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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -42.4007 0) to (21.1986 42.4007 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.98789 4.98789 3.63552 Created 274 atoms create_atoms CPU = 0.000232935 secs 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.98789 4.98789 3.63552 Created 274 atoms create_atoms CPU = 9.48906e-05 secs 274 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 29 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 540 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2186.3803 0 -2186.3803 14465.9 50 0 -2206.4923 0 -2206.4923 -1754.5627 Loop time of 6.09088 on 1 procs for 50 steps with 540 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2186.38031464 -2206.49051055 -2206.49225556 Force two-norm initial, final = 26.1986 0.107343 Force max component initial, final = 9.02059 0.0186994 Final line search alpha, max atom move = 1 0.0186994 Iterations, force evaluations = 50 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0864 | 6.0864 | 6.0864 | 0.0 | 99.93 Neigh | 0.001384 | 0.001384 | 0.001384 | 0.0 | 0.02 Comm | 0.001883 | 0.001883 | 0.001883 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001211 | | | 0.02 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3731 ave 3731 max 3731 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: 41364 ave 41364 max 41364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41364 Ave neighs/atom = 76.6 Neighbor list builds = 1 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2206.4923 0 -2206.4923 -1754.5627 6535.4632 54 0 -2206.5141 0 -2206.5141 -289.59112 6528.804 Loop time of 0.544156 on 1 procs for 4 steps with 540 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2206.49225556 -2206.51296655 -2206.51408064 Force two-norm initial, final = 16.2449 0.14107 Force max component initial, final = 16.1885 0.0203674 Final line search alpha, max atom move = 0.000211358 4.30482e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54349 | 0.54349 | 0.54349 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016069 | 0.00016069 | 0.00016069 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005071 | | | 0.09 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756 ave 3756 max 3756 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: 41420 ave 41420 max 41420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41420 Ave neighs/atom = 76.7037 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2206.5141 0 -2206.5141 -289.59112 Loop time of 9.53674e-07 on 1 procs for 0 steps with 540 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: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756 ave 3756 max 3756 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: 41436 ave 41436 max 41436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41436 Ave neighs/atom = 76.7333 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) = 4.613 | 4.613 | 4.613 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 -2206.5141 -2206.5141 21.138571 84.80148 3.6421226 -289.59112 -289.59112 -2.0911871 -863.66463 -3.0175465 2.3318003 267.79587 Loop time of 9.53674e-07 on 1 procs for 0 steps with 540 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: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756 ave 3756 max 3756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20718 ave 20718 max 20718 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41436 ave 41436 max 41436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41436 Ave neighs/atom = 76.7333 Neighbor list builds = 0 Dangerous builds = 0 540 -1895.24114094041 eV 2.33180030356957 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06