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 = 2.8602 2.8602 2.8602 Created orthogonal box = (0 -46.1221 0) to (23.0596 46.1221 2.8602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9024 3.9024 2.8602 Created 261 atoms create_atoms CPU = 0.000226974 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9024 3.9024 2.8602 Created 261 atoms create_atoms CPU = 8.82149e-05 secs 261 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 518 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.845 | 4.845 | 4.845 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2185.2192 0 -2185.2192 9727.5832 32 0 -2206.6273 0 -2206.6273 71.703729 Loop time of 0.946288 on 1 procs for 32 steps with 518 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2185.21921939 -2206.62533549 -2206.62726619 Force two-norm initial, final = 44.267 0.187813 Force max component initial, final = 18.1187 0.0550438 Final line search alpha, max atom move = 1 0.0550438 Iterations, force evaluations = 32 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94398 | 0.94398 | 0.94398 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014167 | 0.0014167 | 0.0014167 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008929 | | | 0.09 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3712 ave 3712 max 3712 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: 29812 ave 29812 max 29812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29812 Ave neighs/atom = 57.5521 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.845 | 4.845 | 4.845 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2206.6273 0 -2206.6273 71.703729 6083.9749 34 0 -2206.6427 0 -2206.6427 3632.0457 6071.2479 Loop time of 0.0738711 on 1 procs for 2 steps with 518 atoms 94.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2206.62726619 -2206.64069315 -2206.64267688 Force two-norm initial, final = 19.869 1.52334 Force max component initial, final = 16.1154 1.32713 Final line search alpha, max atom move = 0.000262463 0.000348323 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073511 | 0.073511 | 0.073511 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002692 | | | 0.36 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3702 ave 3702 max 3702 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: 29814 ave 29814 max 29814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29814 Ave neighs/atom = 57.556 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2206.6427 0 -2206.6427 3632.0457 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 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: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3702 ave 3702 max 3702 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: 29814 ave 29814 max 29814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29814 Ave neighs/atom = 57.556 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) = 4.982 | 4.982 | 4.982 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 -2206.6427 -2206.6427 23.052995 92.244252 2.855034 3632.0457 3632.0457 350.12394 10355.798 190.21478 2.2684477 265.64251 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 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: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3702 ave 3702 max 3702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14907 ave 14907 max 14907 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29814 ave 29814 max 29814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29814 Ave neighs/atom = 57.556 Neighbor list builds = 0 Dangerous builds = 0 518 -2206.6426768767 eV 2.26844770234578 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01