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 = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -42.1165 0) to (14.8892 42.1165 5.10694) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.13083 6.19308 5.10694 Created 274 atoms create_atoms CPU = 0.000346184 secs 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.13083 6.19308 5.10694 Created 274 atoms create_atoms CPU = 0.000206947 secs 274 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 12 atoms, new total = 536 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.866 | 4.866 | 4.866 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2258.4397 0 -2258.4397 -5289.8656 48 0 -2268.5407 0 -2268.5407 -17755.417 Loop time of 1.17122 on 1 procs for 48 steps with 536 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2258.43969316 -2268.5393226 -2268.54074838 Force two-norm initial, final = 8.38033 0.108957 Force max component initial, final = 1.99992 0.0129702 Final line search alpha, max atom move = 1 0.0129702 Iterations, force evaluations = 48 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1681 | 1.1681 | 1.1681 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016685 | 0.0016685 | 0.0016685 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00141 | | | 0.12 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2584 ave 2584 max 2584 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: 28632 ave 28632 max 28632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28632 Ave neighs/atom = 53.4179 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.866 | 4.866 | 4.866 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2268.5407 0 -2268.5407 -17755.417 6404.9196 52 0 -2268.6693 0 -2268.6693 -8536.5262 6367.823 Loop time of 0.0547769 on 1 procs for 4 steps with 536 atoms 91.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2268.54074838 -2268.66898116 -2268.66931754 Force two-norm initial, final = 62.7325 1.08055 Force max component initial, final = 46.5406 1.06986 Final line search alpha, max atom move = 0.000363018 0.000388378 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054407 | 0.054407 | 0.054407 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.1778e-05 | 8.1778e-05 | 8.1778e-05 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002882 | | | 0.53 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560 ave 2560 max 2560 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: 28848 ave 28848 max 28848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28848 Ave neighs/atom = 53.8209 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2268.6693 0 -2268.6693 -8536.5262 Loop time of 9.53674e-07 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572 ave 2572 max 2572 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: 28848 ave 28848 max 28848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28848 Ave neighs/atom = 53.8209 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) = 5.004 | 5.004 | 5.004 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 -2268.6693 -2268.6693 14.85108 84.233051 5.0903824 -8536.5262 -8536.5262 268.49352 -25868.918 -9.1537302 2.3723722 141.03552 Loop time of 9.53674e-07 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572 ave 2572 max 2572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14424 ave 14424 max 14424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28848 ave 28848 max 28848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28848 Ave neighs/atom = 53.8209 Neighbor list builds = 0 Dangerous builds = 0 536 -2268.66931753554 eV 2.37237221228313 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01