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 -40.3775 0) to (19.7791 40.3775 8.84548) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.27443 4.84487 5.89699 Created 612 atoms create_atoms CPU = 0.000252008 secs 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.27443 4.84487 5.89699 Created 612 atoms create_atoms CPU = 0.000112057 secs 612 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 = 8 31 4 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 48 atoms, new total = 1176 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 = 8 31 4 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) = 5.304 | 5.304 | 5.304 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4941.6223 0 -4941.6223 -8625.0948 30 0 -4968.3803 0 -4968.3803 -24755.847 Loop time of 1.73588 on 1 procs for 30 steps with 1176 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4941.62225725 -4968.37580878 -4968.38033628 Force two-norm initial, final = 2.59461 0.254521 Force max component initial, final = 0.369418 0.0273297 Final line search alpha, max atom move = 1 0.0273297 Iterations, force evaluations = 30 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7326 | 1.7326 | 1.7326 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015764 | 0.0015764 | 0.0015764 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001725 | | | 0.10 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409 ave 3409 max 3409 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: 62304 ave 62304 max 62304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62304 Ave neighs/atom = 52.9796 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.304 | 5.304 | 5.304 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -4968.3803 0 -4968.3803 -24755.847 14128.551 37 0 -4969.1367 0 -4969.1367 -9760.8521 13994.314 Loop time of 0.194545 on 1 procs for 7 steps with 1176 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4968.38033628 -4969.13259105 -4969.13668611 Force two-norm initial, final = 213.526 2.4555 Force max component initial, final = 166.458 1.83487 Final line search alpha, max atom move = 0.000122528 0.000224824 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19368 | 0.19368 | 0.19368 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015783 | 0.00015783 | 0.00015783 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007088 | | | 0.36 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409 ave 3409 max 3409 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: 63072 ave 63072 max 63072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63072 Ave neighs/atom = 53.6327 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 = 8 31 4 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) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4969.1367 0 -4969.1367 -9760.8521 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1176 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: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409 ave 3409 max 3409 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: 63072 ave 63072 max 63072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63072 Ave neighs/atom = 53.6327 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) = 5.442 | 5.442 | 5.442 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 -4969.1367 -4969.1367 19.650704 80.75505 8.8186847 -9760.8521 -9760.8521 -208.7068 -28897.361 -176.48872 2.3248713 347.82631 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1176 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 | | 1.907e-06 | | |100.00 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409 ave 3409 max 3409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31536 ave 31536 max 31536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63072 ave 63072 max 63072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63072 Ave neighs/atom = 53.6327 Neighbor list builds = 0 Dangerous builds = 0 1176 -4969.1366861116 eV 2.32487134895317 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02