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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -33.392 0) to (33.3889 33.392 3.14096) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.43215 4.43215 3.14096 Created 227 atoms create_atoms CPU = 0.000457048 secs 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.43215 4.43215 3.14096 Created 227 atoms create_atoms CPU = 0.000236034 secs 227 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 12 1 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 442 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 4.925 | 4.925 | 4.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2875.2914 0 -2875.2914 19226.825 122 0 -2970.0422 0 -2970.0422 -49464.782 Loop time of 1.37555 on 1 procs for 122 steps with 442 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 = -2875.29144382 -2970.0395124 -2970.04219275 Force two-norm initial, final = 149.995 0.288181 Force max component initial, final = 71.2637 0.0761937 Final line search alpha, max atom move = 0.746528 0.0568807 Iterations, force evaluations = 122 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3472 | 1.3472 | 1.3472 | 0.0 | 97.94 Neigh | 0.01096 | 0.01096 | 0.01096 | 0.0 | 0.80 Comm | 0.013257 | 0.013257 | 0.013257 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004157 | | | 0.30 Nlocal: 442 ave 442 max 442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8082 ave 8082 max 8082 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: 176004 ave 176004 max 176004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176004 Ave neighs/atom = 398.199 Neighbor list builds = 2 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 : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -2970.0422 0 -2970.0422 -49464.782 7003.8635 170 0 -2979.1499 0 -2979.1499 20439.468 6821.1801 Loop time of 0.355721 on 1 procs for 48 steps with 442 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 = -2970.04219275 -2979.14787 -2979.14988451 Force two-norm initial, final = 386.137 5.44177 Force max component initial, final = 384.616 4.51687 Final line search alpha, max atom move = 0.00011303 0.000510541 Iterations, force evaluations = 48 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34409 | 0.34409 | 0.34409 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029027 | 0.0029027 | 0.0029027 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008727 | | | 2.45 Nlocal: 442 ave 442 max 442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8090 ave 8090 max 8090 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: 176002 ave 176002 max 176002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176002 Ave neighs/atom = 398.195 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2979.1499 0 -2979.1499 20439.468 Loop time of 9.53674e-07 on 1 procs for 0 steps with 442 atoms 209.7% 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: 442 ave 442 max 442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8013 ave 8013 max 8013 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: 181796 ave 181796 max 181796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181796 Ave neighs/atom = 411.303 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) = 5.063 | 5.063 | 5.063 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 -2979.1499 -2979.1499 34.012692 66.784067 3.002933 20439.468 20439.468 262.62109 60041.472 1014.3107 2.6147839 288.85626 Loop time of 1.90735e-06 on 1 procs for 0 steps with 442 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: 442 ave 442 max 442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8013 ave 8013 max 8013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90898 ave 90898 max 90898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181796 ave 181796 max 181796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181796 Ave neighs/atom = 411.303 Neighbor list builds = 0 Dangerous builds = 0 442 -2979.14988451368 eV 2.61478392123843 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01