forked from lijiext/lammps
178 lines
13 KiB
Groff
178 lines
13 KiB
Groff
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LAMMPS (18 Jul 2015)
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# 250 butane system for drude polarizability example (Nose-Hoover)
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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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dihedral_style opls
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
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pair_modify mix geometric tail yes
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kspace_style pppm 1.0e-4
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read_data data.butane
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orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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5 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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9 = max dihedrals/atom
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reading bonds ...
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4250 bonds
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reading angles ...
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6000 angles
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reading dihedrals ...
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6750 dihedrals
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5 = max # of 1-2 neighbors
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8 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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17 = max # of special neighbors
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group gBUTANE molecule 1:250
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4500 atoms in group gBUTANE
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group gCORES type 1 2 3
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3500 atoms in group gCORES
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group gDRUDES type 4 5
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1000 atoms in group gDRUDES
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pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
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pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
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pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
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pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
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pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
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pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
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pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
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pair_coeff 1 * thole 1.368000
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pair_coeff 2 * thole 1.368000
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pair_coeff 4 * thole 1.368000
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pair_coeff 5 * thole 1.368000
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neighbor 2.0 bin
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variable vTEMP equal 260.0
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variable vTEMP_D equal 1.0
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variable vPRESS equal 1.0
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velocity gCORES create ${vTEMP} 12345
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velocity gCORES create 260 12345
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velocity gDRUDES create ${vTEMP_D} 12345
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velocity gDRUDES create 1 12345
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fix fDRUDE all drude C C N D D
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fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
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0 = # of size 2 clusters
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500 = # of size 3 clusters
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500 = # of size 4 clusters
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0 = # of frozen angles
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comm_modify vel yes
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compute cTEMP_CORE gCORES temp/com
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compute cTEMP all temp/drude
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fix fDIRECT all drude/transform/direct
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fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
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fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
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fix fNVT1 gCORES nvt temp 260 260 100.0
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fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
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fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
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fix fNVT2 gDRUDES nvt temp 1 1 20.0
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fix fINVERSE all drude/transform/inverse
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fix fMOMENTUM all momentum 100 linear 1 1 1
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thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
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thermo 50
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timestep 0.5
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run 2000
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PPPM initialization ...
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G vector (1/distance) = 0.367867
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.031354
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estimated relative force accuracy = 9.44215e-05
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using double precision FFTs
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3d grid and FFT values/proc = 79507 46656
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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: 17
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New max number of 1-2 to 1-4 neighbors: 17 (+0)
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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master list distance cutoff = 10
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ghost atom cutoff = 10
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Memory usage per processor = 20.1567 Mbytes
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Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
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0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
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50 2.8816051 2130.0808 1490.8248 136.43926 639.25601 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137
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100 5.569447 2172.0554 1656.5476 151.60609 515.50773 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117
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150 8.2248161 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6234 55742.797 218.02975 0.12336382
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200 10.911476 2271.1314 1750.9955 160.2499 520.13587 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.4949 55742.797 220.19714 0.23035017
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250 13.588019 2333.7822 1793.0252 164.09642 540.75705 153.18169 833.95287 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339004
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300 16.26521 2403.6147 1909.3441 174.74185 494.27059 144.27299 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3721 55742.797 239.06243 3.0455686
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350 18.937858 2448.2389 1862.67 170.47027 585.56885 181.70523 821.7917 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806435
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400 21.590191 2498.6994 1942.5496 177.7808 556.14976 168.5792 828.99117 182.0756 0 -1050.149 595296.43 -594869.77 485.86761 55742.797 244.23632 0.3882729
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450 24.247025 2552.9641 1890.0917 172.97989 662.87241 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452669 55742.797 237.65323 0.34464588
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500 26.850275 2608.55 1970.0729 180.29971 638.4771 187.01392 838.62129 176.10775 0 -985.23355 595290.89 -594868.93 3471.1633 55742.797 247.59402 0.66791252
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550 29.482354 2667.002 1875.8227 171.67399 791.17931 178.48765 1003.6885 176.78989 0 -991.21705 595292.35 -594868.92 1767.0543 55742.797 235.34039 1.7252619
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600 32.10773 2715.2399 1883.279 172.35639 831.96094 186.79504 1047.6877 183.04311 0 -1010.5423 595293.27 -594868.29 931.85523 55742.797 236.28437 1.7094253
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650 34.715398 2754.4497 1970.794 180.3657 783.65568 166.02823 963.09399 184.8464 0 -952.45217 595290.25 -594868.11 2640.017 55742.797 247.67755 0.68709275
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700 37.337317 2795.9461 1928.2674 176.4737 867.67874 176.09641 1002.4636 186.11483 0 -920.14356 595291.32 -594868.18 664.78904 55742.797 242.41897 0.44316381
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750 39.927419 2838.2052 2043.2258 186.99461 794.97945 170.34991 941.73148 193.53082 0 -940.49604 595298.1 -594868.23 410.24758 55742.797 256.84035 0.55229077
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800 42.469991 2881.9788 1945.9722 178.09402 936.00667 197.5203 1021.5571 202.83524 0 -915.18511 595297.49 -594868.21 -716.81442 55742.797 244.35112 1.2303511
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850 45.05362 2923.3858 2106.5752 192.79231 816.81052 195.94987 886.41681 184.36064 0 -878.10485 595296.29 -594868.1 -1407.5711 55742.797 264.3276 1.8387296
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900 47.651245 2950.6673 2039.6221 186.6648 911.04515 183.79618 1000.7954 184.49766 0 -890.38965 595299.97 -594867.63 -1085.794 55742.797 256.21167 1.0198208
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950 50.451391 2976.6436 2006.5932 183.64202 970.05039 228.60059 985.21322 206.18529 0 -881.65815 595299.54 -594867.83 -1851.9703 55742.797 252.23637 0.54012241
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1000 53.018937 3003.743 2056.8471 188.24122 946.89587 171.73287 976.85675 207.05097 0 -836.24563 595294.95 -594867.45 282.61914 55742.797 258.5658 0.52076804
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1050 55.532595 3031.3535 2095.4846 191.7773 935.86887 203.54188 945.75569 204.8504 0 -846.10969 595294.45 -594866.62 -376.91112 55742.797 263.27093 0.93584407
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1100 58.115412 3058.5347 2047.3098 187.36838 1011.2249 211.94076 1001.093 223.66214 0 -855.82424 595297.13 -594866.78 -1381.6531 55742.797 256.93409 1.6724456
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1150 60.799698 3078.3996 2123.1811 194.31206 955.21855 189.50189 937.18685 224.21465 0 -823.63222 595294.38 -594866.43 524.70113 55742.797 266.5974 1.3568376
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1200 63.295243 3093.556 2005.8939 183.57802 1087.6621 201.3428 1044.9909 219.39202 0 -805.37122 595293.83 -594866.52 -370.32492 55742.797 252.0829 0.71475597
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1250 65.797931 3108.5155 2175.8972 199.13661 932.61826 156.6571 969.72254 225.30586 0 -850.00503 595297.25 -594866.31 -1015.3093 55742.797 273.53154 0.55100418
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1300 68.300441 3122.9792 2090.3719 191.30939 1032.6073 209.92015 984.36624 236.75408 0 -825.27583 595292.92 -594866.08 -798.51816 55742.797 262.69421 0.75855207
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1350 70.793202 3136.8213 2084.47 190.76925 1052.3513 186.49827 1004.7564 234.55362 0 -798.08335 595290.25 -594865.63 702.53782 55742.797 261.71553 1.3884089
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1400 73.326733 3144.9028 2180.3659 199.54558 964.53687 170.02484 962.43948 235.07761 0 -829.27156 595291.77 -594865.51 1682.2488 55742.797 273.7286 1.5246324
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1450 75.821906 3146.3365 2013.3816 184.26329 1132.9549 193.77936 1084.1403 252.3227 0 -821.23045 595288.54 -594864.6 -160.21484 55742.797 252.96375 0.87780357
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1500 78.325264 3150.6861 2107.4863 192.87569 1043.1998 185.11752 988.72532 245.47682 0 -796.86739 595285.46 -594864.71 2242.3101 55742.797 264.90216 0.61222547
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1550 80.779931 3156.3483 2074.5953 189.86552 1081.7531 166.52863 1062.4971 238.93518 0 -810.65247 595289.34 -594864.9 2224.9015 55742.797 260.73559 0.68881715
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1600 83.275807 3163.8714 2000.6756 183.10045 1163.1958 210.70823 1110.4519 256.16493 0 -840.1463 595290.73 -594864.71 -830.17884 55742.797 251.26533 1.1443116
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1650 85.768304 3169.3489 2056.4309 188.20313 1112.918 214.6419 1021.762 268.00157 0 -815.69477 595289 -594864.8 813.12089 55742.797 258.12835 1.5476743
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1700 88.261463 3168.7666 2119.4079 193.96675 1049.3587 147.25006 1027.6415 246.49221 0 -797.55007 595290.74 -594865.22 412.59618 55742.797 266.23017 1.0703149
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1750 90.746918 3168.2304 2066.7675 189.14913 1101.463 224.44009 1005.0052 243.56874 0 -797.83359 595291.25 -594864.96 -858.91314 55742.797 259.74684 0.69942293
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1800 93.246077 3169.7579 2109.6017 193.06929 1060.1562 204.57678 981.05867 249.37843 0 -801.42006 595291.51 -594864.95 137.05559 55742.797 265.15197 0.65571606
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1850 95.734661 3174.8532 2133.5052 195.25692 1041.348 175.87566 982.18775 244.55231 0 -786.49546 595290.43 -594865.21 882.03323 55742.797 268.02768 1.006296
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1900 98.221874 3180.3842 2106.4808 192.78367 1073.9034 207.8879 977.47746 250.68948 0 -788.04039 595290.55 -594864.66 574.40162 55742.797 264.45175 1.4759897
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1950 100.72148 3182.921 2084.8893 190.80763 1098.0317 207.26976 1007.5583 256.52302 0 -800.37789 595291.76 -594864.71 -981.75066 55742.797 261.81202 1.271779
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2000 103.20588 3185.2881 2079.8136 190.3431 1105.4745 185.44441 1008.6997 251.0561 0 -766.97142 595292.22 -594864.97 661.65951 55742.797 261.35563 0.78600155
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Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms
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Pair time (%) = 60.3651 (58.49)
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Bond time (%) = 16.8315 (16.3087)
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Kspce time (%) = 20.1106 (19.4859)
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Neigh time (%) = 1.52801 (1.48054)
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Comm time (%) = 0.328804 (0.318591)
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Outpt time (%) = 0.00495553 (0.00480159)
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Other time (%) = 4.03695 (3.91155)
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 10060 ave 10060 max 10060 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 774908 ave 774908 max 774908 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 774908
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Ave neighs/atom = 172.202
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Ave special neighs/atom = 13.3333
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Neighbor list builds = 35
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Dangerous builds = 0
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