LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -71.497174 0.0000000) to (43.782899 71.497174 8.8454813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0633284 5.1069410 5.8969875 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.497174 0.0000000) to (43.782899 71.497174 8.8454813) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0633284 5.1069410 5.8969875 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.497174 0.0000000) to (43.782899 71.497174 8.8454813) create_atoms CPU = 0.004 seconds 2358 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 = 17 54 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 0 atoms, new total = 4710 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_137964310702_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) 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 = 17 54 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) = 7.305 | 7.305 | 7.305 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19651.999 0 -19651.999 19575.524 29 0 -19951.886 0 -19951.886 6871.8932 Loop time of 13.0108 on 1 procs for 29 steps with 4710 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 = -19651.9990763392 -19951.8669229009 -19951.8859965832 Force two-norm initial, final = 237.01080 0.51434407 Force max component initial, final = 33.099750 0.033748670 Final line search alpha, max atom move = 1.0000000 0.033748670 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.989 | 12.989 | 12.989 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0076048 | 0.0076048 | 0.0076048 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01384 | | | 0.11 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9478.00 ave 9478 max 9478 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: 254364.0 ave 254364 max 254364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254364 Ave neighs/atom = 54.005096 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) 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 = 17 54 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.305 | 7.305 | 7.305 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -19951.886 0 -19951.886 6871.8932 55378.968 32 0 -19952.431 0 -19952.431 1.0287853 55607.381 Loop time of 1.53125 on 1 procs for 3 steps with 4710 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 = -19951.8859965832 -19952.4154960006 -19952.4305185781 Force two-norm initial, final = 419.31255 4.7720898 Force max component initial, final = 289.01903 3.7977385 Final line search alpha, max atom move = 2.7892255e-05 0.00010592749 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5268 | 1.5268 | 1.5268 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053066 | 0.00053066 | 0.00053066 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003936 | | | 0.26 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9443.00 ave 9443 max 9443 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: 253836.0 ave 253836 max 253836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253836 Ave neighs/atom = 53.892994 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 = 17 54 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.443 | 7.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19952.431 0 -19952.431 1.0287853 Loop time of 2.333e-06 on 1 procs for 0 steps with 4710 atoms 214.3% 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 | | 2.333e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9443.00 ave 9443 max 9443 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: 253800.0 ave 253800 max 253800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253800 Ave neighs/atom = 53.885350 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 = 17 54 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.443 | 7.443 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 -19952.431 -19952.431 43.849726 143.32037 8.8482548 1.0287853 1.0287853 -109.58859 67.946406 44.728542 2.2706254 818.57208 Loop time of 2.428e-06 on 1 procs for 0 steps with 4710 atoms 288.3% 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 | | 2.428e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9443.00 ave 9443 max 9443 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126900.0 ave 126900 max 126900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253800.0 ave 253800 max 253800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253800 Ave neighs/atom = 53.885350 Neighbor list builds = 0 Dangerous builds = 0 4710 -19952.4305185781 eV 2.27062543890896 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16