LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.65334 3.65334 3.65334 Created orthogonal box = (0 -48.4707 0) to (17.1357 48.4707 5.16661) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.23116 5.50762 5.16661 Created 359 atoms create_atoms CPU = 0.000684977 secs 359 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.23116 5.50762 5.16661 Created 359 atoms create_atoms CPU = 0.000575066 secs 359 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 23 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 704 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 4.992 | 4.992 | 4.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2290.7126 0 -2290.7126 3789.083 46 0 -2299.3305 0 -2299.3305 1608.0064 Loop time of 0.403252 on 1 procs for 46 steps with 704 atoms 90.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2290.71256474 -2299.32902428 -2299.33047653 Force two-norm initial, final = 18.4222 0.13333 Force max component initial, final = 3.23198 0.0121036 Final line search alpha, max atom move = 1 0.0121036 Iterations, force evaluations = 46 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39569 | 0.39569 | 0.39569 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052454 | 0.0052454 | 0.0052454 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002313 | | | 0.57 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6793 ave 6793 max 6793 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: 158082 ave 158082 max 158082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158082 Ave neighs/atom = 224.548 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.993 | 4.993 | 4.993 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -2299.3305 0 -2299.3305 1608.0064 8582.5654 48 0 -2299.3348 0 -2299.3348 2562.1238 8576.5272 Loop time of 0.024955 on 1 procs for 2 steps with 704 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2299.33047653 -2299.33471542 -2299.33483383 Force two-norm initial, final = 11.0009 0.139035 Force max component initial, final = 10.989 0.0169261 Final line search alpha, max atom move = 0.000543997 9.20774e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023845 | 0.023845 | 0.023845 | 0.0 | 95.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003078 | 0.0003078 | 0.0003078 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008025 | | | 3.22 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6820 ave 6820 max 6820 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: 157376 ave 157376 max 157376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157376 Ave neighs/atom = 223.545 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.13 | 5.13 | 5.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2299.3348 0 -2299.3348 2562.1238 Loop time of 1.90735e-06 on 1 procs for 0 steps with 704 atoms 157.3% 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6815 ave 6815 max 6815 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: 157376 ave 157376 max 157376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157376 Ave neighs/atom = 223.545 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) = 5.13 | 5.13 | 5.13 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 -2299.3348 -2299.3348 17.137274 96.941478 5.1625003 2562.1238 2562.1238 -3.1622418 7691.1426 -1.6090045 2.4028158 219.34802 Loop time of 1.90735e-06 on 1 procs for 0 steps with 704 atoms 157.3% 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6815 ave 6815 max 6815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78688 ave 78688 max 78688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157376 ave 157376 max 157376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157376 Ave neighs/atom = 223.545 Neighbor list builds = 0 Dangerous builds = 0 704 -2299.33483383431 eV 2.40281581600237 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00