forked from lijiext/lammps
332 lines
18 KiB
Groff
332 lines
18 KiB
Groff
LAMMPS (5 Oct 2016)
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# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
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units metal
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atom_style charge
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dimension 3
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boundary p p p
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lattice diamond 5.431
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 512 atoms
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mass 1 29.0
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change_box all triclinic
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triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
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velocity all create 1.0 277387
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pair_style comb
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pair_coeff * * ffield.comb Si
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Reading potential file ffield.comb with DATE: 2011-02-22
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neighbor 0.5 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all box/relax aniso 0.0 vmax 0.001
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timestep 0.00020
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thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
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thermo_modify norm yes
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thermo 1
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minimize 1.0e-14 1.0e-20 1000 10000
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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 = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25 -> bins = 4 4 4
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Memory usage per processor = 7.52233 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul
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0 1 -4.6295947 -4.6297237 -4.6297237 0
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1 1 -4.6295965 -4.6297255 -4.6297255 0
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2 1 -4.6295965 -4.6297255 -4.6297255 0
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3 1 -4.6295965 -4.6297255 -4.6297255 0
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Loop time of 0.0423422 on 4 procs for 3 steps with 512 atoms
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97.4% 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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-4.62972371535 -4.62972550325 -4.62972550325
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Force two-norm initial, final = 5.86582 3.9583e-08
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Force max component initial, final = 3.38663 2.28585e-08
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Final line search alpha, max atom move = 1 2.28585e-08
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Iterations, force evaluations = 3 6
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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 | 0.026049 | 0.03263 | 0.041219 | 3.0 | 77.06
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00049615 | 0.0090721 | 0.015641 | 5.7 | 21.43
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Output | 3.314e-05 | 3.5107e-05 | 4.1008e-05 | 0.1 | 0.08
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0006052 | | | 1.43
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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min_modify dmax 0.2 line quadratic
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unfix 1
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Neighbor list info ...
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1 neighbor list requests
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25 -> bins = 4 4 4
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Memory usage per processor = 5.89733 Mbytes
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Step Temp TotEng PotEng E_vdwl E_coul
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3 1 -4.6295965 -4.6297255 -4.6297255 0
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4 1 -4.6295965 -4.6297255 -4.6297255 0
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Loop time of 0.00589204 on 4 procs for 1 steps with 512 atoms
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Performance: 2.933 ns/day, 8.183 hours/ns, 169.721 timesteps/s
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101.8% CPU use with 4 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 | 0.003751 | 0.0046486 | 0.0057852 | 1.1 | 78.90
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 7.391e-05 | 0.001206 | 0.0021 | 2.1 | 20.47
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Output | 1.9073e-05 | 2.0742e-05 | 2.1935e-05 | 0.0 | 0.35
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Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.01
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Other | | 1.597e-05 | | | 0.27
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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### copy lines after this to any input script for elastic calculations ###
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## Elastic constants calculations: strain box, measure box stress
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## strain x, measure s_x, s_y, s_z, s_yz:
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## calculates C11, C12, C13 and C14
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fix 2 all deform 1 x scale 1.0001 remap x
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compute perfx all stress/atom NULL pair
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compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
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thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690)
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run 10
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Memory usage per processor = 6.64733 Mbytes
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Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
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4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06
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5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06
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6 21.72835 21.727916 21.727916 0 0 0 146204.21 77325.824 77325.824 2.3636154e-06 -2.6955085e-06 -5.4243912e-06
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7 21.728568 21.727916 21.727916 0 0 0 292407.66 154648.07 154648.07 -1.2891214e-06 -2.3607767e-06 -4.2545106e-06
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8 21.728785 21.727916 21.727916 0 0 0 438610.41 231966.78 231966.78 -1.7378096e-06 -2.0714741e-06 -3.8921893e-06
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9 21.729002 21.727916 21.727916 0 0 0 584812.43 309281.95 309281.95 2.5425006e-06 9.0454362e-06 -7.1598291e-06
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10 21.729219 21.727916 21.727916 0 0 0 731013.74 386593.58 386593.58 -1.6897864e-06 -2.6139147e-06 -5.4137742e-06
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11 21.729437 21.727916 21.727916 0 0 0 877214.34 463901.66 463901.66 -1.8806784e-06 -1.8704431e-06 -4.8350021e-06
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12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06
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13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06
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14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06
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Loop time of 0.0653707 on 4 procs for 10 steps with 512 atoms
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Performance: 2.643 ns/day, 9.079 hours/ns, 152.974 timesteps/s
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99.8% CPU use with 4 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 | 0.041152 | 0.050811 | 0.063103 | 3.5 | 77.73
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00078726 | 0.013075 | 0.02272 | 6.9 | 20.00
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Output | 0.0013869 | 0.0014045 | 0.0014176 | 0.0 | 2.15
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Modify | 2.9087e-05 | 3.32e-05 | 3.5048e-05 | 0.0 | 0.05
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Other | | 4.774e-05 | | | 0.07
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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## strain z, measure s_z: calculates C33
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fix 2 all deform 1 z scale 1.0001 remap x
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compute perfz all stress/atom NULL pair
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compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
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thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
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run 10
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Memory usage per processor = 7.39733 Mbytes
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Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
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14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06
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15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06
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16 21.730089 21.727916 21.72835 0 0 0 1539307.7 850399.78 919275.13 -1.1741349e-06 8.1321584e-06 -2.1634811e-06
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17 21.730089 21.727916 21.728568 0 0 0 1616602.3 927697.4 1065450.9 9.2086349e-07 -2.6001292e-06 -2.9133823e-06
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18 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.5 1211626 1.3356364e-06 -2.794764e-06 -9.2778033e-06
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19 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 -8.7949961e-07 -3.4755821e-06 -7.1758788e-06
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20 21.730089 21.727916 21.729219 0 0 0 1848464.8 1159569 1503974 1.674426e-06 -2.898863e-06 -2.1520562e-06
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21 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.5 1650146.9 -1.7524845e-06 -3.4851467e-06 -1.7806669e-06
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22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06
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23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06
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24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06
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Loop time of 0.065423 on 4 procs for 10 steps with 512 atoms
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Performance: 2.641 ns/day, 9.087 hours/ns, 152.851 timesteps/s
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99.3% CPU use with 4 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 | 0.041187 | 0.050801 | 0.063128 | 3.5 | 77.65
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00077367 | 0.013104 | 0.022709 | 6.9 | 20.03
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Output | 0.0014305 | 0.0014462 | 0.0014589 | 0.0 | 2.21
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Modify | 2.0504e-05 | 2.7299e-05 | 3.1233e-05 | 0.1 | 0.04
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Other | | 4.494e-05 | | | 0.07
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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## strain yz, measure s_yz: calculates C44
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fix 2 all deform 1 yz erate 0.0001 remap x
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compute perfyz all stress/atom NULL pair
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compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
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thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
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run 10
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Memory usage per processor = 8.16262 Mbytes
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Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
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24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07
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25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06
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26 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 -5.49227e-06 -4.2895969e-06 243.66104
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27 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 -6.5461301e-06 -6.5635547e-06 487.32212
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28 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 -6.2913987e-06 -6.8959666e-06 730.98323
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29 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 -6.1650242e-06 -6.374019e-06 974.64422
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30 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 -6.8112674e-06 -6.9206286e-06 1218.3053
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31 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 -6.5914369e-06 -8.6480249e-06 1461.9664
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32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275
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33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885
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34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496
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Loop time of 0.0656388 on 4 procs for 10 steps with 512 atoms
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Performance: 2.633 ns/day, 9.116 hours/ns, 152.349 timesteps/s
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99.8% CPU use with 4 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 | 0.040685 | 0.050668 | 0.063339 | 3.6 | 77.19
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00077748 | 0.013466 | 0.023423 | 7.0 | 20.52
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Output | 0.0013893 | 0.0014307 | 0.001461 | 0.1 | 2.18
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Modify | 2.1935e-05 | 2.6524e-05 | 3.0994e-05 | 0.1 | 0.04
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Other | | 4.733e-05 | | | 0.07
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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Neighbor list builds = 0
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Dangerous builds not checked
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## strain xy, measure s_xy: calculates C66
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fix 2 all deform 1 xy erate 0.0001 remap x
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compute perfxy all stress/atom NULL pair
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compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
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thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
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run 10
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Memory usage per processor = 8.91262 Mbytes
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Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
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34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106
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35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106
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36 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64726 -0.00014128194 2436.6106
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37 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29457 -0.00027206674 2436.6106
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38 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.94189 -0.00040462289 2436.6106
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39 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58915 -0.00053614117 2436.6106
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40 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00066911336 2436.6106
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41 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.00080012128 2436.6106
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|
42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106
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43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106
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|
44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106
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|
Loop time of 0.0657181 on 4 procs for 10 steps with 512 atoms
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|
|
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Performance: 2.629 ns/day, 9.128 hours/ns, 152.165 timesteps/s
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99.3% CPU use with 4 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 | 0.040015 | 0.050405 | 0.063468 | 3.7 | 76.70
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00079203 | 0.013852 | 0.024224 | 7.1 | 21.08
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Output | 0.0013652 | 0.001386 | 0.0014119 | 0.1 | 2.11
|
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Modify | 2.0981e-05 | 2.5392e-05 | 3.2902e-05 | 0.1 | 0.04
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Other | | 4.965e-05 | | | 0.08
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Nlocal: 128 ave 164 max 100 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 3073 ave 3101 max 3037 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 53248 ave 68224 max 41600 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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|
|
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Total # of neighbors = 212992
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Ave neighs/atom = 416
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|
Neighbor list builds = 0
|
|
Dangerous builds not checked
|
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Total wall time: 0:00:00
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