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 = 4.2107185 4.2107185 4.2107185 Created orthogonal box = (0.0000000 -79.447679 0.0000000) to (39.723839 79.447679 4.2107185) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8023586 5.8023586 4.2107185 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -79.447679 0.0000000) to (39.723839 79.447679 4.2107185) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8023586 5.8023586 4.2107185 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -79.447679 0.0000000) to (39.723839 79.447679 4.2107185) create_atoms CPU = 0.002 seconds 714 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 36 1 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_137572817842_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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.513 | 5.513 | 5.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5658.4216 0 -5658.4216 -109267 14 0 -19826.995 0 -19826.995 -265068.94 Loop time of 2.11419 on 1 procs for 14 steps with 1426 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5658.42164638754 -19826.994844685 -19826.994844685 Force two-norm initial, final = 1487.1363 8983.7573 Force max component initial, final = 567.59452 3824.9631 Final line search alpha, max atom move = 1.3590615e-14 5.1983600e-11 Iterations, force evaluations = 14 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0875 | 2.0875 | 2.0875 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016389 | 0.016389 | 0.016389 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01025 | | | 0.48 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10084.0 ave 10084 max 10084 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: 250212.0 ave 250212 max 250212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250212 Ave neighs/atom = 175.46424 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.513 | 5.513 | 5.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -19826.995 0 -19826.995 -265068.94 26577.776 592 0 -108978.5 0 -108978.5 -5080.5729 17593.661 Loop time of 31.1051 on 1 procs for 578 steps with 1426 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -19826.9948446851 -108978.495178052 -108978.495178052 Force two-norm initial, final = 13693.739 13180.196 Force max component initial, final = 10083.255 6959.6760 Final line search alpha, max atom move = 4.3771909e-17 3.0463831e-13 Iterations, force evaluations = 578 694 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.697 | 28.697 | 28.697 | 0.0 | 92.26 Neigh | 1.6042 | 1.6042 | 1.6042 | 0.0 | 5.16 Comm | 0.19893 | 0.19893 | 0.19893 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6047 | | | 1.94 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11299.0 ave 11299 max 11299 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: 374108.0 ave 374108 max 374108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374108 Ave neighs/atom = 262.34783 Neighbor list builds = 38 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.056 | 6.056 | 6.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -108978.5 0 -108978.5 -5080.5729 Loop time of 6.505e-06 on 1 procs for 0 steps with 1426 atoms 199.8% 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 | | 6.505e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11299.0 ave 11299 max 11299 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: 369260.0 ave 369260 max 369260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369260 Ave neighs/atom = 258.94811 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.056 | 6.056 | 6.056 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 -108978.5 -108978.5 31.571782 132.43245 4.2078737 -5080.5729 -5080.5729 4245.6692 10766.785 -30254.173 0.0033675712 675.51323 Loop time of 6.656e-06 on 1 procs for 0 steps with 1426 atoms 300.5% 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 | | 6.656e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11299.0 ave 11299 max 11299 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184630.0 ave 184630 max 184630 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369260.0 ave 369260 max 369260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369260 Ave neighs/atom = 258.94811 Neighbor list builds = 0 Dangerous builds = 0 1426 -108841.529047371 eV 0.00336757117498168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33