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 -51.1198 0) to (25.5583 51.1198 3.17012) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.53885 3.53885 3.17012 Created 261 atoms create_atoms CPU = 0.00020504 secs 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.53885 3.53885 3.17012 Created 261 atoms create_atoms CPU = 6.60419e-05 secs 261 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 = 8 29 1 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 4 atoms, new total = 518 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 = 8 29 1 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5559.4755 0 -5559.4755 7148.5828 56 0 -5604.1357 0 -5604.1357 -3387.8264 Loop time of 8.47709 on 1 procs for 56 steps with 518 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 = -5559.47546865 -5604.13188251 -5604.13569068 Force two-norm initial, final = 73.2686 0.195351 Force max component initial, final = 21.2596 0.032995 Final line search alpha, max atom move = 1 0.032995 Iterations, force evaluations = 56 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.47 | 8.47 | 8.47 | 0.0 | 99.92 Neigh | 0.0026703 | 0.0026703 | 0.0026703 | 0.0 | 0.03 Comm | 0.0029902 | 0.0029902 | 0.0029902 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001467 | | | 0.02 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4540 ave 4540 max 4540 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: 56958 ave 56958 max 56958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56958 Ave neighs/atom = 109.958 Neighbor list builds = 2 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -5604.1357 0 -5604.1357 -3387.8264 8283.7707 58 0 -5604.148 0 -5604.148 -346.15857 8273.8676 Loop time of 0.444179 on 1 procs for 2 steps with 518 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5604.13569068 -5604.14756253 -5604.14796194 Force two-norm initial, final = 26.5976 0.202445 Force max component initial, final = 22.4894 0.0319364 Final line search alpha, max atom move = 0.000391786 1.25122e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4437 | 0.4437 | 0.4437 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012207 | 0.00012207 | 0.00012207 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00036 | | | 0.08 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4550 ave 4550 max 4550 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: 56986 ave 56986 max 56986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56986 Ave neighs/atom = 110.012 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 = 8 29 1 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5604.148 0 -5604.148 -346.15857 Loop time of 2.14577e-06 on 1 procs for 0 steps with 518 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 | | 2.146e-06 | | |100.00 Nlocal: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4550 ave 4550 max 4550 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: 56994 ave 56994 max 56994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56994 Ave neighs/atom = 110.027 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) = 4.627 | 4.627 | 4.627 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 -5604.148 -5604.148 25.535103 102.23969 3.169213 -346.15857 -346.15857 -0.08062674 -1035.3543 -3.0407931 2.5217124 120.68229 Loop time of 9.53674e-07 on 1 procs for 0 steps with 518 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: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4550 ave 4550 max 4550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28497 ave 28497 max 28497 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56994 ave 56994 max 56994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56994 Ave neighs/atom = 110.027 Neighbor list builds = 0 Dangerous builds = 0 518 -3415.36690501201 eV 2.52171237110995 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09