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 = 4.05 4.05 4.05 Created orthogonal box = (0 -52.9647 0) to (24.9659 52.9647 5.72757) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.25597 6.50394 5.72757 Created 464 atoms create_atoms CPU = 0.000360966 secs 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.25597 6.50394 5.72757 Created 464 atoms create_atoms CPU = 0.000268221 secs 464 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 6 25 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 896 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 4.998 | 4.998 | 4.998 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2996.2418 0 -2996.2418 -3297.4987 27 0 -3002.145 0 -3002.145 -9238.6179 Loop time of 0.155835 on 1 procs for 27 steps with 896 atoms 102.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2996.24178009 -3002.14221112 -3002.14497188 Force two-norm initial, final = 2.34454 0.0923363 Force max component initial, final = 0.238434 0.00630004 Final line search alpha, max atom move = 1 0.00630004 Iterations, force evaluations = 27 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15263 | 0.15263 | 0.15263 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020199 | 0.0020199 | 0.0020199 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00119 | | | 0.76 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5633 ave 5633 max 5633 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: 124096 ave 124096 max 124096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124096 Ave neighs/atom = 138.5 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -3002.145 0 -3002.145 -9238.6179 15147.228 33 0 -3002.5178 0 -3002.5178 -1814.4221 15002.412 Loop time of 0.029361 on 1 procs for 6 steps with 896 atoms 68.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3002.14497188 -3002.51710582 -3002.51778489 Force two-norm initial, final = 110.75 1.86722 Force max component initial, final = 80.7228 1.74466 Final line search alpha, max atom move = 0.000343605 0.000599475 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028158 | 0.028158 | 0.028158 | 0.0 | 95.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027275 | 0.00027275 | 0.00027275 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009305 | | | 3.17 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5665 ave 5665 max 5665 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: 125152 ave 125152 max 125152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125152 Ave neighs/atom = 139.679 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3002.5178 0 -3002.5178 -1814.4221 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5665 ave 5665 max 5665 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: 125504 ave 125504 max 125504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125504 Ave neighs/atom = 140.071 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) = 5.136 | 5.136 | 5.136 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 -3002.5178 -3002.5178 24.830807 105.92935 5.7036643 -1814.4221 -1814.4221 67.992241 -5696.8016 185.54317 2.6389545 687.48073 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5665 ave 5665 max 5665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62752 ave 62752 max 62752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 125504 ave 125504 max 125504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125504 Ave neighs/atom = 140.071 Neighbor list builds = 0 Dangerous builds = 0 896 -3002.51778488765 eV 2.63895445442122 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00