forked from lijiext/lammps
460 lines
21 KiB
Groff
460 lines
21 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 2d indenter simulation with minimization instead of dynamics
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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# create geometry
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lattice hex 0.9
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Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
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region box block 0 20 0 10 -0.25 0.25
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create_box 2 box
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Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 420 atoms
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Time spent = 0.000453234 secs
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mass * 1.0
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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# define groups
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region 1 block INF INF INF 1.25 INF INF
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group lower region 1
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60 atoms in group lower
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group mobile subtract all lower
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360 atoms in group mobile
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set group lower type 2
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60 settings made for type
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# initial velocities
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fix 2 lower setforce 0.0 0.0 0.0
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# indenter
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fix 5 all enforce2d
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# minimize with indenter
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thermo 10
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#dump 1 all atom 10 dump.indent
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#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
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#dump_modify 2 pad 4
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#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
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#dump_modify 3 pad 4
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 17 15 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
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10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
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20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
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30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
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35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
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Loop time of 0.00889349 on 1 procs for 35 steps with 420 atoms
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98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-3.17275755126 -3.19093697812 -3.19093855395
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Force two-norm initial, final = 6.74302 0.230475
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Force max component initial, final = 1.46877 0.0236603
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Final line search alpha, max atom move = 1 0.0236603
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Iterations, force evaluations = 35 70
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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 | 0.0073352 | 0.0073352 | 0.0073352 | 0.0 | 82.48
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Neigh | 0.00039649 | 0.00039649 | 0.00039649 | 0.0 | 4.46
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Comm | 9.8944e-05 | 9.8944e-05 | 9.8944e-05 | 0.0 | 1.11
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Output | 2.718e-05 | 2.718e-05 | 2.718e-05 | 0.0 | 0.31
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Modify | 0.00016856 | 0.00016856 | 0.00016856 | 0.0 | 1.90
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Other | | 0.0008671 | | | 9.75
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Nlocal: 420 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 95 ave 95 max 95 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3580 ave 3580 max 3580 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3580
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Ave neighs/atom = 8.52381
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Neighbor list builds = 4
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Dangerous builds = 0
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variable k equal 5000.0/xlat
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variable k1 equal 1000.0/xlat
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fix 4 all indent $k sphere 10 13.0 0 6.0
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fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
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fix_modify 4 energy yes
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
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40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
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50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
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60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
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70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
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80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
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90 0 -3.1810856 0 -3.1803991 -0.1771392 433.03804
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100 0 -3.1812307 0 -3.1805381 -0.15305004 434.96379
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110 0 -3.1812588 0 -3.1805938 -0.12504604 432.50683
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111 0 -3.1812728 0 -3.1805961 -0.12407116 432.50683
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Loop time of 0.0211506 on 1 procs for 76 steps with 420 atoms
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99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-2.17436899358 -3.18059381924 -3.18059607055
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Force two-norm initial, final = 1618.56 0.444006
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Force max component initial, final = 1191.42 0.168708
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Final line search alpha, max atom move = 0.428869 0.0723538
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Iterations, force evaluations = 76 147
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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 | 0.015347 | 0.015347 | 0.015347 | 0.0 | 72.56
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Neigh | 0.002106 | 0.002106 | 0.002106 | 0.0 | 9.96
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Comm | 0.00025511 | 0.00025511 | 0.00025511 | 0.0 | 1.21
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Output | 7.1287e-05 | 7.1287e-05 | 7.1287e-05 | 0.0 | 0.34
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Modify | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 6.55
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Other | | 0.001985 | | | 9.38
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Nlocal: 420 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 95 ave 95 max 95 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3596 ave 3596 max 3596 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3596
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Ave neighs/atom = 8.5619
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Neighbor list builds = 19
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Dangerous builds = 0
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fix 4 all indent ${k1} sphere 10 12.5 0 6.0
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fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
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fix_modify 4 energy yes
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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111 0 -3.1812728 0 -0.21796953 -0.12362158 434.07977
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120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
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130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
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140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
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150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
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160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
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170 0 -3.1032959 0 -3.0962512 1.3134391 432.20445
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180 0 -3.1041304 0 -3.0969544 1.3751461 430.37017
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190 0 -3.1043441 0 -3.0970791 1.392095 430.37017
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193 0 -3.1043345 0 -3.0970891 1.3934777 430.37017
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Loop time of 0.0218823 on 1 procs for 82 steps with 420 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-0.217969533586 -3.09708660422 -3.09708908043
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Force two-norm initial, final = 1754.38 0.648372
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Force max component initial, final = 924.68 0.156564
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Final line search alpha, max atom move = 0.961384 0.150518
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Iterations, force evaluations = 82 156
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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 | 0.016445 | 0.016445 | 0.016445 | 0.0 | 75.15
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Neigh | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 7.27
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Comm | 0.00024986 | 0.00024986 | 0.00024986 | 0.0 | 1.14
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Output | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 | 0.0 | 0.33
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Modify | 0.0014741 | 0.0014741 | 0.0014741 | 0.0 | 6.74
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Other | | 0.002051 | | | 9.37
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Nlocal: 420 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 105 ave 105 max 105 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3666 ave 3666 max 3666 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3666
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Ave neighs/atom = 8.72857
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Neighbor list builds = 14
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Dangerous builds = 0
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fix 4 all indent ${k1} sphere 10 12.0 0 6.0
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fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
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fix_modify 4 energy yes
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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193 0 -3.1043345 0 2.0111862 1.3910056 431.13503
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200 0 -2.5918177 0 -1.931934 5.51119 430.91952
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210 0 -2.8122285 0 -2.7440908 4.2686845 440.18379
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220 0 -2.9102892 0 -2.8879734 3.5957736 444.98944
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230 0 -2.9492295 0 -2.9335905 3.2079493 451.92209
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240 0 -2.9611099 0 -2.9486963 3.1240398 452.59159
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250 0 -2.9644912 0 -2.9549723 3.0493724 455.54273
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260 0 -2.9716881 0 -2.9621479 2.8585653 458.29826
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270 0 -3.0142839 0 -3.0048107 2.1183076 462.48471
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280 0 -3.0666108 0 -3.0590819 1.4342986 470.61174
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290 0 -3.1004306 0 -3.0944504 1.1550298 472.70399
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300 0 -3.1107855 0 -3.1043751 1.0663324 470.76888
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310 0 -3.1124671 0 -3.1059633 1.0375877 473.02275
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316 0 -3.1126981 0 -3.1061297 1.0266662 473.02275
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Loop time of 0.0387044 on 1 procs for 123 steps with 420 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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2.01118618013 -3.10612971775 -3.10612971775
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Force two-norm initial, final = 2329.79 2.56384
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Force max component initial, final = 1038.4 0.558457
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Final line search alpha, max atom move = 6.21371e-07 3.47009e-07
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Iterations, force evaluations = 123 270
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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 | 0.028596 | 0.028596 | 0.028596 | 0.0 | 73.88
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Neigh | 0.0035679 | 0.0035679 | 0.0035679 | 0.0 | 9.22
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Comm | 0.00047278 | 0.00047278 | 0.00047278 | 0.0 | 1.22
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Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.29
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Modify | 0.0025539 | 0.0025539 | 0.0025539 | 0.0 | 6.60
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Other | | 0.003402 | | | 8.79
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Nlocal: 420 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 105 ave 105 max 105 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3583 ave 3583 max 3583 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3583
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Ave neighs/atom = 8.53095
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Neighbor list builds = 29
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Dangerous builds = 0
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fix 4 all indent ${k1} sphere 10 11.4 0 6.0
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fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
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fix_modify 4 energy yes
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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316 0 -3.1126981 0 5.3552772 1.0307152 471.16452
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320 0 -2.7131804 0 0.70918694 3.910187 471.16482
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330 0 -2.5180572 0 -2.2327154 5.9511047 472.82589
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340 0 -2.8183947 0 -2.790733 4.18655 477.34785
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350 0 -2.9132456 0 -2.8943586 3.4322048 481.94491
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360 0 -2.9337359 0 -2.9225123 3.2341233 484.63169
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370 0 -2.9463892 0 -2.9382426 3.0071366 485.20235
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380 0 -2.9682176 0 -2.9597318 2.6056737 490.5653
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390 0 -2.9878255 0 -2.974755 2.3632883 491.02616
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400 0 -3.0033473 0 -2.9915257 2.205124 490.20353
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410 0 -3.0130231 0 -3.001125 2.0531631 492.78365
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420 0 -3.0146089 0 -3.0030496 1.9865701 492.35543
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430 0 -3.0344603 0 -3.0225619 1.6795534 494.30371
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440 0 -3.03943 0 -3.0271752 1.64578 494.30371
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450 0 -3.0420658 0 -3.0294992 1.6461313 493.96169
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460 0 -3.0443144 0 -3.0312966 1.6701433 493.56812
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465 0 -3.0444584 0 -3.0313908 1.6713796 493.56812
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Loop time of 0.046638 on 1 procs for 149 steps with 420 atoms
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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5.35527716926 -3.03139082546 -3.03139082546
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Force two-norm initial, final = 3151.59 4.64631
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Force max component initial, final = 1384.28 2.19626
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Final line search alpha, max atom move = 1.88135e-07 4.13193e-07
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Iterations, force evaluations = 149 323
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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 | 0.034523 | 0.034523 | 0.034523 | 0.0 | 74.02
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Neigh | 0.0042307 | 0.0042307 | 0.0042307 | 0.0 | 9.07
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Comm | 0.00056744 | 0.00056744 | 0.00056744 | 0.0 | 1.22
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Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.30
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Modify | 0.0030701 | 0.0030701 | 0.0030701 | 0.0 | 6.58
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Other | | 0.004109 | | | 8.81
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Nlocal: 420 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 113 ave 113 max 113 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3693 ave 3693 max 3693 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3693
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Ave neighs/atom = 8.79286
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Neighbor list builds = 33
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Dangerous builds = 0
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fix 4 all indent ${k1} sphere 10 11.2 0 6.0
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fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
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fix_modify 4 energy yes
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minimize 1.0e-6 1.0e-6 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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465 0 -3.0444584 0 -2.5580192 1.6715946 493.50462
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470 0 -2.9426683 0 -2.8814986 2.6421083 493.54443
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480 0 -2.9569251 0 -2.9256743 2.6206554 493.55709
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490 0 -2.961805 0 -2.9376884 2.6095523 493.40001
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500 0 -2.9651536 0 -2.9450214 2.6314399 493.06356
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510 0 -2.9667772 0 -2.9489178 2.6710408 492.70775
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520 0 -2.9728188 0 -2.9566496 2.7182742 492.38186
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530 0 -2.9791224 0 -2.9651707 2.7038256 493.19977
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540 0 -2.9968316 0 -2.984276 2.5920672 495.29778
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550 0 -3.0029515 0 -2.9915532 2.4491025 500.52622
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560 0 -3.0160794 0 -3.0057787 2.0399831 513.34527
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570 0 -3.0363001 0 -3.0306173 1.6834763 520.40445
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580 0 -3.0548101 0 -3.0490935 1.501103 521.5353
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590 0 -3.0640876 0 -3.0585539 1.3888581 520.17883
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600 0 -3.0713144 0 -3.0649318 1.3341898 518.99349
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610 0 -3.0727361 0 -3.0662278 1.2983097 519.87058
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620 0 -3.0732598 0 -3.0671664 1.2611866 520.9829
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630 0 -3.076528 0 -3.069576 1.1930176 520.18857
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640 0 -3.0778611 0 -3.0710808 1.1946248 520.31492
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650 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
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651 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
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Loop time of 0.0571101 on 1 procs for 186 steps with 420 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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-2.55801918976 -3.07153633363 -3.07153633363
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Force two-norm initial, final = 440.856 1.45625
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Force max component initial, final = 245.987 0.411517
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Final line search alpha, max atom move = 1.25651e-06 5.17073e-07
|
|
Iterations, force evaluations = 186 403
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.042337 | 0.042337 | 0.042337 | 0.0 | 74.13
|
|
Neigh | 0.0050063 | 0.0050063 | 0.0050063 | 0.0 | 8.77
|
|
Comm | 0.00071383 | 0.00071383 | 0.00071383 | 0.0 | 1.25
|
|
Output | 0.00017142 | 0.00017142 | 0.00017142 | 0.0 | 0.30
|
|
Modify | 0.0038519 | 0.0038519 | 0.0038519 | 0.0 | 6.74
|
|
Other | | 0.005029 | | | 8.81
|
|
|
|
Nlocal: 420 ave 420 max 420 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 116 ave 116 max 116 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3622 ave 3622 max 3622 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3622
|
|
Ave neighs/atom = 8.62381
|
|
Neighbor list builds = 39
|
|
Dangerous builds = 0
|
|
|
|
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
|
|
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
|
|
fix_modify 4 energy yes
|
|
minimize 1.0e-6 1.0e-6 1000 1000
|
|
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
|
|
Per MPI rank memory allocation (min/avg/max) = 4.169 | 4.169 | 4.169 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
|
651 0 -3.0781525 0 -2.6488207 1.2032064 520.29591
|
|
660 0 -3.0085949 0 -2.9796645 1.9715308 520.26872
|
|
670 0 -3.014536 0 -2.9989599 2.0077209 520.35057
|
|
680 0 -3.0193861 0 -3.0073499 2.0050119 520.52555
|
|
690 0 -3.0214256 0 -3.0087927 2.0056587 520.37174
|
|
700 0 -3.0218644 0 -3.0095894 2.0386389 520.05804
|
|
710 0 -3.0262571 0 -3.0142277 2.1356802 520.14691
|
|
720 0 -3.0325017 0 -3.0216037 2.1065924 521.43634
|
|
730 0 -3.0400735 0 -3.0302631 2.0146233 523.09133
|
|
740 0 -3.048476 0 -3.0386288 1.9305047 523.14231
|
|
750 0 -3.0523937 0 -3.042131 1.9025403 522.0453
|
|
760 0 -3.0544932 0 -3.044222 1.9106706 521.73287
|
|
770 0 -3.0587698 0 -3.048907 1.9552463 521.6899
|
|
780 0 -3.065994 0 -3.0566273 1.931796 521.52157
|
|
790 0 -3.0675084 0 -3.0577936 1.9283059 520.99202
|
|
799 0 -3.0677005 0 -3.057959 1.9288603 520.99202
|
|
Loop time of 0.0457094 on 1 procs for 148 steps with 420 atoms
|
|
|
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
Minimization stats:
|
|
Stopping criterion = linesearch alpha is zero
|
|
Energy initial, next-to-last, final =
|
|
-2.64882068661 -3.05795898949 -3.05795898949
|
|
Force two-norm initial, final = 420.333 1.17649
|
|
Force max component initial, final = 194.656 0.28552
|
|
Final line search alpha, max atom move = 1.95857e-06 5.5921e-07
|
|
Iterations, force evaluations = 148 327
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.03413 | 0.03413 | 0.03413 | 0.0 | 74.67
|
|
Neigh | 0.0037162 | 0.0037162 | 0.0037162 | 0.0 | 8.13
|
|
Comm | 0.00058603 | 0.00058603 | 0.00058603 | 0.0 | 1.28
|
|
Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.28
|
|
Modify | 0.0031106 | 0.0031106 | 0.0031106 | 0.0 | 6.81
|
|
Other | | 0.00404 | | | 8.84
|
|
|
|
Nlocal: 420 ave 420 max 420 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 122 ave 122 max 122 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3612 ave 3612 max 3612 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3612
|
|
Ave neighs/atom = 8.6
|
|
Neighbor list builds = 30
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:00
|