LAMMPS (5 Oct 2016) # Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg units metal atom_style charge dimension 3 boundary p p p lattice diamond 5.431 Lattice spacing in x,y,z = 5.431 5.431 5.431 region box block 0 4 0 4 0 4 create_box 1 box Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 512 atoms mass 1 29.0 change_box all triclinic triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0) velocity all create 1.0 277387 pair_style comb pair_coeff * * ffield.comb Si Reading potential file ffield.comb with DATE: 2011-02-22 neighbor 0.5 bin neigh_modify every 20 delay 0 check no fix 1 all box/relax aniso 0.0 vmax 0.001 timestep 0.00020 thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz thermo_modify norm yes thermo 1 minimize 1.0e-14 1.0e-20 1000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 binsize = 6.25 -> bins = 4 4 4 Memory usage per processor = 7.52233 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 0 1 -4.6295947 -4.6297237 -4.6297237 0 1 1 -4.6295965 -4.6297255 -4.6297255 0 2 1 -4.6295965 -4.6297255 -4.6297255 0 3 1 -4.6295965 -4.6297255 -4.6297255 0 Loop time of 0.0423422 on 4 procs for 3 steps with 512 atoms 97.4% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4.62972371535 -4.62972550325 -4.62972550325 Force two-norm initial, final = 5.86582 3.9583e-08 Force max component initial, final = 3.38663 2.28585e-08 Final line search alpha, max atom move = 1 2.28585e-08 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026049 | 0.03263 | 0.041219 | 3.0 | 77.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049615 | 0.0090721 | 0.015641 | 5.7 | 21.43 Output | 3.314e-05 | 3.5107e-05 | 4.1008e-05 | 0.1 | 0.08 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006052 | | | 1.43 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked min_modify dmax 0.2 line quadratic unfix 1 run 1 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 binsize = 6.25 -> bins = 4 4 4 Memory usage per processor = 5.89733 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 3 1 -4.6295965 -4.6297255 -4.6297255 0 4 1 -4.6295965 -4.6297255 -4.6297255 0 Loop time of 0.00589204 on 4 procs for 1 steps with 512 atoms Performance: 2.933 ns/day, 8.183 hours/ns, 169.721 timesteps/s 101.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.003751 | 0.0046486 | 0.0057852 | 1.1 | 78.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.391e-05 | 0.001206 | 0.0021 | 2.1 | 20.47 Output | 1.9073e-05 | 2.0742e-05 | 2.1935e-05 | 0.0 | 0.35 Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.01 Other | | 1.597e-05 | | | 0.27 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked ### copy lines after this to any input script for elastic calculations ### ## Elastic constants calculations: strain box, measure box stress ## strain x, measure s_x, s_y, s_z, s_yz: ## calculates C11, C12, C13 and C14 fix 2 all deform 1 x scale 1.0001 remap x compute perfx all stress/atom NULL pair compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6] 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] WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) run 10 Memory usage per processor = 6.64733 Mbytes 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] 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 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 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 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 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 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 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 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 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 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 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 Loop time of 0.0653707 on 4 procs for 10 steps with 512 atoms Performance: 2.643 ns/day, 9.079 hours/ns, 152.974 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041152 | 0.050811 | 0.063103 | 3.5 | 77.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078726 | 0.013075 | 0.02272 | 6.9 | 20.00 Output | 0.0013869 | 0.0014045 | 0.0014176 | 0.0 | 2.15 Modify | 2.9087e-05 | 3.32e-05 | 3.5048e-05 | 0.0 | 0.05 Other | | 4.774e-05 | | | 0.07 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked ## strain z, measure s_z: calculates C33 fix 2 all deform 1 z scale 1.0001 remap x compute perfz all stress/atom NULL pair compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6] 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] run 10 Memory usage per processor = 7.39733 Mbytes 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] 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 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 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 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 18 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.5 1211626 1.3356364e-06 -2.794764e-06 -9.2778033e-06 19 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 -8.7949961e-07 -3.4755821e-06 -7.1758788e-06 20 21.730089 21.727916 21.729219 0 0 0 1848464.8 1159569 1503974 1.674426e-06 -2.898863e-06 -2.1520562e-06 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 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 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 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 Loop time of 0.065423 on 4 procs for 10 steps with 512 atoms Performance: 2.641 ns/day, 9.087 hours/ns, 152.851 timesteps/s 99.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041187 | 0.050801 | 0.063128 | 3.5 | 77.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077367 | 0.013104 | 0.022709 | 6.9 | 20.03 Output | 0.0014305 | 0.0014462 | 0.0014589 | 0.0 | 2.21 Modify | 2.0504e-05 | 2.7299e-05 | 3.1233e-05 | 0.1 | 0.04 Other | | 4.494e-05 | | | 0.07 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked ## strain yz, measure s_yz: calculates C44 fix 2 all deform 1 yz erate 0.0001 remap x compute perfyz all stress/atom NULL pair compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6] 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] run 10 Memory usage per processor = 8.16262 Mbytes 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] 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 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 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 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 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 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 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 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 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 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 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 Loop time of 0.0656388 on 4 procs for 10 steps with 512 atoms Performance: 2.633 ns/day, 9.116 hours/ns, 152.349 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040685 | 0.050668 | 0.063339 | 3.6 | 77.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077748 | 0.013466 | 0.023423 | 7.0 | 20.52 Output | 0.0013893 | 0.0014307 | 0.001461 | 0.1 | 2.18 Modify | 2.1935e-05 | 2.6524e-05 | 3.0994e-05 | 0.1 | 0.04 Other | | 4.733e-05 | | | 0.07 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked ## strain xy, measure s_xy: calculates C66 fix 2 all deform 1 xy erate 0.0001 remap x compute perfxy all stress/atom NULL pair compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6] 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] run 10 Memory usage per processor = 8.91262 Mbytes 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] 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 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 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 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 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 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 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 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 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 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 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 Loop time of 0.0657181 on 4 procs for 10 steps with 512 atoms Performance: 2.629 ns/day, 9.128 hours/ns, 152.165 timesteps/s 99.3% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040015 | 0.050405 | 0.063468 | 3.7 | 76.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079203 | 0.013852 | 0.024224 | 7.1 | 21.08 Output | 0.0013652 | 0.001386 | 0.0014119 | 0.1 | 2.11 Modify | 2.0981e-05 | 2.5392e-05 | 3.2902e-05 | 0.1 | 0.04 Other | | 4.965e-05 | | | 0.08 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 3073 ave 3101 max 3037 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 53248 ave 68224 max 41600 min Histogram: 1 0 0 2 0 0 0 0 0 1 Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked Total wall time: 0:00:00