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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -51.4223 0) to (12.1194 51.4223 5.71314) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.733 5.71314 5.71314 Created 218 atoms create_atoms CPU = 0.000705957 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.733 5.71314 5.71314 Created 218 atoms create_atoms CPU = 0.000475883 secs 218 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 18 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 430 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1209.3579 0 -1209.3579 9225.3056 149 0 -1236.367 0 -1236.367 -1382.4978 Loop time of 1.91866 on 1 procs for 149 steps with 430 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 = -1209.35788914 -1236.36575089 -1236.36697799 Force two-norm initial, final = 35.1499 0.111255 Force max component initial, final = 10.4341 0.0170245 Final line search alpha, max atom move = 1 0.0170245 Iterations, force evaluations = 149 281 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.873 | 1.873 | 1.873 | 0.0 | 97.62 Neigh | 0.021162 | 0.021162 | 0.021162 | 0.0 | 1.10 Comm | 0.01864 | 0.01864 | 0.01864 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005849 | | | 0.30 Nlocal: 430 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7450 ave 7450 max 7450 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: 173274 ave 173274 max 173274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173274 Ave neighs/atom = 402.963 Neighbor list builds = 3 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 : 149 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 149 0 -1236.367 0 -1236.367 -1382.4978 7120.9342 151 0 -1236.3716 0 -1236.3716 -580.76478 7113.3586 Loop time of 0.0220051 on 1 procs for 2 steps with 430 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 = -1236.36697799 -1236.37143115 -1236.37162069 Force two-norm initial, final = 7.75636 0.118322 Force max component initial, final = 7.75351 0.0204588 Final line search alpha, max atom move = 0.000868379 1.7766e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021334 | 0.021334 | 0.021334 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019717 | 0.00019717 | 0.00019717 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004737 | | | 2.15 Nlocal: 430 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7515 ave 7515 max 7515 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: 173182 ave 173182 max 173182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173182 Ave neighs/atom = 402.749 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1236.3716 0 -1236.3716 -580.76478 Loop time of 9.53674e-07 on 1 procs for 0 steps with 430 atoms 314.6% 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: 430 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7521 ave 7521 max 7521 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: 173860 ave 173860 max 173860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173860 Ave neighs/atom = 404.326 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) = 5.126 | 5.126 | 5.126 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 -1236.3716 -1236.3716 12.121046 102.84456 5.7062825 -580.76478 -580.76478 2.7822804 -1749.6791 4.6025085 2.6900918 351.58409 Loop time of 2.14577e-06 on 1 procs for 0 steps with 430 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: 430 ave 430 max 430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7521 ave 7521 max 7521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86930 ave 86930 max 86930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 173860 ave 173860 max 173860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173860 Ave neighs/atom = 404.326 Neighbor list builds = 0 Dangerous builds = 0 430 -1236.37162069087 eV 2.69009181184041 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02