forked from lijiext/lammps
231 lines
11 KiB
Groff
231 lines
11 KiB
Groff
LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for thermal conductivity of liquid LJ
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# Green-Kubo method via compute heat/flux and fix ave/correlate
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# settings
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variable x equal 10
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variable y equal 10
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variable z equal 10
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variable rho equal 0.6
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variable t equal 1.35
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variable rc equal 2.5
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#variable rho equal 0.85
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#variable t equal 0.7
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#variable rc equal 3.0
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variable p equal 200 # correlation length
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variable s equal 10 # sample interval
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variable d equal $p*$s # dump interval
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variable d equal 200*$s
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variable d equal 200*10
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# setup problem
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units lj
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atom_style atomic
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lattice fcc ${rho}
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lattice fcc 0.6
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Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
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region box block 0 $x 0 $y 0 $z
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region box block 0 10 0 $y 0 $z
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region box block 0 10 0 10 0 $z
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
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2 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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mass 1 1.0
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velocity all create $t 87287
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velocity all create 1.35 87287
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1
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# 1st equilibration run
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fix 1 all nvt temp $t $t 0.5
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fix 1 all nvt temp 1.35 $t 0.5
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fix 1 all nvt temp 1.35 1.35 0.5
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thermo 100
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run 1000
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Neighbor list info ...
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1 neighbor list requests
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 14 14 14
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Memory usage per processor = 2.52285 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.35 -4.1241917 0 -2.0996979 -3.1962625
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100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
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200 1.271238 -3.7354981 0 -1.8291178 0.6873844
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300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
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400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
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500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
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600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
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700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
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800 1.3489121 -3.7082852 0 -1.6854229 0.86438061
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900 1.3708803 -3.6966168 0 -1.6408103 0.921415
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1000 1.3640742 -3.7075319 0 -1.6619322 0.86651332
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Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms
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Performance: 943316.262 tau/day, 2183.602 timesteps/s
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98.9% CPU use with 8 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 | 0.23307 | 0.24263 | 0.2466 | 1.0 | 52.98
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Neigh | 0.10661 | 0.11011 | 0.11166 | 0.5 | 24.04
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Comm | 0.069595 | 0.075354 | 0.087444 | 2.2 | 16.45
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Output | 0.00028014 | 0.00028831 | 0.00031686 | 0.1 | 0.06
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Modify | 0.01694 | 0.01904 | 0.021602 | 1.2 | 4.16
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Other | | 0.01053 | | | 2.30
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Nlocal: 500 ave 510 max 479 min
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Histogram: 1 0 0 0 0 2 1 1 0 3
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Nghost: 1519 ave 1539 max 1509 min
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Histogram: 2 0 4 0 0 0 0 1 0 1
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Neighs: 13553.8 ave 14051 max 12567 min
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Histogram: 1 0 0 0 1 0 2 1 1 2
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Total # of neighbors = 108430
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Ave neighs/atom = 27.1075
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Neighbor list builds = 155
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Dangerous builds = 0
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velocity all scale $t
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velocity all scale 1.35
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unfix 1
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# thermal conductivity calculation
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reset_timestep 0
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compute myKE all ke/atom
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compute myPE all pe/atom
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compute myStress all stress/atom NULL virial
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compute flux all heat/flux myKE myPE myStress
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variable Jx equal c_flux[1]/vol
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variable Jy equal c_flux[2]/vol
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variable Jz equal c_flux[3]/vol
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fix 1 all nve
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fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
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fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
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fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
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fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
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variable scale equal $s*dt/$t/$t/vol
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variable scale equal 10*dt/$t/$t/vol
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variable scale equal 10*dt/1.35/$t/vol
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variable scale equal 10*dt/1.35/1.35/vol
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variable k11 equal trap(f_JJ[3])*${scale}
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variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
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variable k22 equal trap(f_JJ[4])*${scale}
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variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
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variable k33 equal trap(f_JJ[5])*${scale}
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variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
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thermo $d
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thermo 2000
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thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
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run 100000
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Memory usage per processor = 4.39785 Mbytes
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Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
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0 1.35 0.012561273 -0.087295611 -0.037041124 0.014429409 0.69689289 0.12547278
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2000 1.3455113 -0.034571206 -0.17570902 -0.057218308 -1.6110148 7.9287556 8.5035767
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4000 1.3477761 -0.029528723 0.018790489 0.056107464 7.698411 1.9459053 9.9605272
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6000 1.3411436 -0.20281149 0.2184806 0.036024028 4.6533075 1.6223216 3.7246529
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8000 1.3561682 0.12038719 0.034930957 0.12173601 4.6450263 1.9032849 2.7566363
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10000 1.3397694 -0.14241489 -0.10956496 0.053088086 6.4191535 3.1582257 2.2786677
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12000 1.3410756 0.0033462395 0.14337321 0.16381733 5.9663779 1.6774436 1.7442075
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14000 1.3484928 0.0080419803 -0.080232102 0.039035519 4.9483626 1.6210893 1.6103343
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16000 1.3414836 -0.11063045 -0.031557643 0.032060333 6.1381241 1.438198 1.5831541
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18000 1.3488617 0.15908507 -0.021418806 -0.13992507 5.9198613 1.1016464 1.2905478
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20000 1.3535727 0.13217689 0.071933521 -0.028452943 6.3746606 1.003194 1.7007101
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22000 1.3408534 -0.078953557 -0.0022323663 -0.22979033 5.0105241 1.1489328 1.720847
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24000 1.34722 0.074784199 -0.071218632 0.15238165 4.4835452 0.94086945 3.1603615
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26000 1.3539218 0.052534363 0.10419096 0.1866213 4.2233104 1.3973253 3.2802881
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28000 1.3510105 0.0080425673 -0.03723976 0.20758595 5.261917 1.1931088 3.498831
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30000 1.3410807 -0.043957884 0.065683978 0.015386362 4.3815277 1.5000017 3.2237565
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32000 1.34766 -0.060481287 0.17142383 0.034367135 4.0974942 1.1637027 3.3771953
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34000 1.3417583 -0.10055844 0.050237668 0.06974988 4.1478021 1.0235517 2.9440249
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36000 1.3468728 0.09375756 -0.17875264 -0.063513807 4.4412987 0.71084371 3.4316313
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38000 1.3496868 -0.038635804 0.117965 0.018050271 4.962332 0.41701129 3.4690212
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40000 1.3403452 -0.092158116 0.14432655 -0.062258229 4.9980486 0.3762815 3.1688552
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42000 1.3498661 0.085807945 0.010256385 -0.002956898 4.8200626 0.29278287 3.094633
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44000 1.3564084 -0.07415163 -0.051327929 -0.18457986 4.7070907 0.3358167 3.0741797
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46000 1.3435866 -0.013911463 0.081813372 0.022628846 4.6043718 0.3682401 2.9956189
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48000 1.350611 0.036512747 0.080481423 -0.22973181 4.5648715 0.32728516 3.8573343
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50000 1.3421783 0.057665789 0.075597141 0.17377918 4.4278473 0.5383886 3.5866168
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52000 1.3473497 -0.11159587 -0.09688769 0.19876168 4.3876613 0.43408155 3.4786305
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54000 1.3459495 -0.15341705 0.063996148 -0.0038254597 4.8434026 0.62047297 3.445187
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56000 1.3545654 -0.082406034 0.089232864 -0.024355614 4.546051 0.7367607 3.3694561
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58000 1.3577504 0.082844384 0.019500036 0.073721698 4.4061886 1.4575694 3.2754066
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60000 1.348614 -0.16190321 -0.048576343 0.093820555 4.2946463 1.3416919 3.1159234
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62000 1.3551143 0.097443296 -0.04420265 -0.25713945 4.1260882 1.2550603 3.063215
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64000 1.346239 0.019198575 -0.095746619 0.18383922 4.5691519 1.2615165 2.9935539
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66000 1.3535383 -0.0035547901 -0.1753318 0.014025292 4.5371394 1.0740671 2.9362916
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68000 1.3421249 -0.18217113 0.077901408 0.04314081 5.1644747 1.0218342 2.9789097
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70000 1.3446114 0.029565781 -0.13771336 0.050328878 5.4811405 1.0430806 2.9748623
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72000 1.3692655 0.005711741 0.13966773 -0.062638787 5.3033385 1.1040582 2.7599218
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74000 1.3405365 -0.054281977 0.038019086 -0.024980877 5.1246258 2.0782965 2.725331
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76000 1.3644178 0.040847675 -0.051968108 -0.12259032 5.1218657 1.8504273 2.6804003
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78000 1.353792 -0.093663092 0.018784967 -0.073871437 5.025196 1.7789709 2.5339006
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80000 1.3520982 -0.09407101 0.010328039 0.0028841073 5.1410049 1.855057 2.6935895
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82000 1.3447597 -0.11935066 -0.2184608 0.073543056 5.2645334 1.7883077 4.2012292
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84000 1.3712151 -0.064367612 0.021246872 -0.033571866 5.0479674 1.8947341 4.3856536
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86000 1.3453867 -0.029842112 -0.042297039 0.05422886 5.0667777 2.0365983 4.4542311
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88000 1.3439543 -0.21625828 -0.028119372 -0.010320332 4.9946428 2.3095763 4.3429587
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90000 1.3472579 0.058391002 0.037139373 0.03424008 5.0599004 2.8132794 4.4503426
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92000 1.361788 0.028891114 0.072799744 -0.12035229 4.8759851 2.5130025 4.2747068
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94000 1.3440566 0.043421348 0.049653856 -0.060444094 4.8884081 2.5072981 4.3105221
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96000 1.3537566 0.088733517 -0.11449828 -0.049852036 4.8115085 2.4780963 4.2213579
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98000 1.3373399 0.25457663 -0.041723778 0.00084565184 4.7163394 2.4100822 4.485536
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100000 1.3487502 0.046333889 0.1247351 0.063467467 4.6563279 2.4049358 4.5742925
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Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms
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Performance: 872163.631 tau/day, 2018.897 timesteps/s
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99.6% CPU use with 8 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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Pair | 27.027 | 27.478 | 28.167 | 6.9 | 55.48
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Neigh | 11.257 | 11.369 | 11.491 | 2.3 | 22.95
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Comm | 6.6783 | 7.6942 | 8.2758 | 19.3 | 15.53
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Output | 0.0075166 | 0.024356 | 0.026799 | 4.1 | 0.05
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Modify | 1.7374 | 1.7617 | 1.7845 | 1.0 | 3.56
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Other | | 1.205 | | | 2.43
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Nlocal: 500 ave 505 max 491 min
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Histogram: 1 0 0 1 0 1 0 2 2 1
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Nghost: 1529.88 ave 1548 max 1508 min
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Histogram: 1 1 0 0 1 1 2 0 0 2
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Neighs: 13569.8 ave 13906 max 13235 min
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Histogram: 1 1 0 1 1 1 1 1 0 1
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Total # of neighbors = 108558
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Ave neighs/atom = 27.1395
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Neighbor list builds = 16041
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Dangerous builds = 0
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variable kappa equal (v_k11+v_k22+v_k33)/3.0
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print "running average conductivity: ${kappa}"
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running average conductivity: 3.8785187495769
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Total wall time: 0:00:50
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