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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -69.681995 0.0000000) to (42.669178 69.681995 8.6204757) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9345308 4.9770340 5.7469838 Created 2356 atoms using lattice units in orthogonal box = (0.0000000 -69.681995 0.0000000) to (42.669178 69.681995 8.6204757) create_atoms CPU = 0.003 seconds 2356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9345308 4.9770340 5.7469838 Created 2356 atoms using lattice units in orthogonal box = (0.0000000 -69.681995 0.0000000) to (42.669178 69.681995 8.6204757) create_atoms CPU = 0.003 seconds 2356 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 4678 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_677715648236_000#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20676.528 0 -20676.528 7599.7805 69 0 -20752.119 0 -20752.119 -2599.2364 Loop time of 4.78501 on 1 procs for 69 steps with 4678 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20676.5276071713 -20752.1011569565 -20752.1193567511 Force two-norm initial, final = 113.08071 0.48143406 Force max component initial, final = 17.339135 0.088293101 Final line search alpha, max atom move = 0.77458888 0.068390855 Iterations, force evaluations = 69 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7399 | 4.7399 | 4.7399 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018204 | 0.018204 | 0.018204 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02693 | | | 0.56 Nlocal: 4678.00 ave 4678 max 4678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14696.0 ave 14696 max 14696 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: 817020.0 ave 817020 max 817020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 817020 Ave neighs/atom = 174.65156 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -20752.119 0 -20752.119 -2599.2364 51262.062 71 0 -20752.225 0 -20752.225 596.53541 51169.815 Loop time of 0.183908 on 1 procs for 2 steps with 4678 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 = -20752.1193567511 -20752.224664025 -20752.2253103577 Force two-norm initial, final = 165.83754 0.49264113 Force max component initial, final = 120.76026 0.094306373 Final line search alpha, max atom move = 0.00015489808 1.4607876e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18038 | 0.18038 | 0.18038 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054269 | 0.00054269 | 0.00054269 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002985 | | | 1.62 Nlocal: 4678.00 ave 4678 max 4678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14833.0 ave 14833 max 14833 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: 816226.0 ave 816226 max 816226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816226 Ave neighs/atom = 174.48183 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 11.83 | 11.83 | 11.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20752.225 0 -20752.225 596.53541 Loop time of 2.093e-06 on 1 procs for 0 steps with 4678 atoms 191.1% 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 | | 2.093e-06 | | |100.00 Nlocal: 4678.00 ave 4678 max 4678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14850.0 ave 14850 max 14850 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: 816376.0 ave 816376 max 816376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816376 Ave neighs/atom = 174.51389 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 11.83 | 11.83 | 11.83 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 -20752.225 -20752.225 42.625243 139.36399 8.6138322 596.53541 596.53541 0.73842623 1789.0039 -0.13611928 2.1468305 1682.13 Loop time of 2.258e-06 on 1 procs for 0 steps with 4678 atoms 265.7% 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 | | 2.258e-06 | | |100.00 Nlocal: 4678.00 ave 4678 max 4678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14850.0 ave 14850 max 14850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 408188.0 ave 408188 max 408188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 816376.0 ave 816376 max 816376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816376 Ave neighs/atom = 174.51389 Neighbor list builds = 0 Dangerous builds = 0 4678 -20752.2253103577 eV 2.14683050829266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05