237 lines
23 KiB
Groff
237 lines
23 KiB
Groff
LAMMPS (8 Jul 2015)
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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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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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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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1 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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master list distance cutoff = 14
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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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comm_modify vel yes
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compute TATOM ATOMS temp/com
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compute TEMP all temp/drude
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fix DTDIR all drude/transform/direct
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fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
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fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
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fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
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fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
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fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 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_modify RIGID temp TATOM press thermo_press
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WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
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fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
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fix NVT DRUDES nvt temp 1 ${TDK} 100.0
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fix NVT DRUDES nvt temp 1 1 100.0
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fix DTINV all drude/transform/inverse
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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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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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Memory usage per processor = 15.0906 Mbytes
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Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] 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 0.60629702 3742.7991 5338.7966 -1595.9975 567.29055 0 662.23349 155098.48 -157924 31679.046 13979.575 1194.8336 1690.2267 201.65776
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40 1.2431891 2752.9388 4407.9332 -1654.9944 792.86725 0 870.27523 154593.92 -157912.06 27392.302 14278.564 986.5045 1450.7624 56.079837
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60 1.875339 1995.9775 3980.851 -1984.8735 660.64216 0 750.43214 154538.47 -157934.42 22242.676 14691.413 890.92262 1315.3403 40.305321
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80 2.471236 1377.1261 3449.7879 -2072.6618 617.64243 0 605.75693 154628.63 -157924.69 17345.214 15201.397 772.06962 1146.6088 21.44718
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100 3.0357449 886.38995 3038.4108 -2152.0208 537.89929 0 450.99962 154789.13 -157930.05 13299.227 15783.335 680.00257 1011.6773 15.016231
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120 3.585844 488.055 2928.1336 -2440.0786 536.23164 0 334.88597 154620.05 -157931.25 8694.3472 16409.509 655.3223 977.40122 9.8538294
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140 4.117424 160.14918 2538.5116 -2378.3624 509.19396 0 249.89205 154793.34 -157930.79 6363.1137 17053.486 568.1241 847.92526 7.2744139
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160 4.6321139 -103.57595 2403.1613 -2506.7372 494.69822 0 144.07174 154790.83 -157936.34 4017.2005 17699.095 537.83243 803.44775 5.3901399
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180 5.126441 -315.61252 2216.7944 -2532.4069 477.29447 0 80.852363 154842.41 -157932.96 1958.1627 18336.716 496.12314 741.4685 4.440167
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200 5.6090059 -490.61276 2058.9074 -2549.5202 470.23217 0 80.799455 154831.63 -157932.18 1260.1943 18960.132 460.78771 688.92684 3.5878733
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220 6.0495639 -644.09355 2001.1189 -2645.2125 494.11524 0 53.071997 154741.65 -157934.05 -16.373549 19564.819 447.85452 669.94663 2.7746068
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240 6.5042329 -773.76581 1911.0759 -2684.8417 491.56501 0 36.579309 154722.88 -157935.86 -773.18555 20144.755 427.70271 639.97688 2.2989541
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260 6.9512041 -886.818 1719.7038 -2606.5218 462.97731 0 47.595907 154814.45 -157931.55 -696.23419 20696.487 384.87324 575.96351 1.9229602
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280 7.3921249 -983.57561 1659.2167 -2642.7923 476.06924 0 65.542713 154749.27 -157933.68 -1099.4208 21220.613 371.3361 555.78067 1.7042918
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300 7.8054619 -1069.4015 1531.598 -2600.9995 487.38132 0 130.06616 154709.03 -157927.47 -548.86446 21717.521 342.77477 513.11788 1.4030219
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320 8.2272029 -1144.9139 1562.933 -2707.8469 509.00464 0 127.16899 154591.31 -157935.33 -1516.7077 22190.692 349.78761 523.61225 1.4145866
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340 8.6145689 -1216.4369 1511.7737 -2728.2106 518.42214 0 144.71934 154541.92 -157933.27 -1345.493 22636.556 338.33806 506.55234 1.2328234
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360 9.0159991 -1279.8637 1435.4044 -2715.2681 525.01973 0 153.83119 154536.21 -157930.33 -1447.797 23056.471 321.24646 480.9789 1.1390786
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380 9.4004741 -1340.2241 1391.5909 -2731.815 536.93555 0 180.52081 154483.31 -157932.58 -1315.0222 23450.141 311.4409 466.34776 1.004293
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400 9.7971771 -1398.7544 1401.1636 -2799.918 547.12264 0 190.99461 154394.23 -157932.27 -1686.7786 23818.238 313.5833 469.59825 0.92621346
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420 10.175245 -1450.5676 1355.0166 -2805.5842 555.43355 0 178.57277 154392.99 -157932.58 -1948.3006 24158.665 303.2555 454.12588 0.90821389
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440 10.550016 -1501.2755 1336.6037 -2837.8792 573.29095 0 195.76657 154324.78 -157931.72 -1845.698 24470.004 299.13465 447.99648 0.8127319
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460 10.93798 -1551.1246 1327.3311 -2878.4557 580.57019 0 206.92238 154267.88 -157933.83 -2059.7154 24752.911 297.05944 444.88976 0.80466605
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480 11.304226 -1597.9166 1280.274 -2878.1906 596.27629 0 247.5201 154210.94 -157932.93 -1714.1239 25006.108 286.52794 429.10945 0.79188456
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500 11.66949 -1645.4221 1303.9947 -2949.4168 620.22431 0 275.42964 154086.38 -157931.45 -1833.6239 25232.592 291.83668 437.06941 0.78754301
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520 12.030775 -1692.7733 1261.2365 -2954.0098 639.32812 0 295.13753 154045.85 -157934.32 -1715.0443 25432.412 282.26732 422.73896 0.75950535
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540 12.389967 -1739.3602 1247.1301 -2986.4903 666.88476 0 341.37591 153937.16 -157931.91 -1556.9492 25607.225 279.11027 418.00746 0.75767537
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560 12.765452 -1783.4916 1212.3647 -2995.8563 669.09681 0 366.501 153899.16 -157930.62 -1543.0147 25758.368 271.3297 406.37068 0.70509124
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580 13.122579 -1824.6061 1200.7205 -3025.3267 699.41498 0 409.47507 153794.95 -157929.16 -1053.8519 25887.592 268.72372 402.43012 0.77346975
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600 13.47702 -1864.0982 1206.4231 -3070.5213 726.9912 0 439.25863 153695.5 -157932.27 -1130.6737 26000.4 269.99996 404.33899 0.78190692
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620 13.82937 -1902.6883 1167.061 -3069.7493 741.54351 0 453.21801 153667.95 -157932.46 -921.61026 26097.341 261.19065 391.14672 0.7561126
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640 14.180362 -1941.2814 1168.4808 -3109.7622 758.6291 0 484.81029 153578.39 -157931.59 -1084.6877 26180.233 261.50841 391.64626 0.70968727
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660 14.527615 -1977.9114 1159.1979 -3137.1094 746.51288 0 452.2958 153598.59 -157934.51 -1424.6628 26247.07 259.43088 388.52145 0.73088365
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680 14.875155 -2015.8231 1149.125 -3164.9481 730.41157 0 417.95266 153620.83 -157934.15 -1485.3138 26293.983 257.17653 385.144 0.72723522
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700 15.22063 -2052.4439 1175.9011 -3228.345 735.43016 0 393.72125 153577.95 -157935.44 -1936.2883 26318.916 263.16908 394.10321 0.77446426
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720 15.565813 -2092.4868 1137.4051 -3229.892 739.27374 0 431.22089 153537.92 -157938.3 -1669.6367 26318.64 254.5536 381.18868 0.77432854
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740 15.926298 -2128.2671 1117.2535 -3245.5206 763.39303 0 451.2336 153475.75 -157935.89 -1554.5185 26294.984 250.04362 374.42691 0.77695221
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760 16.273413 -2164.5578 1132.9117 -3297.4695 791.93983 0 493.17297 153351.43 -157934.01 -1464.3621 26250.086 253.54797 379.63211 0.87260304
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780 16.620524 -2201.7367 1138.2941 -3340.0308 832.89022 0 542.69718 153217.14 -157932.76 -1185.0268 26186.538 254.75255 381.43046 0.88724559
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800 16.968419 -2236.9734 1127.0464 -3364.0197 849.94855 0 579.03844 153137.36 -157930.36 -957.1991 26107.922 252.23529 377.65702 0.8873688
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820 17.320858 -2274.0191 1152.6791 -3426.6982 878.53555 0 605.98285 153020.89 -157932.1 -1004.5494 26016.264 257.97196 386.24526 0.90940959
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840 17.671788 -2312.5555 1157.6702 -3470.2257 915.53242 0 653.69994 152892.11 -157931.56 -793.45868 25912.528 259.08897 387.88866 0.97141875
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860 18.021136 -2351.0088 1136.5124 -3487.5212 921.37408 0 665.09396 152857.19 -157931.18 -528.38134 25800.163 254.35382 380.78143 0.98986969
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880 18.370286 -2387.3364 1155.2826 -3542.619 934.02359 0 660.06761 152795.05 -157931.76 -775.58796 25681.702 258.55463 386.99987 1.1470186
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900 18.737898 -2425.9324 1151.5543 -3577.4867 936.00838 0 670.95003 152749.78 -157934.22 -883.49007 25555.357 257.72021 385.72656 1.1920669
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920 19.09607 -2461.264 1119.906 -3581.17 931.8496 0 682.4928 152739.5 -157935.01 -890.93067 25420.635 250.63726 375.12148 1.1675653
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940 19.45002 -2496.7293 1081.4763 -3578.2056 971.61744 0 731.21429 152653.33 -157934.36 -483.6151 25277.795 242.03662 362.20568 1.2144341
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960 19.805087 -2527.097 1111.841 -3638.938 964.7058 0 704.68407 152623.89 -157932.22 -841.64397 25129.524 248.8323 372.33505 1.3291216
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980 20.160533 -2560.1354 1096.9132 -3657.0486 954.19645 0 693.42648 152627.51 -157932.19 -949.1276 24974.275 245.49142 367.3853 1.2126954
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1000 20.518917 -2592.9079 1053.7186 -3646.6266 959.23242 0 684.31399 152644.74 -157934.91 -869.15319 24811.035 235.8244 352.90011 1.2013298
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1020 20.849072 -2623.091 1066.4493 -3689.5404 998.09604 0 709.32917 152535.4 -157932.37 -881.38225 24640.265 238.67355 357.17132 1.2006706
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1040 21.194962 -2652.822 1083.618 -3736.44 1011.32 0 727.70427 152458.99 -157934.45 -815.2175 24461.841 242.51594 362.90994 1.2429114
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1060 21.530151 -2683.6347 1074.3994 -3758.0341 1029.3659 0 763.93884 152381.4 -157932.73 -616.78933 24277.069 240.45279 359.82116 1.235143
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1080 21.868091 -2715.2991 1094.3032 -3809.6022 1068.1764 0 785.28284 152272.57 -157935.63 -541.23611 24088.232 244.9073 366.48583 1.2604348
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1100 22.209137 -2747.0371 1066.1644 -3813.2016 1080.2369 0 833.94072 152208.13 -157935.51 -217.98411 23897.246 238.60979 357.0619 1.2283546
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1120 22.551618 -2774.9066 1084.3361 -3859.2427 1113.055 0 847.43384 152114.69 -157934.42 -77.787494 23707.475 242.67665 363.13214 1.2803322
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1140 22.899431 -2803.21 1072.4113 -3875.6213 1090.9217 0 807.02034 152161.17 -157934.73 -668.47773 23520.606 240.00786 359.14316 1.2572349
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1160 23.252016 -2834.8697 1052.5943 -3887.464 1096.5034 0 789.77107 152162.88 -157936.62 -589.78074 23331.777 235.57277 352.55512 1.1369148
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1180 23.609597 -2863.7817 1031.8109 -3895.5926 1087.1932 0 789.79657 152165.44 -157938.03 -586.94333 23140.391 230.92139 345.60929 1.0837566
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1200 23.970129 -2891.3631 1042.111 -3933.4741 1093.7082 0 775.83298 152136.1 -157939.12 -1109.7168 22947.229 233.22659 349.07035 1.0726257
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1220 24.3333 -2919.3393 1043.3795 -3962.7187 1095.6802 0 760.56643 152121.29 -157940.25 -1189.6331 22748.747 233.51046 349.50414 1.0560945
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1240 24.699158 -2942.4201 1015.5889 -3958.009 1114.7861 0 821.20595 152042.69 -157936.69 -581.49954 22545.116 227.29088 340.1868 1.0444581
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1260 25.06694 -2965.9906 1011.5209 -3977.5115 1137.3984 0 850.69736 151972.34 -157937.95 -557.09399 22340.759 226.38045 338.85243 0.98374803
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1280 25.506043 -2989.5484 1016.7798 -4006.3282 1160.9102 0 882.24024 151890.5 -157939.98 -93.844073 22136.859 227.55742 340.60408 1.0089629
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1300 25.885481 -3011.5964 1043.7628 -4055.3592 1184.2311 0 891.6381 151808.85 -157940.08 -307.32007 21936.757 233.59626 349.6133 1.0504806
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1320 26.286564 -3035.1132 1037.5333 -4072.6466 1179.597 0 903.59052 151784.33 -157940.16 -91.53774 21739.794 232.20209 347.62923 0.8833997
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1340 26.707803 -3061.1043 1034.7198 -4095.8241 1231.5568 0 955.77666 151655.57 -157938.72 53.261099 21546.978 231.57242 346.58931 1.0307605
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1360 27.133179 -3085.252 983.77833 -4069.0303 1230.971 0 968.86383 151669.63 -157938.5 197.66951 21360.266 220.17161 329.49241 1.002352
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1380 27.554558 -3101.9696 1037.9918 -4139.9614 1216.6215 0 897.01691 151685.79 -157939.39 -392.64446 21180.32 232.3047 347.61632 1.0380526
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1400 27.956349 -3124.8379 1003.328 -4128.1659 1199.4883 0 863.54306 151748.07 -157939.27 -548.32584 21003.378 224.54686 336.16828 0.85494391
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1420 28.361482 -3146.8927 1020.9417 -4167.8344 1210.319 0 850.57584 151710.13 -157938.86 -1093.8532 20825.938 228.48885 342.04449 0.9178739
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1440 28.768238 -3170.6554 993.33274 -4163.9882 1239.5959 0 893.87046 151642.2 -157939.65 -436.10089 20645.122 222.30991 332.79717 0.88336557
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1460 29.177687 -3191.0873 980.2106 -4171.2979 1257.3639 0 955.42122 151554.27 -157938.35 -139.1763 20465.429 219.37314 328.30589 0.99602014
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1480 29.586943 -3208.4185 993.92387 -4202.3424 1243.9183 0 936.28667 151555.9 -157938.45 -261.1948 20289.512 222.4422 333.01034 0.85071989
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1500 29.995233 -3229.0775 1028.0284 -4257.1059 1272.6443 0 960.80911 151449.75 -157940.31 -307.25416 20116.744 230.07487 344.43881 0.88683413
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1520 30.435761 -3250.8294 998.11977 -4248.9491 1282.1976 0 990.08774 151419.81 -157941.05 64.772936 19947.298 223.38125 334.38841 0.90320757
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1540 30.853458 -3268.3168 1004.1599 -4272.4768 1299.4164 0 987.20608 151381.91 -157941.01 -80.22578 19782.738 224.73305 336.30685 1.007422
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1560 31.279241 -3289.0826 966.08591 -4255.1685 1287.1272 0 982.95309 151416.22 -157941.47 198.4371 19622.918 216.21201 323.54353 0.99939162
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1580 31.708028 -3306.2125 979.26815 -4285.4807 1288.5111 0 952.23769 151415.68 -157941.91 -206.26434 19467.717 219.16222 328.0518 0.90689318
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1600 32.140092 -3325.1219 984.21128 -4309.3331 1308.258 0 963.95207 151360.81 -157942.35 -284.04656 19314.766 220.2685 329.66568 0.9610293
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1620 32.5727 -3340.9024 1013.5306 -4354.433 1318.1025 0 944.3489 151325.17 -157942.05 -653.005 19163.698 226.83023 339.47468 1.0097397
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1640 32.982791 -3360.2312 974.13546 -4334.3667 1312.594 0 986.63361 151308.68 -157942.28 343.78235 19013.496 218.01352 326.28924 0.99083786
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1660 33.419277 -3375.6484 982.60503 -4358.2535 1345.3148 0 970.47388 151266.28 -157940.32 -374.81541 18867.836 219.90902 329.06869 1.0301828
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1680 33.858902 -3394.428 981.74052 -4376.1685 1319.3919 0 955.09161 151289.81 -157940.47 -162.3498 18724.14 219.71554 328.81202 0.99514477
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1700 34.30191 -3412.8462 973.87976 -4386.7259 1341.294 0 965.41854 151248.54 -157941.98 -351.70824 18582.062 217.95629 326.03525 1.1973975
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1720 34.776698 -3429.9352 986.76909 -4416.7043 1362.6752 0 1013.2358 151149.58 -157942.2 37.299904 18441.349 220.84095 330.4706 1.0534043
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1740 35.222457 -3446.5561 971.25044 -4417.8065 1381.6012 0 1046.8608 151096.61 -157942.88 336.29665 18304.289 217.36784 325.28479 1.0839935
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1760 35.644247 -3463.1798 999.75562 -4462.9354 1395.5442 0 1012.1296 151070.28 -157940.88 -252.71902 18172.322 223.74736 334.82695 1.1205298
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1780 36.095301 -3481.5453 991.5153 -4473.0606 1403.686 0 1029.7008 151037.13 -157943.57 -108.73918 18043.082 221.90316 332.00846 1.1669904
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1800 36.548801 -3496.9886 965.33662 -4462.3252 1390.3088 0 1050.6761 151040.12 -157943.43 539.62368 17917.488 216.04432 323.23991 1.1447201
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1820 37.00671 -3510.113 991.32596 -4501.439 1392.0482 0 1034.7898 151015.68 -157943.96 152.36115 17797.781 221.86078 332.04409 1.050451
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1840 37.465953 -3528.9352 974.95032 -4503.8855 1387.6457 0 1012.5199 151036.63 -157940.68 -250.11127 17681.765 218.19588 326.4633 1.104675
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1860 37.926741 -3545.3967 970.46573 -4515.8624 1391.3683 0 1035.1551 151000.11 -157942.49 -218.15781 17567.52 217.19222 325.05524 1.0190724
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1880 38.391252 -3561.7398 933.83134 -4495.5711 1404.458 0 1032.7156 151010.9 -157943.64 -1.9885562 17454.833 208.99337 312.70412 1.1301542
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1900 38.856336 -3574.6165 984.6503 -4559.2668 1422.0814 0 1060.3245 150900.79 -157942.46 190.15103 17344.24 220.36676 329.66505 1.2027369
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1920 39.32352 -3589.0687 963.85062 -4552.9193 1427.8662 0 1075.6986 150887.22 -157943.7 506.81653 17237.394 215.71175 322.81523 1.0733524
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1940 39.79544 -3604.8214 970.89136 -4575.7128 1416.926 0 1037.9197 150913.56 -157944.12 -60.261935 17135.412 217.28748 325.12481 1.144127
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1960 40.270815 -3620.548 963.48434 -4584.0323 1401.1546 0 1016.5609 150941.43 -157943.17 -388.03612 17035.264 215.62977 322.67138 1.1152888
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1980 40.749353 -3638.3971 977.90456 -4616.3017 1415.5473 0 1009.486 150904.71 -157946.04 -640.67547 16934.97 218.85705 327.48198 1.1614525
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2000 41.229238 -3654.2588 957.08437 -4611.3432 1418.1059 0 1031.2688 150883.23 -157943.95 -595.60403 16834.098 214.19745 320.55039 1.0631632
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Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms
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Pair time (%) = 23.5391 (57.0932)
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Bond time (%) = 0.0153775 (0.0372976)
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Kspce time (%) = 3.17798 (7.70806)
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Neigh time (%) = 2.51543 (6.10108)
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Comm time (%) = 1.6585 (4.02262)
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Outpt time (%) = 0.00876421 (0.0212572)
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Other time (%) = 10.3141 (25.0165)
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Nlocal: 625 ave 632 max 619 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 12577 ave 12644 max 12511 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 532752 ave 581561 max 492708 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Total # of neighbors = 2131009
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Ave neighs/atom = 852.404
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Ave special neighs/atom = 4
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Neighbor list builds = 120
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Dangerous builds = 16
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