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 = 3.17012 3.17012 3.17012 Created orthogonal box = (0 -51.5116 0) to (18.211 51.5116 4.48323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.96663 5.46301 4.48323 Created 266 atoms create_atoms CPU = 0.000337124 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.96663 5.46301 4.48323 Created 266 atoms create_atoms CPU = 0.000202894 secs 266 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 6 29 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 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 524 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5626.2611 0 -5626.2611 6299.6235 41 0 -5664.711 0 -5664.711 -6768.1204 Loop time of 5.86279 on 1 procs for 41 steps with 524 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 = -5626.26107576 -5664.7060037 -5664.71098014 Force two-norm initial, final = 65.3237 0.242131 Force max component initial, final = 20.2981 0.0566183 Final line search alpha, max atom move = 1 0.0566183 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8585 | 5.8585 | 5.8585 | 0.0 | 99.93 Neigh | 0.001524 | 0.001524 | 0.001524 | 0.0 | 0.03 Comm | 0.0017037 | 0.0017037 | 0.0017037 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001031 | | | 0.02 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3736 ave 3736 max 3736 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: 57544 ave 57544 max 57544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57544 Ave neighs/atom = 109.817 Neighbor list builds = 1 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -5664.711 0 -5664.711 -6768.1204 8411.2093 43 0 -5664.7451 0 -5664.7451 -1421.35 8393.2319 Loop time of 0.34833 on 1 procs for 2 steps with 524 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5664.71098014 -5664.74490011 -5664.74506393 Force two-norm initial, final = 45.0603 0.256655 Force max component initial, final = 32.0124 0.0502542 Final line search alpha, max atom move = 0.000445631 2.23948e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34798 | 0.34798 | 0.34798 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002601 | | | 0.07 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3760 ave 3760 max 3760 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: 57664 ave 57664 max 57664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57664 Ave neighs/atom = 110.046 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 6 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.632 | 4.632 | 4.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5664.7451 0 -5664.7451 -1421.35 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3764 ave 3764 max 3764 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: 57696 ave 57696 max 57696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57696 Ave neighs/atom = 110.107 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) = 4.632 | 4.632 | 4.632 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 -5664.7451 -5664.7451 18.191434 103.0231 4.4784494 -1421.35 -1421.35 9.5012001 -4268.2921 -5.2591173 2.4865359 332.09703 Loop time of 1.19209e-06 on 1 procs for 0 steps with 524 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 | | 1.192e-06 | | |100.00 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3764 ave 3764 max 3764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28848 ave 28848 max 28848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57696 ave 57696 max 57696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57696 Ave neighs/atom = 110.107 Neighbor list builds = 0 Dangerous builds = 0 524 -3450.61133066858 eV 2.48653586170812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06