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 = 3.48714 3.48714 3.48714 Created orthogonal box = (0 -35.5655 0) to (30.7976 35.5655 6.03991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.52778 5.47108 6.03991 Created 627 atoms create_atoms CPU = 0.000473976 secs 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.52778 5.47108 6.03991 Created 629 atoms create_atoms CPU = 0.000324965 secs 629 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 19 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1228 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.457 | 5.457 | 5.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5389.9114 0 -5389.9114 10379.262 125 0 -5431.9901 0 -5431.9901 -12513.707 Loop time of 3.35128 on 1 procs for 125 steps with 1228 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5389.91142356 -5431.98475047 -5431.9900762 Force two-norm initial, final = 62.9316 0.306932 Force max component initial, final = 13.5431 0.0986042 Final line search alpha, max atom move = 0.726764 0.071662 Iterations, force evaluations = 125 244 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3157 | 3.3157 | 3.3157 | 0.0 | 98.94 Neigh | 0.016438 | 0.016438 | 0.016438 | 0.0 | 0.49 Comm | 0.011757 | 0.011757 | 0.011757 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007431 | | | 0.22 Nlocal: 1228 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6896 ave 6896 max 6896 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: 213220 ave 213220 max 213220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213220 Ave neighs/atom = 173.632 Neighbor list builds = 3 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 : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.457 | 5.457 | 5.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -5431.9901 0 -5431.9901 -12513.707 13231.433 129 0 -5432.1484 0 -5432.1484 -5312.281 13175.768 Loop time of 0.108869 on 1 procs for 4 steps with 1228 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5431.9900762 -5432.14815456 -5432.14842544 Force two-norm initial, final = 103.138 0.356315 Force max component initial, final = 82.1569 0.0874825 Final line search alpha, max atom move = 0.000323201 2.82744e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10752 | 0.10752 | 0.10752 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030375 | 0.00030375 | 0.00030375 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001043 | | | 0.96 Nlocal: 1228 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6863 ave 6863 max 6863 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: 213222 ave 213222 max 213222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213222 Ave neighs/atom = 173.634 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.594 | 5.594 | 5.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5432.1484 0 -5432.1484 -5312.281 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1228 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: 1228 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6893 ave 6893 max 6893 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: 213378 ave 213378 max 213378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213378 Ave neighs/atom = 173.761 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) = 5.594 | 5.594 | 5.594 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 -5432.1484 -5432.1484 30.715111 71.131039 6.0306579 -5312.281 -5312.281 0.0051060359 -15931.467 -5.3813453 2.2368615 918.38041 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1228 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: 1228 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6893 ave 6893 max 6893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106689 ave 106689 max 106689 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213378 ave 213378 max 213378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213378 Ave neighs/atom = 173.761 Neighbor list builds = 0 Dangerous builds = 0 1228 -5432.14842543887 eV 2.2368615457369 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03