211 lines
14 KiB
Groff
211 lines
14 KiB
Groff
LAMMPS (30 Apr 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
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using 1 OpenMP thread(s) per MPI task
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# Initialization
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units metal
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boundary p p p
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atom_style atomic
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use 2 atom types so that inter- and intra-layer
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# interactions can be specified separately
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read_data data.bilayer-graphene # read lammps data file
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orthogonal box = (0 0 -20) to (17.04 19.6761 40)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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256 atoms
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read_data CPU = 0.000291348 secs
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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# Separate atom groups
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group membrane type 1
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128 atoms in group membrane
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group adsorbant type 2
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128 atoms in group adsorbant
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
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####################################################################
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pair_coeff * * rebo CH.rebo C C # chemical
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Reading potential file CH.rebo with DATE: 2018-7-3
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pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
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####################################################################
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#### Simulation settings ####
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timestep 0.0001
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velocity all create 300.0 12345
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fix thermostat all nve
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compute COM1 membrane com
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compute COM2 adsorbant com
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############################
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# Output
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#dump 1 all xyz 100 trajec.xyz
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#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
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thermo 10
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thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
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thermo_modify line one format float %14.8f
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 3 3 8
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair rebo, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
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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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(3) neighbor class addition, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
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Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
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0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000
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10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126
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20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357
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30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673
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40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055
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50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486
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60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952
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70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441
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80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946
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90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458
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100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973
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110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489
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120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004
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130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519
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140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038
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150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562
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160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099
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170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654
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180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235
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190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851
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200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512
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210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230
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220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016
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230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883
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240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845
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250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913
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260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097
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270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408
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280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849
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290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424
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300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129
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310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957
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320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898
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330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935
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340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046
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350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207
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360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390
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370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561
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380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688
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390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734
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400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664
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410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442
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420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033
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430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405
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440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527
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450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373
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460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918
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470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143
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480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030
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490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565
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500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740
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510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547
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520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981
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530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040
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540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724
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550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032
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560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963
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570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517
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580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691
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590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478
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600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871
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610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856
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620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416
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630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531
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640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176
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650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323
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660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937
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670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986
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680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430
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690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229
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700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343
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710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729
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720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344
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730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148
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740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098
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750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156
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760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282
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770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441
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780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599
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790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726
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800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792
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810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773
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820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647
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830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393
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840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995
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850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439
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860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713
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870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805
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880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706
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890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408
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900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904
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910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186
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920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247
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930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078
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940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670
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950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015
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960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101
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970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915
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980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444
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990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672
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1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581
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Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms
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Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 timesteps/s
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99.7% CPU use with 1 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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---------------------------------------------------------------
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Pair | 2.5864 | 2.5864 | 2.5864 | 0.0 | 99.30
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0079134 | 0.0079134 | 0.0079134 | 0.0 | 0.30
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Output | 0.0027175 | 0.0027175 | 0.0027175 | 0.0 | 0.10
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Modify | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.16
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Other | | 0.00331 | | | 0.13
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Nlocal: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1721 ave 1721 max 1721 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 37312 ave 37312 max 37312 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 94592 ave 94592 max 94592 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 94592
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Ave neighs/atom = 369.5
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:02
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