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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -38.923932 0.0000000) to (18.347434 38.923932 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3963041 5.3420685 4.4499064 Created 206 atoms create_atoms CPU = 0.000 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3963041 5.3420685 4.4499064 Created 206 atoms create_atoms CPU = 0.000 seconds 206 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 24 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 408 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2560.1617 0 -2560.1617 134964.24 34 0 -2761.8204 0 -2761.8204 9909.5577 Loop time of 0.85575 on 1 procs for 34 steps with 408 atoms 45.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2560.16169889245 -2761.81779335038 -2761.8203985692 Force two-norm initial, final = 249.29618 0.30541636 Force max component initial, final = 78.344431 0.075320876 Final line search alpha, max atom move = 0.71897958 0.054154172 Iterations, force evaluations = 34 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85355 | 0.85355 | 0.85355 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010861 | 0.0010861 | 0.0010861 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001117 | | | 0.13 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2456.00 ave 2456 max 2456 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: 26376.0 ave 26376 max 26376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26376 Ave neighs/atom = 64.647059 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -2761.8204 0 -2761.8204 9909.5577 6355.8392 37 0 -2761.865 0 -2761.865 2857.5618 6372.809 Loop time of 0.0892364 on 1 procs for 3 steps with 408 atoms 46.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2761.8203985692 -2761.86451348418 -2761.86498097033 Force two-norm initial, final = 45.609320 0.31397652 Force max component initial, final = 36.190965 0.081224398 Final line search alpha, max atom move = 0.00041700932 3.3871331e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088788 | 0.088788 | 0.088788 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.4e-05 | 9.4e-05 | 9.4e-05 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003541 | | | 0.40 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2420.00 ave 2420 max 2420 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: 26144.0 ave 26144 max 26144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26144 Ave neighs/atom = 64.078431 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2761.865 0 -2761.865 2857.5618 Loop time of 2.20002e-06 on 1 procs for 0 steps with 408 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2420.00 ave 2420 max 2420 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: 26144.0 ave 26144 max 26144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26144 Ave neighs/atom = 64.078431 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) = 4.580 | 4.580 | 4.580 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 -2761.865 -2761.865 18.380765 77.847863 4.4536966 2857.5618 2857.5618 -8.6773951 8579.0855 2.2773261 2.4925207 309.67199 Loop time of 2.0999e-06 on 1 procs for 0 steps with 408 atoms 190.5% 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: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2420.00 ave 2420 max 2420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13072.0 ave 13072 max 13072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26144.0 ave 26144 max 26144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26144 Ave neighs/atom = 64.078431 Neighbor list builds = 0 Dangerous builds = 0 408 -2761.86498097033 eV 2.49252072276282 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01