190 lines
12 KiB
Plaintext
190 lines
12 KiB
Plaintext
LAMMPS (30 Nov 2020)
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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 charge
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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 different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data hBN-momolayer-5nm.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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880 atoms
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read_data CPU = 0.008 seconds
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mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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######################## Potential defition ########################
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pair_style tersoff shift 0.00
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pair_coeff * * BNC.tersoff B N
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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####################################################################
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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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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke temp
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#thermo_modify lost warn
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thermo_modify line one format float %20.16g lost warn
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###### Run molecular dynamics ######
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run 10000
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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 = 4.1
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ghost atom cutoff = 4.1
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binsize = 2.05, bins = 23 24 49
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -6517.75168416643 -6551.83758440293 34.08590023649997 299.9999999999998
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100 -6517.591757868635 -6540.779491471579 23.18773360294392 204.0820407446414
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200 -6517.542257518233 -6546.334231680467 28.79197416223492 253.4066047468253
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300 -6517.547026665019 -6552.017766231997 34.47073956697721 303.3870837602092
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400 -6517.549880169609 -6554.168239147238 36.61835897762826 322.2889117514031
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500 -6517.548226470739 -6553.394824124983 35.84659765424357 315.4964141084193
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600 -6517.543822188257 -6557.804430840637 40.26060865238051 354.3454188362772
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700 -6517.548850551941 -6554.896250559415 37.34740000747415 328.7054155678276
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800 -6517.542638411757 -6557.375983041433 39.83334462967532 350.5849429232983
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900 -6517.55075885843 -6557.111484488137 39.56072562970743 348.1855431884253
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1000 -6517.54273795102 -6559.298879744795 41.75614179377518 367.5080444176888
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1100 -6517.549343783575 -6560.886093997487 43.33675021391144 381.4194424664666
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1200 -6517.542423332176 -6558.676768888114 41.13434555593687 362.0354334537062
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1300 -6517.545344075701 -6561.204696269845 43.65935219414447 384.258757062778
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1400 -6517.550486308486 -6559.652130027128 42.10164371864144 370.5489081396594
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1500 -6517.547348144133 -6560.675578342398 43.12823019826496 379.5841966827288
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1600 -6517.543563176833 -6558.851478162317 41.30791498548372 363.5630688836865
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1700 -6517.542623115538 -6561.609360337041 44.06673722150263 387.8442721103335
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1800 -6517.554833588377 -6561.212435833928 43.65760224555111 384.2433552522239
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1900 -6517.549071422489 -6560.38241286512 42.83334144263117 376.9887943000331
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2000 -6517.545980266263 -6557.338387626354 39.79240736009128 350.2246420132446
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2100 -6517.554095104669 -6559.87721259204 42.32311748737136 372.4981637015772
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2200 -6517.541910494127 -6557.900141553543 40.35823105941543 355.2046222578467
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2300 -6517.543741229654 -6555.791430728012 38.24768949835712 336.629127290004
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2400 -6517.555255788205 -6560.723935042218 43.16867925401336 379.940200679699
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2500 -6517.555074792246 -6557.544526593844 39.98945180159846 351.9588879050065
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2600 -6517.549903118179 -6557.918564784741 40.3686616665621 355.2964250889964
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2700 -6517.539742897031 -6557.945682615683 40.40593971865226 355.6245201532153
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2800 -6517.547251676093 -6556.865915617517 39.31866394142421 346.0550873113292
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2900 -6517.545299736506 -6559.862692054109 42.31739231760382 372.4477748041638
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3000 -6517.55560248467 -6560.792536373287 43.23693388861683 380.5409297271634
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3100 -6517.552205940511 -6558.067955972071 40.51575003156001 356.590992907162
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3200 -6517.552750237322 -6559.663276613887 42.11052637656611 370.627087015937
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3300 -6517.556463580721 -6559.886913646993 42.33045006627206 372.5626998779712
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3400 -6517.553240930869 -6559.759847990668 42.20660705979942 371.4727212743841
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3500 -6517.548452643367 -6558.30850296424 40.76005032087284 358.7411513681483
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3600 -6517.554196218421 -6559.440190093303 41.88599387488308 368.6509106486549
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3700 -6517.55327428666 -6559.20140683827 41.64813255160946 366.5574234153127
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3800 -6517.553265790113 -6559.320999047847 41.76773325773447 367.6100642899428
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3900 -6517.557526995435 -6558.935061683234 41.37753468779878 364.1758122922397
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4000 -6517.555340791266 -6559.073176508879 41.51783571761353 365.4106427838033
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4100 -6517.553854213419 -6558.263385298808 40.70953108538969 358.2965167673373
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4200 -6517.553680788039 -6558.14054442872 40.58686364068086 357.2168846274402
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4300 -6517.558042018571 -6556.578721922002 39.02067990343117 343.4324424412317
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4400 -6517.563739283292 -6558.500306214708 40.93656693141579 360.2947258020188
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4500 -6517.547020963956 -6555.377454255585 37.83043329162872 332.9567330991509
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4600 -6517.548172986324 -6558.772744519205 41.22457153288104 362.8295387258405
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4700 -6517.558584079818 -6557.969788651196 40.41120457137863 355.6708576654109
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4800 -6517.559372552759 -6557.310265979464 39.75089342670537 349.8592657160261
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4900 -6517.55923597315 -6558.176827172919 40.61759119976872 357.4873268825193
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5000 -6517.56212653515 -6557.374748952199 39.81262241704939 350.4025606554209
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5100 -6517.555552632631 -6557.497202980329 39.94165034769875 351.5381732966079
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5200 -6517.561569541295 -6558.157238110723 40.59566856942829 357.2943793864433
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5300 -6517.564502194116 -6558.421999422868 40.85749722875147 359.5988101701971
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5400 -6517.556534594537 -6557.267621790594 39.71108719605641 349.5089194111953
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5500 -6517.563877256539 -6557.142752156087 39.57887489954838 348.345280232614
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5600 -6517.56686938866 -6557.809180900105 40.24231151144559 354.1843803352434
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5700 -6517.558039039658 -6559.133111388302 41.57507234864435 365.9143991519822
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5800 -6517.555738279771 -6557.908663173967 40.35292489419648 355.1579211422933
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5900 -6517.561084510689 -6557.042738405876 39.4816538951864 347.4896096736371
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6000 -6517.55801940098 -6557.892645435926 40.33462603494598 354.9968675178603
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6100 -6517.564254724593 -6558.224594979722 40.66034025512962 357.8635738503061
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6200 -6517.560641752437 -6558.21020654546 40.64956479302306 357.7687358495627
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6300 -6517.566017136221 -6559.578738119577 42.01272098335624 369.7662730794008
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6400 -6517.556093448701 -6556.104820300268 38.54872685156678 339.2786452823787
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6500 -6517.560982934479 -6557.084136152714 39.52315321823437 347.8548573809885
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6600 -6517.564245932257 -6558.046609845879 40.48236391362233 356.2971518963097
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6700 -6517.566290721775 -6557.727671715245 40.16138099347028 353.472087122386
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6800 -6517.570284071772 -6557.990328296512 40.42004422474062 355.748658045926
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6900 -6517.565184634684 -6556.035668256965 38.47048362228119 338.5900036850376
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7000 -6517.559098587035 -6555.986507687455 38.42740910041999 338.2108921911735
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7100 -6517.558005558503 -6556.912239013785 39.35423345528209 346.3681450297208
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7200 -6517.571145809251 -6556.350273356944 38.77912754769311 341.3064693491723
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7300 -6517.561021218117 -6556.99807608988 39.43705487176288 347.0970805946272
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7400 -6517.564526723936 -6556.561549105003 38.99702238106649 343.22422565188
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7500 -6517.573591127068 -6559.064299272126 41.49070814505833 365.1718850655065
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7600 -6517.560285401078 -6556.032090011901 38.47180461082385 338.6016300924391
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7700 -6517.560367395816 -6556.511797795351 38.95143039953437 342.8229572574783
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7800 -6517.573020066369 -6556.924913541821 39.35189347545233 346.347550181292
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7900 -6517.566299833051 -6556.577995911533 39.01169607848268 343.3533731643211
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8000 -6517.570136763681 -6557.582657078253 40.01252031457137 352.1619206500376
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8100 -6517.575674117457 -6558.320029386858 40.74435526940069 358.6030146192588
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8200 -6517.571493793849 -6558.305152064342 40.73365827049295 358.5088671961291
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8300 -6517.5784508572 -6559.057530922976 41.47908006577681 365.0695429310681
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8400 -6517.571529794804 -6556.983706108324 39.41217631352003 346.8781171105746
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8500 -6517.573679430778 -6558.010837981697 40.4371585509185 355.8992862475501
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8600 -6517.569221385932 -6557.925020755149 40.35579936921761 355.1832202395844
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8700 -6517.577852436772 -6557.081904802895 39.50405236612336 347.6867451822922
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8800 -6517.580643488045 -6557.09464429535 39.514000807305 347.7743043294406
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8900 -6517.578100930365 -6556.390740011451 38.81263908108628 341.601414178213
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9000 -6517.580194960002 -6559.786353631432 42.20615867143003 371.4687748769035
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9100 -6517.564119644257 -6558.263714946205 40.69959530194826 358.209069024671
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9200 -6517.569716055186 -6557.301587884572 39.73187182938527 349.6918510619774
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9300 -6517.57904099131 -6558.208366761209 40.62932576989919 357.5906062741362
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9400 -6517.579849744588 -6556.949796893357 39.3699471487698 346.5064458524541
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9500 -6517.573257994172 -6556.659853832866 39.0865958386938 344.0125879102258
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9600 -6517.571031994579 -6556.369911317095 38.79887932251565 341.4803105094658
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9700 -6517.574140115361 -6556.924661161591 39.35052104622968 346.3354710293865
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9800 -6517.580185525737 -6557.018312552581 39.43812702684369 347.1065169457875
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9900 -6517.573201214946 -6558.960816834054 41.3876156191084 364.2645375238429
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10000 -6517.575226749958 -6558.46352748641 40.88830073645191 359.8699208712792
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Loop time of 15.95 on 1 procs for 10000 steps with 880 atoms
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Performance: 54.169 ns/day, 0.443 hours/ns, 626.959 timesteps/s
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99.6% CPU use with 1 MPI tasks x no 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 | 15.508 | 15.508 | 15.508 | 0.0 | 97.23
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Neigh | 0.12432 | 0.12432 | 0.12432 | 0.0 | 0.78
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Comm | 0.11079 | 0.11079 | 0.11079 | 0.0 | 0.69
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Output | 0.0090941 | 0.0090941 | 0.0090941 | 0.0 | 0.06
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Modify | 0.12027 | 0.12027 | 0.12027 | 0.0 | 0.75
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Other | | 0.07801 | | | 0.49
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Nlocal: 880.000 ave 880 max 880 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1569.00 ave 1569 max 1569 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 15844.0 ave 15844 max 15844 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15844
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Ave neighs/atom = 18.004545
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Neighbor list builds = 140
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Dangerous builds = 0
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Total wall time: 0:00:15
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