forked from lijiext/lammps
446 lines
20 KiB
Groff
446 lines
20 KiB
Groff
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LAMMPS (5 Oct 2016)
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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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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 420 atoms
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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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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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 = 17 15 1
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Memory usage per processor = 3.60136 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 0.00329685 on 4 procs for 35 steps with 420 atoms
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75.8% CPU use with 4 MPI tasks x no 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 | 0.0018942 | 0.0019329 | 0.0019758 | 0.1 | 58.63
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Neigh | 0.00011587 | 0.000121 | 0.00012612 | 0.0 | 3.67
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Comm | 0.00034523 | 0.00040966 | 0.00046587 | 0.3 | 12.43
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Output | 4.3869e-05 | 4.667e-05 | 5.2929e-05 | 0.1 | 1.42
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Modify | 2.4796e-05 | 3.7432e-05 | 5.0306e-05 | 0.2 | 1.14
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Other | | 0.0007492 | | | 22.73
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Nlocal: 105 ave 111 max 99 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 84 ave 90 max 78 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Neighs: 895 ave 999 max 798 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Memory usage per processor = 3.60136 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 -0.17713919 433.03804
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100 0 -3.1812307 0 -3.1805381 -0.15305002 434.96379
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110 0 -3.1812588 0 -3.1805938 -0.12504601 432.50683
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111 0 -3.1812728 0 -3.1805961 -0.12407115 432.50683
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Loop time of 0.00908947 on 4 procs for 76 steps with 420 atoms
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96.2% CPU use with 4 MPI tasks x no 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 -3.18059381928 -3.18059607058
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Force two-norm initial, final = 1618.56 0.444005
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Force max component initial, final = 1191.42 0.168709
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Final line search alpha, max atom move = 0.428871 0.0723543
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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 | 0.0037253 | 0.0040306 | 0.0043435 | 0.5 | 44.34
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Neigh | 0.00058532 | 0.00061685 | 0.00064421 | 0.1 | 6.79
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Comm | 0.0012383 | 0.0015994 | 0.0019143 | 0.8 | 17.60
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Output | 0.00012493 | 0.0001325 | 0.00015235 | 0.1 | 1.46
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Modify | 0.00026274 | 0.00028539 | 0.00030255 | 0.1 | 3.14
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Other | | 0.002425 | | | 26.68
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Nlocal: 105 ave 111 max 99 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 87 ave 90 max 84 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 899 ave 1001 max 797 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Memory usage per processor = 3.60136 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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111 0 -3.1812728 0 -0.21796955 -0.12362156 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 1.3134388 432.20444
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180 0 -3.1041304 0 -3.0969544 1.3751455 430.37021
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190 0 -3.1043441 0 -3.0970791 1.3920926 430.37021
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193 0 -3.1043346 0 -3.0970891 1.3934753 430.37021
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Loop time of 0.00948715 on 4 procs for 82 steps with 420 atoms
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100.1% CPU use with 4 MPI tasks x no 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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-0.217969552445 -3.09708660005 -3.09708907864
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Force two-norm initial, final = 1754.38 0.649535
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Force max component initial, final = 924.68 0.156756
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Final line search alpha, max atom move = 0.962047 0.150807
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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 | 0.0037739 | 0.0042151 | 0.0046482 | 0.6 | 44.43
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Neigh | 0.00041008 | 0.0004425 | 0.00048161 | 0.1 | 4.66
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Comm | 0.0013449 | 0.0018466 | 0.0023468 | 1.1 | 19.46
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Output | 0.00012422 | 0.00013196 | 0.00015044 | 0.1 | 1.39
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Modify | 0.00026131 | 0.00028855 | 0.00030518 | 0.1 | 3.04
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Other | | 0.002563 | | | 27.01
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Nlocal: 105 ave 112 max 98 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Nghost: 94 ave 97 max 91 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 916.5 ave 1013 max 831 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Memory usage per processor = 3.60136 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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193 0 -3.1043346 0 2.0111873 1.3910032 431.13505
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200 0 -2.5918062 0 -1.93191 5.511262 430.91953
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210 0 -2.8122299 0 -2.7440894 4.2686747 440.18337
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220 0 -2.910295 0 -2.8879715 3.5956981 444.98997
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230 0 -2.949231 0 -2.9335905 3.2079519 451.9225
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240 0 -2.9611012 0 -2.9486911 3.1241334 452.5907
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250 0 -2.9644798 0 -2.9549529 3.0499305 455.51712
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260 0 -2.9716705 0 -2.9621358 2.8593553 458.27346
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270 0 -3.0143454 0 -3.0048234 2.1158458 462.52748
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280 0 -3.0656896 0 -3.0590412 1.4428324 470.69566
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290 0 -3.1008608 0 -3.0951203 1.1487473 472.80734
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300 0 -3.1109522 0 -3.1046995 1.064904 470.50807
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310 0 -3.1123989 0 -3.105985 1.0430839 470.40952
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313 0 -3.1125022 0 -3.1060453 1.0390872 470.40952
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Loop time of 0.016437 on 4 procs for 120 steps with 420 atoms
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95.8% CPU use with 4 MPI tasks x no 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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2.01118731028 -3.10604533837 -3.10604533837
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Force two-norm initial, final = 2329.79 2.39232
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Force max component initial, final = 1038.4 0.571422
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Final line search alpha, max atom move = 7.76258e-07 4.43571e-07
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Iterations, force evaluations = 120 264
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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 | 0.0060949 | 0.0071945 | 0.008219 | 1.2 | 43.77
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Neigh | 0.00081253 | 0.00092614 | 0.0010352 | 0.3 | 5.63
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Comm | 0.0022275 | 0.0035025 | 0.0047491 | 2.1 | 21.31
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Output | 0.00018907 | 0.00019854 | 0.00022316 | 0.1 | 1.21
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Modify | 0.00045967 | 0.00049853 | 0.0005331 | 0.1 | 3.03
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Other | | 0.004117 | | | 25.05
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Nlocal: 105 ave 123 max 90 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 91 ave 100 max 85 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Neighs: 892.25 ave 1107 max 699 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 3569
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Ave neighs/atom = 8.49762
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Neighbor list builds = 28
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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: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Memory usage per processor = 3.60136 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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313 0 -3.1125022 0 5.3341053 1.0377311 471.02427
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320 0 -2.402824 0 -0.86170235 6.1550233 471.02943
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330 0 -2.5964265 0 -2.4563494 5.5893601 473.87197
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340 0 -2.857458 0 -2.8325789 3.9156904 478.37268
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350 0 -2.923244 0 -2.9056267 3.3461026 481.81668
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360 0 -2.9355414 0 -2.924236 3.2437289 484.05209
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370 0 -2.9486011 0 -2.9405396 2.9295065 487.64545
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380 0 -2.9695687 0 -2.9616077 2.5116249 491.53648
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390 0 -2.991356 0 -2.9786736 2.2788393 491.056
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400 0 -3.0098108 0 -2.9963408 2.0798685 490.87751
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410 0 -3.0142937 0 -3.0017605 2.0015139 491.52711
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417 0 -3.0148998 0 -3.0024932 1.9909706 492.48053
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Loop time of 0.0132418 on 4 procs for 104 steps with 420 atoms
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94.4% CPU use with 4 MPI tasks x no 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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5.33410533222 -3.00249023582 -3.00249317367
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Force two-norm initial, final = 3147.64 2.97401
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Force max component initial, final = 1384.36 0.679769
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Final line search alpha, max atom move = 0.14124 0.0960107
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Iterations, force evaluations = 104 200
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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 | 0.0043645 | 0.0054896 | 0.0065427 | 1.4 | 41.46
|
||
|
|
Neigh | 0.00071716 | 0.00088716 | 0.0010509 | 0.5 | 6.70
|
||
|
|
Comm | 0.0017078 | 0.0030243 | 0.0044179 | 2.3 | 22.84
|
||
|
|
Output | 0.00015879 | 0.00016719 | 0.00018978 | 0.1 | 1.26
|
||
|
|
Modify | 0.00033998 | 0.00038028 | 0.00042176 | 0.2 | 2.87
|
||
|
|
Other | | 0.003293 | | | 24.87
|
||
|
|
|
||
|
|
Nlocal: 105 ave 121 max 89 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
Nghost: 93.5 ave 101 max 86 min
|
||
|
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||
|
|
Neighs: 936 ave 1121 max 741 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
|
||
|
|
Total # of neighbors = 3744
|
||
|
|
Ave neighs/atom = 8.91429
|
||
|
|
Neighbor list builds = 27
|
||
|
|
Dangerous builds = 0
|
||
|
|
|
||
|
|
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
|
||
|
|
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
|
||
|
|
fix_modify 4 energy yes
|
||
|
|
minimize 1.0e-6 1.0e-6 1000 1000
|
||
|
|
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||
|
|
Memory usage per processor = 3.60141 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
417 0 -3.0148998 0 -2.4816986 1.9918498 492.26314
|
||
|
|
420 0 -2.9209943 0 -2.7871779 2.8201475 492.26417
|
||
|
|
430 0 -2.9210322 0 -2.8866221 3.0115293 492.22119
|
||
|
|
440 0 -2.930174 0 -2.9072946 3.0289241 491.74253
|
||
|
|
450 0 -2.9423694 0 -2.9251127 3.0269322 491.55578
|
||
|
|
460 0 -2.9595882 0 -2.9424058 2.8769376 491.29122
|
||
|
|
470 0 -2.9716874 0 -2.9531385 2.7820875 491.71167
|
||
|
|
480 0 -2.9967793 0 -2.9798492 2.5135722 493.20335
|
||
|
|
490 0 -3.0077594 0 -2.9927399 2.3652753 495.90598
|
||
|
|
500 0 -3.0156527 0 -3.0064227 2.2002124 502.94121
|
||
|
|
510 0 -3.0389075 0 -3.0316863 1.8518803 512.1298
|
||
|
|
520 0 -3.0533374 0 -3.0444153 1.6968184 511.35747
|
||
|
|
530 0 -3.0643133 0 -3.0573978 1.5165159 516.34223
|
||
|
|
540 0 -3.0958216 0 -3.0905446 1.0627598 519.02979
|
||
|
|
550 0 -3.1051578 0 -3.1009512 1.0050567 517.17039
|
||
|
|
560 0 -3.1119271 0 -3.1069923 0.92711525 515.78315
|
||
|
|
570 0 -3.114104 0 -3.1090684 0.9237051 515.34157
|
||
|
|
580 0 -3.114576 0 -3.1094219 0.9181339 515.34157
|
||
|
|
590 0 -3.114722 0 -3.1095528 0.90665975 515.99746
|
||
|
|
600 0 -3.1149189 0 -3.1096744 0.88783587 515.99746
|
||
|
|
605 0 -3.1149612 0 -3.1097106 0.88187936 515.99746
|
||
|
|
Loop time of 0.0257494 on 4 procs for 188 steps with 420 atoms
|
||
|
|
|
||
|
|
98.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
Minimization stats:
|
||
|
|
Stopping criterion = linesearch alpha is zero
|
||
|
|
Energy initial, next-to-last, final =
|
||
|
|
-2.48169863396 -3.10971061979 -3.10971061979
|
||
|
|
Force two-norm initial, final = 470.636 1.194
|
||
|
|
Force max component initial, final = 222.162 0.376608
|
||
|
|
Final line search alpha, max atom move = 2.92234e-06 1.10058e-06
|
||
|
|
Iterations, force evaluations = 188 401
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.0080748 | 0.010793 | 0.013608 | 2.6 | 41.91
|
||
|
|
Neigh | 0.000983 | 0.0012598 | 0.0015397 | 0.8 | 4.89
|
||
|
|
Comm | 0.003365 | 0.0064785 | 0.0095432 | 3.8 | 25.16
|
||
|
|
Output | 0.0002985 | 0.00031477 | 0.00035667 | 0.1 | 1.22
|
||
|
|
Modify | 0.00062346 | 0.0007531 | 0.00086522 | 0.4 | 2.92
|
||
|
|
Other | | 0.00615 | | | 23.89
|
||
|
|
|
||
|
|
Nlocal: 105 ave 125 max 84 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
Nghost: 94.25 ave 104 max 84 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
Neighs: 895.75 ave 1159 max 648 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
|
||
|
|
Total # of neighbors = 3583
|
||
|
|
Ave neighs/atom = 8.53095
|
||
|
|
Neighbor list builds = 38
|
||
|
|
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: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||
|
|
Memory usage per processor = 3.60141 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
605 0 -3.1149612 0 -2.7562264 0.88153856 516.19694
|
||
|
|
610 0 -3.0480145 0 -3.0046036 1.5377628 516.18952
|
||
|
|
620 0 -3.0581364 0 -3.0393996 1.5790644 516.23694
|
||
|
|
630 0 -3.058957 0 -3.0461523 1.6279637 515.82575
|
||
|
|
640 0 -3.0608654 0 -3.0476936 1.631809 515.82575
|
||
|
|
650 0 -3.059954 0 -3.0488507 1.7016953 514.58992
|
||
|
|
660 0 -3.0601043 0 -3.0495387 1.7749452 513.2301
|
||
|
|
670 0 -3.0600329 0 -3.0503272 1.8525614 512.87295
|
||
|
|
680 0 -3.0618342 0 -3.0532875 1.9461671 512.7735
|
||
|
|
690 0 -3.0681709 0 -3.0588644 1.8339583 513.83989
|
||
|
|
700 0 -3.0723671 0 -3.0624663 1.7080165 515.99424
|
||
|
|
710 0 -3.0738836 0 -3.0635305 1.6674853 516.40455
|
||
|
|
720 0 -3.0744809 0 -3.0640016 1.6430059 516.40455
|
||
|
|
729 0 -3.074692 0 -3.0641622 1.6351234 517.12194
|
||
|
|
Loop time of 0.017405 on 4 procs for 124 steps with 420 atoms
|
||
|
|
|
||
|
|
97.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
Minimization stats:
|
||
|
|
Stopping criterion = linesearch alpha is zero
|
||
|
|
Energy initial, next-to-last, final =
|
||
|
|
-2.75622643697 -3.06416218566 -3.06416218566
|
||
|
|
Force two-norm initial, final = 387.971 1.75423
|
||
|
|
Force max component initial, final = 226.888 0.425447
|
||
|
|
Final line search alpha, max atom move = 9.47831e-07 4.03252e-07
|
||
|
|
Iterations, force evaluations = 124 275
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.0049167 | 0.0073144 | 0.0095913 | 2.7 | 42.02
|
||
|
|
Neigh | 0.00037408 | 0.00051659 | 0.00065827 | 0.6 | 2.97
|
||
|
|
Comm | 0.0021894 | 0.0047411 | 0.0072858 | 3.6 | 27.24
|
||
|
|
Output | 0.00018907 | 0.0001967 | 0.00021863 | 0.1 | 1.13
|
||
|
|
Modify | 0.00040865 | 0.00051677 | 0.00060606 | 0.4 | 2.97
|
||
|
|
Other | | 0.004119 | | | 23.67
|
||
|
|
|
||
|
|
Nlocal: 105 ave 131 max 78 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
Nghost: 97.25 ave 110 max 84 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
Neighs: 900.25 ave 1197 max 607 min
|
||
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||
|
|
|
||
|
|
Total # of neighbors = 3601
|
||
|
|
Ave neighs/atom = 8.57381
|
||
|
|
Neighbor list builds = 16
|
||
|
|
Dangerous builds = 0
|
||
|
|
Total wall time: 0:00:00
|