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 = 4.02485 4.02485 4.02485 Created orthogonal box = (0 -46.246 0) to (32.698 46.246 5.69199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.95424 6.30572 5.69199 Created 532 atoms create_atoms CPU = 0.000243187 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.95424 6.30572 5.69199 Created 532 atoms create_atoms CPU = 0.000146866 secs 532 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 23 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2734.7882 0 -2734.7882 3132.0831 51 0 -2764.8433 0 -2764.8433 -1043.7959 Loop time of 0.378788 on 1 procs for 51 steps with 1048 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2734.78821135 -2764.84067112 -2764.84332406 Force two-norm initial, final = 21.9466 0.120146 Force max component initial, final = 4.19481 0.0114266 Final line search alpha, max atom move = 1 0.0114266 Iterations, force evaluations = 51 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36748 | 0.36748 | 0.36748 | 0.0 | 97.01 Neigh | 0.0047991 | 0.0047991 | 0.0047991 | 0.0 | 1.27 Comm | 0.0039637 | 0.0039637 | 0.0039637 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002548 | | | 0.67 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5971 ave 5971 max 5971 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: 146656 ave 146656 max 146656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146656 Ave neighs/atom = 139.939 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -2764.8433 0 -2764.8433 -1043.7959 17214.298 53 0 -2764.8695 0 -2764.8695 821.5219 17173.826 Loop time of 0.011586 on 1 procs for 2 steps with 1048 atoms 172.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2764.84332406 -2764.86806505 -2764.86948953 Force two-norm initial, final = 31.4172 1.88494 Force max component initial, final = 24.2693 1.71725 Final line search alpha, max atom move = 0.000154903 0.000266006 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011185 | 0.011185 | 0.011185 | 0.0 | 96.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001092 | 0.0001092 | 0.0001092 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002918 | | | 2.52 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947 ave 5947 max 5947 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: 146480 ave 146480 max 146480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146480 Ave neighs/atom = 139.771 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.152 | 5.152 | 5.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2764.8695 0 -2764.8695 821.5219 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947 ave 5947 max 5947 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: 146528 ave 146528 max 146528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146528 Ave neighs/atom = 139.817 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) = 5.152 | 5.152 | 5.152 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 -2764.8695 -2764.8695 32.653206 92.491955 5.686398 821.5219 821.5219 -71.429229 2375.9474 160.04751 2.5990918 670.80366 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947 ave 5947 max 5947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73264 ave 73264 max 73264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146528 ave 146528 max 146528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146528 Ave neighs/atom = 139.817 Neighbor list builds = 0 Dangerous builds = 0 1048 -2732.65998179251 eV 2.5990917808369 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00