LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -47.253847 0.0000000) to (22.273974 47.253847 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6892576 5.8026602 5.1100000 Created 463 atoms create_atoms CPU = 0.001 seconds 463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6892576 5.8026602 5.1100000 Created 463 atoms create_atoms CPU = 0.002 seconds 463 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 28 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 904 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3170.7695 0 -3170.7695 3418.7256 33 0 -3187.1793 0 -3187.1793 -3879.1053 Loop time of 0.965422 on 1 procs for 33 steps with 904 atoms 87.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3170.76953566721 -3187.1769731887 -3187.17933106492 Force two-norm initial, final = 25.372435 0.14168672 Force max component initial, final = 4.8007608 0.034355308 Final line search alpha, max atom move = 1.0000000 0.034355308 Iterations, force evaluations = 33 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96205 | 0.96205 | 0.96205 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019475 | 0.0019475 | 0.0019475 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001425 | | | 0.15 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5408.00 ave 5408 max 5408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119502.0 ave 119502 max 119502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119502 Ave neighs/atom = 132.19248 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -3187.1793 0 -3187.1793 -3879.1053 10756.866 35 0 -3187.2004 0 -3187.2004 -1159.3992 10735.938 Loop time of 0.0645618 on 1 procs for 2 steps with 904 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 = -3187.17933106492 -3187.20038328102 -3187.20043983166 Force two-norm initial, final = 30.567891 0.25109781 Force max component initial, final = 23.343235 0.15625687 Final line search alpha, max atom move = 0.00084636479 0.00013225031 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063986 | 0.063986 | 0.063986 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001343 | 0.0001343 | 0.0001343 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004413 | | | 0.68 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5464.00 ave 5464 max 5464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119700.0 ave 119700 max 119700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119700 Ave neighs/atom = 132.41150 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3187.2004 0 -3187.2004 -1159.3992 Loop time of 1.90001e-06 on 1 procs for 0 steps with 904 atoms 105.3% 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 | | 1.9e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5464.00 ave 5464 max 5464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119728.0 ave 119728 max 119728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119728 Ave neighs/atom = 132.44248 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) = 5.125 | 5.125 | 5.125 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 -3187.2004 -3187.2004 22.25393 94.507693 5.1046517 -1159.3992 -1159.3992 -18.432553 -3483.0595 23.29457 2.3480178 557.36597 Loop time of 2.10002e-06 on 1 procs for 0 steps with 904 atoms 142.9% 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 | | 2.1e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5464.00 ave 5464 max 5464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59864.0 ave 59864 max 59864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119728.0 ave 119728 max 119728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119728 Ave neighs/atom = 132.44248 Neighbor list builds = 0 Dangerous builds = 0 904 -3187.20043983166 eV 2.34801783231515 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01