forked from lijiext/lammps
200 lines
14 KiB
Groff
200 lines
14 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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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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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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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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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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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 = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 8 8 8
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2 neighbor lists, perpetual/occasional/extra = 2 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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(2) pair thole, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 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 c_cTEMP[1] c_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 4439.7916 55742.797 334.61375 18.435655
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50 0.63524747 2090.3465 1466.1274 134.17896 624.2191 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015
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100 1.2804167 2131.9774 1633.3979 149.48744 498.57955 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587
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150 1.9264774 2177.6381 1711.4959 156.63492 466.14218 134.74039 700.59917 168.27759 0 -965.58407 595300.38 -594872.27 4413.0227 55742.797 215.26856 0.12192187
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200 2.5798194 2233.5217 1730.4557 158.3701 503.06601 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5944 55742.797 217.61368 0.22886584
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250 3.234822 2297.3011 1773.2292 162.28471 524.07191 151.5359 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0577 55742.797 222.691 1.0389643
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300 3.9885037 2368.3956 1891.828 173.13879 476.56759 142.49027 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9227 55742.797 236.85673 3.0511439
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350 4.7276039 2414.4804 1843.9331 168.75548 570.54727 181.42277 808.6796 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5954 55742.797 231.57282 1.0738212
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400 5.3416793 2466.7094 1924.3089 176.11142 542.40044 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79737 55742.797 241.94266 0.38534799
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450 6.0018888 2522.7872 1875.8855 171.67974 646.90169 133.40906 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.40141 55742.797 235.86638 0.34369111
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500 6.6298664 2580.2771 1955.7507 178.98895 624.52635 185.08445 827.39297 175.04156 0 -984.94513 595290.88 -594868.93 3484.9216 55742.797 245.79119 0.67067791
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550 7.2369561 2640.6835 1866.035 170.77823 774.64858 176.89609 988.92025 176.49761 0 -991.07212 595292.32 -594868.91 1773.3486 55742.797 234.10561 1.7344207
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600 7.8453741 2690.8569 1876.0664 171.6963 814.7905 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72487 55742.797 235.38014 1.7010285
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650 8.4387105 2732.1825 1963.5421 179.70202 768.64035 165.39219 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9017 55742.797 246.76774 0.68037827
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700 9.0765064 2775.7294 1921.9362 175.89427 853.79318 175.21242 987.66712 186.48684 0 -918.75413 595291.36 -594868.18 670.06264 55742.797 241.62283 0.44222019
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750 9.6925657 2820.0741 2038.1504 186.53011 781.92376 168.58531 929.80574 193.62706 0 -939.9379 595298.09 -594868.25 398.72752 55742.797 256.20117 0.55407442
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800 10.302839 2865.959 1943.5754 177.87467 922.38359 197.16019 1009.2236 201.50386 0 -914.81706 595297.54 -594868.23 -717.10975 55742.797 244.0452 1.2420644
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850 10.916842 2909.1138 2101.5572 192.33306 807.55656 195.18897 876.12792 184.47417 0 -876.31499 595296.17 -594868.09 -1403.4232 55742.797 263.69793 1.8344028
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900 11.513051 2938.1376 2038.9242 186.60093 899.21343 183.32681 989.01659 184.31258 0 -889.86018 595300.05 -594867.63 -1087.2761 55742.797 256.12732 1.0106144
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950 12.11419 2965.6942 2007.942 183.76546 957.75216 227.45503 972.71506 206.37949 0 -880.4232 595299.46 -594867.83 -1848.7603 55742.797 252.40653 0.53885876
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1000 12.740639 2994.2317 2058.0187 188.34845 936.21302 170.68957 965.88085 205.36589 0 -833.14441 595294.86 -594867.44 327.6391 55742.797 258.71295 0.52143283
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1050 13.346812 3022.9501 2095.3848 191.76817 927.56526 203.90712 935.91396 205.08197 0 -845.07232 595294.32 -594866.59 -355.70418 55742.797 263.25608 0.94198602
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1100 13.938097 3051.1769 2047.7199 187.4059 1003.457 212.39892 989.65684 227.20812 0 -856.11277 595297.04 -594866.74 -1402.022 55742.797 256.98383 1.6773742
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1150 14.508841 3071.8157 2127.8626 194.74051 943.95311 188.38445 926.24309 223.28071 0 -821.63207 595294.06 -594866.38 550.31236 55742.797 267.1915 1.3431353
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1200 15.110682 3087.7694 2015.2955 184.43845 1072.4739 199.90932 1034.9531 215.15511 0 -804.43314 595293.38 -594866.49 -333.57793 55742.797 253.26777 0.70913778
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1250 15.728746 3102.5825 2176.9518 199.23312 925.63076 155.81519 956.83624 230.0728 0 -847.47674 595296.65 -594866.26 -932.66685 55742.797 273.66551 0.54750805
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1300 16.365541 3116.8403 2087.6045 191.05612 1029.2357 209.96201 974.81053 241.13608 0 -823.38398 595292.74 -594866.03 -825.75383 55742.797 262.34486 0.76175709
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1350 16.943579 3131.0787 2089.6524 191.24354 1041.4264 186.48189 998.11168 233.71019 0 -801.37003 595290.06 -594865.57 684.79151 55742.797 262.36797 1.3871293
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1400 17.542898 3138.996 2186.2582 200.08483 952.73785 168.60338 957.20178 227.71944 0 -826.52269 595291.08 -594865.34 1796.7295 55742.797 274.47403 1.5135537
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1450 18.144658 3139.5791 2010.7377 184.02132 1128.8414 192.8015 1074.5205 245.37206 0 -807.3159 595288.01 -594864.55 -16.504608 55742.797 252.63135 0.87723467
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1500 18.759382 3143.8991 2099.4529 192.14048 1044.4462 186.04014 980.83524 242.01309 0 -784.81131 595285 -594864.63 2343.8986 55742.797 263.89145 0.61241549
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1550 19.331644 3149.7316 2086.068 190.9155 1063.6635 165.80546 1056.0893 230.89463 0 -813.37768 595289.09 -594864.84 2260.7364 55742.797 262.17666 0.69483626
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1600 19.91757 3156.535 2013.4276 184.2675 1143.1073 210.65881 1098.2892 243.94955 0 -835.62037 595290.47 -594864.64 -838.57356 55742.797 252.86585 1.1542996
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1650 20.503137 3160.0031 2081.0656 190.45768 1078.9375 212.2197 1005.7509 250.38023 0 -813.71955 595289.15 -594864.85 796.21731 55742.797 261.22447 1.5557945
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1700 21.130273 3155.5677 2113.3761 193.41472 1042.1916 146.036 1019.0909 249.77802 0 -798.16357 595290.59 -594865.14 359.69262 55742.797 265.46995 1.074008
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1750 21.735444 3151.796 2063.5487 188.85455 1088.2472 224.89093 997.02075 247.36817 0 -807.87592 595291.82 -594864.98 -1081.2667 55742.797 259.34362 0.69484916
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1800 22.302735 3150.4232 2097.9294 192.00105 1052.4938 202.22751 974.42358 248.58229 0 -799.53722 595291.6 -594864.8 94.58692 55742.797 263.68474 0.65252808
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1850 22.902581 3153.4477 2106.6272 192.79706 1046.8205 177.57166 971.73469 249.90348 0 -777.13298 595289.76 -594865.02 881.42516 55742.797 264.65016 0.99601444
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1900 23.480426 3159.2037 2092.2693 191.48304 1066.9343 198.78895 969.41309 260.03288 0 -787.26163 595290.41 -594864.45 606.40366 55742.797 262.66088 1.4839893
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1950 24.086136 3164.5139 2059.5653 188.48999 1104.9485 214.12027 1000.4493 263.39543 0 -799.45067 595291.13 -594864.69 -1248.7209 55742.797 258.62963 1.2624825
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2000 24.655188 3171.2963 2080.1555 190.37439 1091.1408 179.21892 996.41486 248.41626 0 -760.00877 595292.04 -594864.94 940.70366 55742.797 261.39948 0.7837686
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Loop time of 24.6553 on 4 procs for 2000 steps with 4500 atoms
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Performance: 3.504 ns/day, 6.849 hours/ns, 81.119 timesteps/s
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96.3% 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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Pair | 11.825 | 12.439 | 13.012 | 12.2 | 50.45
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Bond | 0.82239 | 0.89713 | 0.95859 | 5.7 | 3.64
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Kspace | 6.6353 | 7.2001 | 7.8139 | 15.7 | 29.20
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Neigh | 0.44976 | 0.44994 | 0.45003 | 0.0 | 1.82
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Comm | 0.55452 | 0.62432 | 0.70013 | 6.6 | 2.53
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Output | 0.003664 | 0.0043042 | 0.0061252 | 1.6 | 0.02
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Modify | 2.9457 | 2.959 | 2.9736 | 0.7 | 12.00
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Other | | 0.08099 | | | 0.33
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Nlocal: 1125 ave 1166 max 1096 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 5867.25 ave 5956 max 5793 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 193608 ave 200510 max 186198 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 774433
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Ave neighs/atom = 172.096
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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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Total wall time: 0:00:24
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