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 = 3.52221 3.52221 3.52221 Created orthogonal box = (0 -53.6522 0) to (26.8244 53.6522 3.52221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.62489 4.62489 3.52221 Created 466 atoms create_atoms CPU = 0.000283003 secs 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.62489 4.62489 3.52221 Created 466 atoms create_atoms CPU = 0.000138998 secs 466 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 33 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 920 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5294.4447 0 -5294.4447 -1811.7223 12 0 -5300.1289 0 -5300.1289 -4065.8325 Loop time of 5.61835 on 1 procs for 12 steps with 920 atoms 79.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5294.44473643 -5300.12382003 -5300.12893292 Force two-norm initial, final = 12.82 0.218126 Force max component initial, final = 3.66443 0.0433883 Final line search alpha, max atom move = 1 0.0433883 Iterations, force evaluations = 12 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6171 | 5.6171 | 5.6171 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074744 | 0.00074744 | 0.00074744 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004919 | | | 0.01 Nlocal: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5986 ave 5986 max 5986 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: 121032 ave 121032 max 121032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121032 Ave neighs/atom = 131.557 Neighbor list builds = 0 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -5300.1289 0 -5300.1289 -4065.8325 10138.239 14 0 -5300.1519 0 -5300.1519 -607.20166 10119.536 Loop time of 1.05578 on 1 procs for 2 steps with 920 atoms 75.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5300.12893292 -5300.15139806 -5300.15192904 Force two-norm initial, final = 34.9935 2.36365 Force max component initial, final = 29.1059 2.2339 Final line search alpha, max atom move = 0.000279812 0.000625071 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0553 | 1.0553 | 1.0553 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012088 | 0.00012088 | 0.00012088 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003839 | | | 0.04 Nlocal: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5986 ave 5986 max 5986 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: 116368 ave 116368 max 116368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116368 Ave neighs/atom = 126.487 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5300.1519 0 -5300.1519 -607.20166 Loop time of 9.53674e-07 on 1 procs for 0 steps with 920 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: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5986 ave 5986 max 5986 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: 117552 ave 117552 max 117552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117552 Ave neighs/atom = 127.774 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) = 5.114 | 5.114 | 5.114 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 -5300.1519 -5300.1519 26.790399 107.30448 3.5201695 -607.20166 -607.20166 116.83114 -2291.9131 353.477 2.2305244 406.494 Loop time of 9.53674e-07 on 1 procs for 0 steps with 920 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: 920 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5986 ave 5986 max 5986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58776 ave 58776 max 58776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117552 ave 117552 max 117552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117552 Ave neighs/atom = 127.774 Neighbor list builds = 0 Dangerous builds = 0 920 -2603.02190761129 eV 2.23052443480889 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07