.649713 -3798.9041 894.49834 -4693.4024 1387.2314 0 908.98338 150956.58 -157946.2 -1336.2681 15939.126 200.19057 299.08979 1.99336
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1440 26.019568 -3770.2203 926.96956 -4697.1899 1408.3234 0 930.94218 150909.09 -157945.54 -1479.4839 15931.76 207.45769 309.99863 1.9420101
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1460 26.391048 -3765.611 925.8388 -4691.4498 1453.7458 0 991.60997 150809.05 -157945.85 -840.19764 15915.083 207.20462 309.58977 2.0206113
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1480 26.764417 -3775.5533 897.45722 -4673.0106 1448.3682 0 1017.1514 150806.55 -157945.08 -350.56805 15893.71 200.85277 300.10571 1.945031
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1500 27.13281 -3774.5729 890.65309 -4665.226 1446.7764 0 1001.4176 150830.42 -157943.84 -410.46342 15870.464 199.32999 297.86004 1.8712264
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1520 27.500265 -3789.599 873.98319 -4663.5822 1442.1868 0 1012.8814 150826.03 -157944.68 24.399796 15844.317 195.59923 292.31265 1.7812003
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1540 27.868039 -3799.4214 879.9876 -4679.409 1470.7765 0 1043.5857 150751.8 -157945.57 -117.3494 15817.531 196.94303 294.27937 1.8764714
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1560 28.237804 -3808.5737 884.02221 -4692.5959 1476.2544 0 1031.065 150745.8 -157945.71 -134.38328 15790.497 197.84599 295.60533 1.9624808
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1580 28.614069 -3810.3826 881.02258 -4691.4052 1494.8044 0 1056.2914 150703.91 -157946.41 143.72796 15761.802 197.17466 294.61532 1.9194335
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1600 28.98594 -3811.3999 900.38301 -4711.7829 1484.7896 0 1008.1585 150740.82 -157945.55 -606.18902 15732.936 201.50757 301.08426 1.975131
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1620 29.390152 -3806.3652 923.83116 -4730.1964 1451.5712 0 974.75532 150788.99 -157945.52 -803.66402 15700.793 206.75531 308.94868 1.9548773
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1640 29.770757 -3780.4823 926.08598 -4706.5682 1473.3966 0 1001.2541 150764.99 -157946.2 -267.61953 15664.228 207.25994 309.69886 1.9804041
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1660 30.150359 -3781.8554 904.38999 -4686.2453 1480.8669 0 1044.4828 150733.32 -157944.92 334.93631 15626.039 202.40434 302.41882 1.9682532
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1680 30.535691 -3806.1604 913.1776 -4719.338 1495.1709 0 1047.1796 150684.96 -157946.64 187.42287 15589.003 204.37102 305.37701 1.9489831
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1700 30.914774 -3833.9683 889.78762 -4723.756 1506.0651 0 1085.1426 150631.7 -157946.67 484.91155 15553.147 199.1363 297.62268 1.7777001
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|
1720 31.295628 -3842.1369 894.05081 -4736.1877 1523.554 0 1111.0586 150574.13 -157944.93 644.7439 15520.678 200.09041 298.99568 1.8760829
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|
1740 31.688478 -3846.6021 868.65036 -4715.2525 1537.3591 0 1138.8056 150555.14 -157946.56 899.91638 15492.771 194.40573 290.47895 1.8712221
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|
1760 32.046871 -3857.9528 883.26637 -4741.2192 1542.993 0 1087.2616 150575.49 -157946.97 551.51344 15470.089 197.67683 295.29782 2.0345443
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|
1780 32.474213 -3871.4941 935.07928 -4806.5734 1526.7468 0 1036.0478 150576.57 -157945.93 -636.02229 15449.192 209.27266 312.71251 1.9801693
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|
1800 32.86394 -3840.4408 916.271 -4756.7118 1576.9326 0 1100.9058 150511.02 -157945.57 628.83596 15425.726 205.06333 306.41471 1.9480945
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|
1820 33.2544 -3863.8057 928.94676 -4792.7524 1566.8662 0 1091.867 150492.97 -157944.46 127.39479 15404.045 207.90019 310.61713 2.0438685
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1840 33.654639 -3866.4315 882.39729 -4748.8287 1571.1231 0 1116.2191 150510.49 -157946.66 775.21837 15384.034 197.48232 295.08631 1.8701078
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|
1860 34.049358 -3854.7362 943.50575 -4798.2419 1598.0765 0 1094.2606 150455.31 -157945.89 -185.76137 15367.771 211.15852 315.55119 1.9664963
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|
1880 34.452703 -3862.4907 910.1166 -4772.6073 1551.4788 0 1069.6982 150551.3 -157945.09 75.157314 15353.364 203.68596 304.30419 2.0643731
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|
1900 34.820253 -3879.6568 921.99593 -4801.6528 1541.8636 0 1071.1404 150530.01 -157944.67 -243.29034 15340.544 206.34458 308.28647 2.0409636
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|
1920 35.24159 -3914.6053 894.91511 -4809.5205 1545.6295 0 1087.8419 150502.25 -157945.24 585.4907 15327.629 200.28384 299.29163 1.8721306
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|
1940 35.641894 -3916.7204 893.69522 -4810.4157 1558.0228 0 1078.6893 150498.47 -157945.6 -213.58892 15315.774 200.01082 298.82901 1.9662798
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|
1960 36.036489 -3916.4155 889.43523 -4805.8507 1569.5342 0 1087.2216 150483.46 -157946.07 197.26075 15304.142 199.05743 297.4414 1.897782
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|
1980 36.439917 -3885.2222 890.76008 -4775.9823 1562.1737 0 1087.3549 150520.37 -157945.88 448.96019 15293.261 199.35393 297.81895 2.0239285
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|
2000 36.842032 -3890.9997 883.71903 -4774.7187 1561.3244 0 1092.1688 150517.76 -157945.97 292.74093 15284.861 197.77813 295.50959 1.9186189
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Loop time of 36.8421 on 4 procs for 2000 steps with 2500 atoms
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Performance: 4.690 ns/day, 5.117 hours/ns, 54.286 timesteps/s
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97.8% 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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---------------------------------------------------------------
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Pair | 24.965 | 26.526 | 28.829 | 27.6 | 72.00
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Bond | 0.011653 | 0.012315 | 0.013344 | 0.6 | 0.03
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Kspace | 1.5367 | 3.8315 | 5.3771 | 72.2 | 10.40
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Neigh | 2.6221 | 2.6225 | 2.6227 | 0.0 | 7.12
|
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Comm | 1.2339 | 1.2536 | 1.2758 | 1.3 | 3.40
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Output | 0.0057538 | 0.0073775 | 0.012186 | 3.2 | 0.02
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Modify | 2.4848 | 2.5068 | 2.5296 | 1.2 | 6.80
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|
Other | | 0.08209 | | | 0.22
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Nlocal: 625 ave 639 max 613 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Nghost: 13529.2 ave 13635 max 13449 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Neighs: 587190 ave 645917 max 526348 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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|
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Total # of neighbors = 2348759
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Ave neighs/atom = 939.504
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Ave special neighs/atom = 4
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Neighbor list builds = 102
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Dangerous builds = 7
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Total wall time: 0:00:36
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