LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52152 3.52152 3.52152 Created orthogonal box = (0 -40.7681 0) to (28.8249 40.7681 4.98018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.59289 6.08426 4.98018 Created 538 atoms create_atoms CPU = 0.000468969 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.59289 6.08426 4.98018 Created 538 atoms create_atoms CPU = 0.000322104 secs 538 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1060 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6089.0066 0 -6089.0066 -2884.5484 79 0 -6116.1857 0 -6116.1857 -18188.113 Loop time of 114.216 on 1 procs for 79 steps with 1060 atoms 57.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6089.00663564 -6116.17985949 -6116.18572736 Force two-norm initial, final = 26.1645 0.245683 Force max component initial, final = 7.4562 0.0274406 Final line search alpha, max atom move = 1 0.0274406 Iterations, force evaluations = 79 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 114.18 | 114.18 | 114.18 | 0.0 | 99.97 Neigh | 0.0057921 | 0.0057921 | 0.0057921 | 0.0 | 0.01 Comm | 0.025153 | 0.025153 | 0.025153 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003641 | | | 0.00 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4981 ave 4981 max 4981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85216 ave 85216 max 85216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85216 Ave neighs/atom = 80.3925 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -6116.1857 0 -6116.1857 -18188.113 11704.785 87 0 -6116.889 0 -6116.889 -2654.0443 11615.557 Loop time of 7.0285 on 1 procs for 8 steps with 1060 atoms 61.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6116.18572736 -6116.8873137 -6116.88898161 Force two-norm initial, final = 206.277 3.79205 Force max component initial, final = 185.966 3.62337 Final line search alpha, max atom move = 0.000127275 0.000461163 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0271 | 7.0271 | 7.0271 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028586 | 0.00028586 | 0.00028586 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001094 | | | 0.02 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4981 ave 4981 max 4981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85232 ave 85232 max 85232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85232 Ave neighs/atom = 80.4075 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.746 | 4.746 | 4.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6116.889 0 -6116.889 -2654.0443 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1060 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4995 ave 4995 max 4995 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86432 ave 86432 max 86432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86432 Ave neighs/atom = 81.5396 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.746 | 4.746 | 4.746 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -6116.889 -6116.889 28.619888 81.536166 4.9776212 -2654.0443 -2654.0443 -496.23 -7317.5747 -148.32836 2.3216662 668.02074 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1060 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.907e-06 | | |100.00 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4995 ave 4995 max 4995 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43216 ave 43216 max 43216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86432 ave 86432 max 86432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86432 Ave neighs/atom = 81.5396 Neighbor list builds = 0 Dangerous builds = 0 1060 -3049.71232118215 eV 2.32166624863821 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:04