forked from lijiext/lammps
172 lines
13 KiB
Groff
172 lines
13 KiB
Groff
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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2 by 1 by 2 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 = 26875 11664
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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 = 14.7792 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 0.91017509 3449.6475 2040.7698 186.76984 1408.8777 836.85155 816.32124 115.24642 0 -758.7276 595242.44 -594843.26 3042.2937 55742.797 199.51659 152.7045
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100 1.829694 2917.9137 1947.102 178.19743 970.81176 363.96553 932.94225 165.60761 0 -931.00296 595306.34 -594867.04 1697.0127 55742.797 226.24749 49.885738
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150 2.6620312 2853.3142 1959.0731 179.29301 894.24108 244.19792 978.17893 187.28366 0 -941.03478 595295.44 -594869.82 4597.2005 55742.797 241.05848 14.405808
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200 3.4969041 2885.6715 1928.6381 176.50762 957.03347 227.09245 1066.5297 186.6858 0 -949.52603 595296.49 -594870.24 2602.8275 55742.797 240.70211 5.1458056
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250 4.621171 2905.8961 1939.7876 177.52802 966.10847 215.77945 1122.1238 195.98218 0 -993.52132 595296.54 -594870.79 1808.1681 55742.797 243.04306 2.643716
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300 5.5216351 2968.5517 1974.9277 180.74402 993.624 210.11413 1158.7871 194.142 0 -996.53154 595297.91 -594870.79 3371.8618 55742.797 247.7682 1.8321312
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350 6.3789251 2996.151 1992.9982 182.39782 1003.1527 217.80518 1150.726 205.32316 0 -996.14478 595296.05 -594870.61 3022.9945 55742.797 250.15947 1.5176819
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400 7.208317 2991.7201 1975.3852 180.78589 1016.3349 221.46133 1169.8254 213.90874 0 -1016.9906 595298.44 -594870.31 753.59124 55742.797 247.99744 1.3743032
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450 8.0359671 3061.6051 2009.1302 183.87421 1052.4749 212.54169 1234.7697 205.71762 0 -1028.2259 595297.95 -594870.28 996.71341 55742.797 252.23801 1.3870863
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500 8.8456361 3127.3783 2009.8033 183.93581 1117.5749 222.16507 1246.5854 215.82607 0 -994.66665 595298.3 -594870.63 2537.6157 55742.797 252.32947 1.367397
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550 9.6647151 3181.037 2069.9836 189.44346 1111.0534 218.00575 1246.961 212.55852 0 -992.83597 595296.16 -594869.79 1333.8768 55742.797 259.86467 1.4641506
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600 10.484356 3194.2009 2007.5349 183.7282 1186.666 228.93838 1309.4718 215.93595 0 -995.70641 595297.81 -594869.79 1336.7994 55742.797 252.00698 1.4677515
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650 11.30116 3145.4387 2028.2544 185.62444 1117.1843 209.73722 1277.9793 217.12799 0 -1015.2398 595297.88 -594870.3 1442.6875 55742.797 254.61499 1.4639962
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700 12.106719 3163.3345 2053.2645 187.91335 1110.07 209.45249 1257.3108 216.7541 0 -1000.1505 595296.63 -594869.92 1093.9724 55742.797 257.76091 1.4652884
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750 12.924665 3145.6215 2010.7195 184.01966 1134.902 224.53065 1248.3301 222.25374 0 -988.4479 595298.83 -594870.59 470.73988 55742.797 252.39115 1.5116555
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800 13.736913 3191.2614 2043.4195 187.01234 1147.842 225.71717 1239.3564 234.89539 0 -980.97352 595299.07 -594870.22 1472.0305 55742.797 256.53524 1.4309304
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850 14.550736 3157.6279 2004.8472 183.48223 1152.7806 217.72587 1269.3398 224.40554 0 -987.51794 595299.15 -594870.32 293.76575 55742.797 251.69397 1.4007963
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900 15.344895 3188.5027 2077.065 190.09155 1111.4377 216.92608 1251.4141 213.7672 0 -1000.1269 595299.5 -594870.05 702.56821 55742.797 260.7853 1.3847905
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950 16.157597 3205.6761 2090.9807 191.3651 1114.6954 223.7729 1252.7887 225.91029 0 -1016.3682 595299.15 -594870.56 -19.492925 55742.797 262.50762 1.4603579
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1000 16.969809 3231.5931 2078.7058 190.24172 1152.8873 228.77504 1273.1611 219.28923 0 -995.58473 595296.82 -594869.57 1292.4071 55742.797 260.98775 1.3954023
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1050 17.771785 3264.2837 2106.0113 192.7407 1158.2724 224.16481 1278.5557 212.91309 0 -985.93386 595298.71 -594870.14 1357.1588 55742.797 264.40381 1.4463397
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1100 18.572331 3243.3355 2125.1664 194.49376 1118.1691 227.38559 1247.5134 210.61488 0 -996.85878 595299.68 -594870.17 650.53225 55742.797 266.82195 1.4240918
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1150 19.40463 3255.4144 2096.5982 191.87922 1158.8162 234.11389 1267.4257 217.02225 0 -989.70892 595299.81 -594869.84 688.78475 55742.797 263.2133 1.4631154
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1200 20.321045 3266.2609 2088.3727 191.12642 1177.8882 225.40174 1284.1097 225.77008 0 -985.63518 595297.81 -594869.57 182.80287 55742.797 262.21901 1.3550749
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1250 21.233994 3277.4365 2093.1481 191.56346 1184.2884 250.33569 1267.9985 235.70102 0 -999.80819 595299.96 -594869.9 780.87528 55742.797 262.80001 1.4077597
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1300 22.113268 3280.4141 2121.4996 194.15818 1158.9145 228.23585 1259.7304 230.65174 0 -989.06345 595298.99 -594869.63 932.19341 55742.797 266.34543 1.4646736
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1350 23.007421 3272.2214 2088.047 191.09662 1184.1744 224.66504 1284.656 217.03214 0 -970.5252 595297.72 -594869.37 63.097535 55742.797 262.16781 1.3823451
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1400 23.903494 3239.3096 2099.1837 192.11584 1140.1259 221.3215 1252.8691 215.64014 0 -978.70393 595298.89 -594869.89 1125.3057 55742.797 263.59141 1.3221979
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1450 24.833224 3226.293 2042.7354 186.94973 1183.5576 241.40449 1273.025 233.66813 0 -994.70934 595299.55 -594869.38 -412.31857 55742.797 256.45155 1.4245996
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1500 25.736203 3245.4596 2097.0431 191.91994 1148.4164 250.3854 1248.1507 212.36871 0 -990.48467 595297.36 -594869.36 245.49743 55742.797 263.28349 1.4252034
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1550 26.633033 3308.5518 2113.8467 193.45778 1194.7051 234.5293 1286.7563 233.20552 0 -987.36764 595297.06 -594869.48 1324.7098 55742.797 265.37419 1.4864431
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1600 27.530123 3319.786 2130.8949 195.01803 1188.8911 234.06508 1292.3987 225.94876 0 -992.81161 595299.1 -594869.81 343.14209 55742.797 267.51024 1.5104547
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1650 28.41116 3239.0425 2066.8485 189.15654 1172.194 219.46922 1303.0071 210.00869 0 -989.28577 595298.63 -594869.64 -505.97551 55742.797 259.48305 1.4300292
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1700 29.313339 3281.3023 2054.581 188.03383 1226.7213 224.72686 1339.1948 208.65914 0 -974.24634 595297.79 -594869.4 331.11846 55742.797 257.92342 1.4735531
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1750 30.216241 3237.8348 2043.3835 187.00904 1194.4513 238.16066 1281.9383 221.74494 0 -976.72731 595299.4 -594870.06 612.69867 55742.797 256.53793 1.4116726
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1800 31.113153 3242.1274 2087.94 191.08683 1154.1873 240.53142 1256.6966 210.49591 0 -983.16111 595299.34 -594869.72 -8.1277769 55742.797 262.14149 1.4166426
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1850 31.993161 3249.8016 2079.8947 190.35052 1169.9069 233.21641 1269.4077 215.23716 0 -975.12835 595296.5 -594869.33 1156.1724 55742.797 261.13101 1.4122227
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1900 32.891621 3251.9579 2097.6037 191.97124 1154.3541 243.13703 1228.3357 235.37914 0 -983.06313 595300.37 -594869.8 293.60486 55742.797 263.33664 1.4715416
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1950 33.791255 3202.0703 2076.0894 190.00227 1125.9809 233.71337 1217.6976 227.58496 0 -981.8352 595298.07 -594869.25 -544.65606 55742.797 260.61868 1.5018224
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2000 34.690323 3215.7987 2015.5993 184.46625 1200.1994 242.43605 1281.6846 227.48326 0 -980.70325 595298.82 -594869.52 248.82508 55742.797 253.04055 1.4169879
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Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms
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Pair time (%) = 16.514 (47.6038)
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Bond time (%) = 4.35555 (12.5555)
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Kspce time (%) = 10.6198 (30.613)
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Neigh time (%) = 0.393407 (1.13405)
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Comm time (%) = 1.18699 (3.42165)
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Outpt time (%) = 0.00467861 (0.0134867)
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Other time (%) = 1.6161 (4.65863)
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Nlocal: 1125 ave 1219 max 1009 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 5768 ave 5890 max 5664 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 215002 ave 223956 max 206872 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 860008
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Ave neighs/atom = 191.113
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Ave special neighs/atom = 13.3333
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Neighbor list builds = 29
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Dangerous builds = 0
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