forked from lijiext/lammps
172 lines
13 KiB
Groff
172 lines
13 KiB
Groff
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LAMMPS (18 Jul 2015)
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# 250 butane system for drude polarizability example (Langevin)
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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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comm_modify vel yes
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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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fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
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fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
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fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
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fix fNPH all nve
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compute cTEMP all temp/drude
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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 2.8944459 3475.1575 2067.5082 189.21692 1407.6493 846.00752 810.92425 115.58516 0 -764.28457 595242.38 -594842.96 3029.5187 55742.797 202.89871 152.54291
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100 5.6009829 2975.2938 1988.4777 181.98411 986.81605 358.65377 931.63831 175.54125 0 -919.10691 595306.8 -594866.71 2010.6143 55742.797 231.36532 50.118891
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150 8.2652578 2904.7202 1962.6821 179.62331 942.03808 234.91712 997.34884 195.22618 0 -909.31364 595293.23 -594869.37 4956.5664 55742.797 241.54715 14.313437
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200 10.97319 2905.616 1909.813 174.78477 995.80302 228.33514 1082.3513 200.51771 0 -943.19777 595298.16 -594870.37 2973.6338 55742.797 238.34584 5.1137785
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250 13.676164 2934.0626 1952.0155 178.6471 982.0471 212.76463 1131.5055 194.94566 0 -983.79846 595297.63 -594871 1591.8677 55742.797 244.66672 2.4161409
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300 16.381759 2995.4781 2017.7772 184.66557 977.70088 213.25867 1133.9492 195.13329 0 -992.6543 595299.31 -594871.29 2817.7518 55742.797 253.21545 1.6812532
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350 19.14905 3058.4882 1982.338 181.4222 1076.1502 228.54692 1197.9766 205.68279 0 -982.30502 595297.25 -594871 1408.2609 55742.797 248.83728 1.4672371
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400 21.914272 3016.5895 1998.3531 182.8879 1018.2363 238.06518 1169.309 197.52924 0 -1014.8678 595298.98 -594870.78 1454.1926 55742.797 250.8778 1.3985907
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450 24.629148 3014.232 1979.0496 181.12125 1035.1824 216.45567 1198.2831 197.81853 0 -1005.5029 595298.68 -594870.56 1296.2887 55742.797 248.44786 1.4025051
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500 27.390589 3054.4694 2023.8824 185.22432 1030.587 220.97548 1197.2137 199.51957 0 -1014.3543 595298.28 -594871.05 2481.3102 55742.797 254.08894 1.4000969
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550 30.147365 3088.0877 2020.1967 184.887 1067.8909 221.93439 1216.8427 213.27263 0 -1012.4867 595299.44 -594871.11 1697.8283 55742.797 253.63701 1.3687703
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600 32.854639 3112.7966 2031.7038 185.94013 1081.0928 220.37419 1254.8806 208.09272 0 -1030.3329 595298.95 -594870.87 -75.358619 55742.797 255.05809 1.439614
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650 35.725004 3155.4753 2025.6962 185.39031 1129.7792 221.82928 1284.1281 210.16702 0 -1015.1565 595299.63 -594870.82 1286.1601 55742.797 254.30974 1.4197689
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700 38.70379 3134.5524 2054.9292 188.0657 1079.6232 225.36387 1243.5643 191.53984 0 -1010.9148 595301.25 -594871.18 700.78109 55742.797 257.97902 1.4421042
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750 41.679769 3189.6098 2103.3042 192.49294 1086.3056 219.5641 1243.9772 203.81533 0 -1010.2161 595299.86 -594870.7 482.90086 55742.797 264.08828 1.3795515
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800 44.637671 3173.7718 2053.4131 187.92694 1120.3587 219.52183 1256.8457 218.62858 0 -1003.175 595299.34 -594870.81 538.9293 55742.797 257.80398 1.4002525
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850 47.531367 3221.5884 2084.0326 190.72922 1137.5559 224.32279 1277.7167 218.74781 0 -1011.3685 595298.54 -594870.4 145.40179 55742.797 261.66451 1.3777132
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900 50.379314 3214.7916 2054.2398 188.00261 1160.5518 222.07439 1296.738 225.4151 0 -1013.6054 595300.61 -594870.68 490.09072 55742.797 257.90629 1.4047863
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950 53.038527 3213.4974 2122.2134 194.2235 1091.284 221.85551 1252.3002 201.89089 0 -1014.1089 595300.04 -594870.69 1203.4321 55742.797 266.42418 1.4941572
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1000 55.653448 3212.7244 2079.8287 190.34449 1132.8956 225.42816 1261.5078 204.71764 0 -986.95829 595298.68 -594870.48 790.47665 55742.797 261.10437 1.4611106
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1050 58.290098 3216.1124 2106.2454 192.76212 1109.8669 213.54607 1261.1068 207.93437 0 -1001.5715 595299.05 -594870.2 69.145866 55742.797 264.43815 1.4332898
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1100 60.921228 3218.0797 2082.4185 190.5815 1135.6611 236.95827 1266.8625 198.25038 0 -995.08857 595298.88 -594870.2 694.35787 55742.797 261.43907 1.4374087
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1150 63.510285 3208.3968 2119.1968 193.94742 1089.2 210.20908 1236.1825 202.19163 0 -988.56762 595299.35 -594870.17 1528.4475 55742.797 266.08185 1.3950176
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1200 66.140576 3219.1289 2078.071 190.18362 1141.0579 234.57015 1268.2146 206.93186 0 -997.01686 595298.32 -594869.97 939.70203 55742.797 260.89628 1.4263352
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1250 68.774998 3268.5006 2115.3231 193.5929 1153.1775 241.50662 1262.3711 220.71001 0 -1000.1626 595298.37 -594869.62 -187.61926 55742.797 265.57695 1.4418423
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1300 71.409732 3324.099 2138.7146 195.73368 1185.3844 242.3031 1279.7915 223.94399 0 -989.04901 595298.47 -594870.08 258.69655 55742.797 268.51674 1.4497832
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1350 73.990336 3290.8471 2103.0993 192.47419 1187.7477 219.60844 1312.8653 221.57552 0 -993.69832 595297.61 -594870.21 1651.4259 55742.797 264.03877 1.4428477
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1400 76.620059 3227.0141 2052.6998 187.86167 1174.3143 236.01325 1272.4804 217.65692 0 -979.6779 595297.5 -594869.66 595.11702 55742.797 257.67276 1.5108922
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1450 79.249466 3253.5975 2107.984 192.92124 1145.6135 248.51645 1261.8304 208.79164 0 -1002.8333 595299.15 -594869.84 170.12671 55742.797 264.66781 1.4041436
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1500 81.830899 3276.1976 2101.6206 192.33886 1174.577 242.38394 1288.61 204.9722 0 -989.7383 595298.02 -594869.67 619.26135 55742.797 263.84288 1.4691362
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1550 84.449908 3271.9376 2117.6914 193.80965 1154.2463 234.62432 1268.5368 202.02117 0 -979.66071 595298.65 -594869.92 568.43047 55742.797 265.86458 1.4693675
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1600 87.073373 3281.1387 2105.1447 192.66139 1175.994 219.69265 1288.3244 205.52796 0 -966.68015 595298.79 -594869.67 1351.6273 55742.797 264.27256 1.5056051
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1650 89.695136 3287.675 2131.7955 195.10045 1155.8795 235.54527 1262.9178 220.26583 0 -991.68887 595298.56 -594869.72 -750.34342 55742.797 267.63101 1.4905169
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1700 92.342235 3295.9626 2079.4982 190.31424 1216.4644 232.74928 1329.4691 218.51323 0 -992.04439 595297.16 -594869.38 589.94184 55742.797 261.06357 1.4590401
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1750 94.911541 3315.2639 2097.2605 191.93983 1218.0035 241.24927 1312.3575 214.88139 0 -978.98823 595298.34 -594869.84 -92.971422 55742.797 263.26817 1.5389785
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1800 97.525025 3241.5219 2086.8653 190.98847 1154.6566 221.03432 1282.1774 209.03793 0 -986.54668 595299 -594870.05 456.17335 55742.797 261.96332 1.5311996
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1850 100.13804 3222.7069 2040.0335 186.70245 1182.6734 242.74754 1272.8794 221.80974 0 -982.51665 595296.99 -594869.24 279.00233 55742.797 256.09213 1.4766233
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1900 102.70693 3190.3766 2032.3946 186.00335 1157.9819 213.06329 1268.187 220.21025 0 -971.50314 595297.54 -594869.51 499.15225 55742.797 255.16226 1.3935863
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1950 105.30868 3208.3096 2053.9844 187.97923 1154.3252 212.46296 1277.2726 210.16078 0 -974.19087 595298.44 -594869.82 807.22906 55742.797 257.85261 1.4622515
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2000 107.9105 3231.8811 2053.6913 187.9524 1178.1899 229.11239 1280.6492 220.1084 0 -979.25259 595297.02 -594869.45 474.05197 55742.797 257.80782 1.4833297
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Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms
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Pair time (%) = 65.8442 (61.0173)
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Bond time (%) = 16.6061 (15.3887)
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Kspce time (%) = 20.7451 (19.2244)
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Neigh time (%) = 1.24307 (1.15195)
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Comm time (%) = 0.386346 (0.358024)
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Outpt time (%) = 0.00603366 (0.00559135)
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Other time (%) = 3.07976 (2.854)
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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: 8739 ave 8739 max 8739 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 860638 ave 860638 max 860638 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 860638
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Ave neighs/atom = 191.253
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Ave special neighs/atom = 13.3333
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Neighbor list builds = 28
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Dangerous builds = 0
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