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 = 2.88265 2.88265 2.88265 Created orthogonal box = (0 -49.5979 0) to (24.7975 49.5979 2.88265) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.02122 4.02122 2.88265 Created 298 atoms create_atoms CPU = 0.000589848 secs 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.02122 4.02122 2.88265 Created 298 atoms create_atoms CPU = 0.000325918 secs 298 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 6 23 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2215.2149 0 -2215.2149 16934.982 116 0 -2273.1427 0 -2273.1427 -4286.9738 Loop time of 1.14687 on 1 procs for 116 steps with 588 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2215.2148971 -2273.14063409 -2273.14274045 Force two-norm initial, final = 111.645 0.192114 Force max component initial, final = 37.0337 0.0234716 Final line search alpha, max atom move = 1 0.0234716 Iterations, force evaluations = 116 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1193 | 1.1193 | 1.1193 | 0.0 | 97.59 Neigh | 0.0058091 | 0.0058091 | 0.0058091 | 0.0 | 0.51 Comm | 0.01599 | 0.01599 | 0.01599 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005814 | | | 0.51 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8157 ave 8157 max 8157 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: 139764 ave 139764 max 139764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139764 Ave neighs/atom = 237.694 Neighbor list builds = 1 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 : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -2273.1427 0 -2273.1427 -4286.9738 7090.7605 136 0 -2274.1513 0 -2274.1513 9532.6223 7031.5485 Loop time of 0.12602 on 1 procs for 20 steps with 588 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2273.14274045 -2274.15091693 -2274.15130165 Force two-norm initial, final = 89.1861 2.7178 Force max component initial, final = 84.8112 2.20752 Final line search alpha, max atom move = 0.00281047 0.00620418 Iterations, force evaluations = 20 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11933 | 0.11933 | 0.11933 | 0.0 | 94.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015342 | 0.0015342 | 0.0015342 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005159 | | | 4.09 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8169 ave 8169 max 8169 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: 139632 ave 139632 max 139632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139632 Ave neighs/atom = 237.469 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2274.1513 0 -2274.1513 9532.6223 Loop time of 1.90735e-06 on 1 procs for 0 steps with 588 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 | | 1.907e-06 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8110 ave 8110 max 8110 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: 139468 ave 139468 max 139468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139468 Ave neighs/atom = 237.19 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) = 5.089 | 5.089 | 5.089 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 -2274.1513 -2274.1513 25.075207 99.195746 2.8269192 9532.6223 9532.6223 310.80479 27793.791 493.27063 2.3899714 222.67069 Loop time of 2.14577e-06 on 1 procs for 0 steps with 588 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8110 ave 8110 max 8110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69734 ave 69734 max 69734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139468 ave 139468 max 139468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139468 Ave neighs/atom = 237.19 Neighbor list builds = 0 Dangerous builds = 0 588 -2274.15130164501 eV 2.38997135326986 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01