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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -53.8044 0) to (43.9282 53.8044 8.90517) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4158 5.15898 5.93678 Created 1758 atoms create_atoms CPU = 0.000488043 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4158 5.15898 5.93678 Created 1758 atoms create_atoms CPU = 0.000375032 secs 1758 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 15 37 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, cut 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 44 atoms, new total = 3472 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 15 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.636 | 5.636 | 5.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14158.014 0 -14158.014 447.47723 37 0 -14195.592 0 -14195.592 -5240.9961 Loop time of 19.1268 on 1 procs for 37 steps with 3472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14158.0142408 -14195.5799709 -14195.5923498 Force two-norm initial, final = 39.3889 0.355655 Force max component initial, final = 6.15931 0.0502949 Final line search alpha, max atom move = 0.664744 0.0334332 Iterations, force evaluations = 37 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.108 | 19.108 | 19.108 | 0.0 | 99.90 Neigh | 0.012508 | 0.012508 | 0.012508 | 0.0 | 0.07 Comm | 0.0025189 | 0.0025189 | 0.0025189 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003566 | | | 0.02 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7619 ave 7619 max 7619 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: 267074 ave 267074 max 267074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267074 Ave neighs/atom = 76.9222 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.637 | 5.637 | 5.637 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -14195.592 0 -14195.592 -5240.9961 42095.307 40 0 -14195.77 0 -14195.77 -1146.6267 41972.935 Loop time of 1.94623 on 1 procs for 3 steps with 3472 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14195.5923498 -14195.7689836 -14195.7696248 Force two-norm initial, final = 171.553 0.364021 Force max component initial, final = 123.581 0.0603739 Final line search alpha, max atom move = 0.000218917 1.32169e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.945 | 1.945 | 1.945 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021577 | 0.00021577 | 0.00021577 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009682 | | | 0.05 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7632 ave 7632 max 7632 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: 267100 ave 267100 max 267100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267100 Ave neighs/atom = 76.9297 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 15 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.775 | 5.775 | 5.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14195.77 0 -14195.77 -1146.6267 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3472 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 | | 1.192e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7659 ave 7659 max 7659 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: 267242 ave 267242 max 267242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267242 Ave neighs/atom = 76.9706 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) = 5.775 | 5.775 | 5.775 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 -14195.77 -14195.77 43.854657 107.60889 8.894171 -1146.6267 -1146.6267 -1.5342551 -3436.0441 -2.3017235 2.3108582 1613.9509 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7659 ave 7659 max 7659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133621 ave 133621 max 133621 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267242 ave 267242 max 267242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267242 Ave neighs/atom = 76.9706 Neighbor list builds = 0 Dangerous builds = 0 3472 -12194.3999087892 eV 2.31085819055039 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22